1
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Yang H, Zingaro VA, Lincoff J, Tom H, Oikawa S, Oses-Prieto JA, Edmondson Q, Seiple I, Shah H, Kajimura S, Burlingame AL, Grabe M, Ruggero D. Remodelling of the translatome controls diet and its impact on tumorigenesis. Nature 2024; 633:189-197. [PMID: 39143206 DOI: 10.1038/s41586-024-07781-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/03/2024] [Indexed: 08/16/2024]
Abstract
Fasting is associated with a range of health benefits1-6. How fasting signals elicit changes in the proteome to establish metabolic programmes remains poorly understood. Here we show that hepatocytes selectively remodel the translatome while global translation is paradoxically downregulated during fasting7,8. We discover that phosphorylation of eukaryotic translation initiation factor 4E (P-eIF4E) is induced during fasting. We show that P-eIF4E is responsible for controlling the translation of genes involved in lipid catabolism and the production of ketone bodies. Inhibiting P-eIF4E impairs ketogenesis in response to fasting and a ketogenic diet. P-eIF4E regulates those messenger RNAs through a specific translation regulatory element within their 5' untranslated regions (5' UTRs). Our findings reveal a new signalling property of fatty acids, which are elevated during fasting. We found that fatty acids bind and induce AMP-activated protein kinase (AMPK) kinase activity that in turn enhances the phosphorylation of MAP kinase-interacting protein kinase (MNK), the kinase that phosphorylates eIF4E. The AMPK-MNK-eIF4E axis controls ketogenesis, revealing a new lipid-mediated kinase signalling pathway that links ketogenesis to translation control. Certain types of cancer use ketone bodies as an energy source9,10 that may rely on P-eIF4E. Our findings reveal that on a ketogenic diet, treatment with eFT508 (also known as tomivosertib; a P-eIF4E inhibitor) restrains pancreatic tumour growth. Thus, our findings unveil a new fatty acid-induced signalling pathway that activates selective translation, which underlies ketogenesis and provides a tailored diet intervention therapy for cancer.
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Affiliation(s)
- Haojun Yang
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- School of Medicine and Department of Urology, UCSF, San Francisco, CA, USA
| | - Vincenzo Andrea Zingaro
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- School of Medicine and Department of Urology, UCSF, San Francisco, CA, USA
| | - James Lincoff
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
- Cardiovascular Research Institute, UCSF, San Francisco, CA, USA
| | - Harrison Tom
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- School of Medicine and Department of Urology, UCSF, San Francisco, CA, USA
| | - Satoshi Oikawa
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA
| | | | - Quinn Edmondson
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
- Cardiovascular Research Institute, UCSF, San Francisco, CA, USA
| | - Ian Seiple
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
- Cardiovascular Research Institute, UCSF, San Francisco, CA, USA
| | - Hardik Shah
- Metabolomics Platform, Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
| | - Shingo Kajimura
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA
| | - Alma L Burlingame
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
| | - Michael Grabe
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
- Cardiovascular Research Institute, UCSF, San Francisco, CA, USA
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA.
- School of Medicine and Department of Urology, UCSF, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA, USA.
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2
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Wan YX, Qi XW, Lian YY, Liu ZY, Wang H, Qiu YQ, Zhang CG, Li WN, Jiang HL, Yang DH, Zhao W, Chen ZS, Huang JC. Electroacupuncture facilitates vascular normalization by inhibiting Glyoxalase1 in endothelial cells to attenuate glycolysis and angiogenesis in triple-negative breast cancer. Cancer Lett 2024; 598:217094. [PMID: 38945204 DOI: 10.1016/j.canlet.2024.217094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 06/13/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
Recent therapeutic strategies for the treatment of triple-negative breast cancer (TNBC) have shifted the focus from vascular growth factors to endothelial cell metabolism. This study highlights the underexplored therapeutic potential of peri-tumoral electroacupuncture, a globally accepted non-pharmacological intervention for TNBC, and molecular mechanisms. Our study showed that peri-tumoral electroacupuncture effectively reduced the density of microvasculature and enhanced vascular functionality in 4T1 breast cancer xenografts, with optimal effects on day 3 post-acupuncture. The timely integration of peri-tumoral electroacupuncture amplified the anti-tumor efficacy of paclitaxel. Multi-omics analysis revealed Glyoxalase 1 (Glo1) and the associated methylglyoxal-glycolytic pathway as key mediators of electroacupuncture-induced vascular normalization. Peri-tumoral electroacupuncture notably reduced Glo1 expression in the endothelial cells of 4T1 xenografts. Using an in vivo matrigel plug angiogenesis assay, we demonstrated that either Glo1 knockdown or electroacupuncture inhibited angiogenesis. In contrast, Glo1 overexpression increased blood vessel formation. In vitro pharmacological inhibition and genetic knockdown of Glo1 in human umbilical vein endothelial cells inhibited proliferation and promoted apoptosis via downregulating the methylglyoxal-glycolytic pathway. The study using the Glo1-silenced zebrafish model further supported the role of Glo1 in vascular development. This study underscores the pivotal role of Glo1 in peri-tumoral electroacupuncture, spotlighting a promising avenue for enhancing vascular normalization and improving TNBC treatment outcomes.
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Affiliation(s)
- Yu-Xiang Wan
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xue-Wei Qi
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 100029, China
| | - Yan-Yan Lian
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Ze-Yu Liu
- Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Hui Wang
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yu-Qin Qiu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Chun-Guang Zhang
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Wen-Na Li
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Hong-Lin Jiang
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Dong-Hua Yang
- New York College of Traditional Chinese Medicine, Mineola, NY, 11501, USA
| | - Wei Zhao
- Guanganmen Hospital, Chinese Academy of Traditional Chinese Medicine, Beijing, 100029, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA.
| | - Jin-Chang Huang
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029, China.
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3
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Busquets-Hernández C, Ribó S, Gratacós-Batlle E, Carbajo D, Tsiotsia A, Blanco-Canosa JB, Chamberlain LH, Triola G. Quantitative analysis of protein lipidation and acyl-CoAs reveals substrate preferences of the S-acylation machinery. Chem Sci 2024; 15:12845-12855. [PMID: 39148806 PMCID: PMC11322976 DOI: 10.1039/d4sc02235a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/08/2024] [Indexed: 08/17/2024] Open
Abstract
Protein palmitoylation or S-acylation has emerged as a key regulator of cellular processes. Increasing evidence shows that this modification is not restricted to palmitate but it can include additional fatty acids, raising the possibility that differential S-acylation contributes to the fine-tuning of protein activity. However, methods to profile the acyl moieties attached to proteins are scarce. Herein, we report a method for the identification and quantification of lipids bound to proteins that relies on hydroxylamine treatment and mass spectrometry analysis of fatty acid hydroxamates. This method has enabled unprecedented and extensive profiling of the S-acylome in different cell lines and tissues and has shed light on the substrate specificity of some S-acylating enzymes. Moreover, we could extend it to quantify also the acyl-CoAs, which are thioesters formed between a fatty acid and a coenzyme A, overcoming many of the previously described challenges for the detection of such species. Importantly, the simultaneous analysis of the lipid fraction and the proteome allowed us to establish, for the first time, a direct correlation between the endogenous levels of acyl-CoAs and the S-acylation profile of its proteome.
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Affiliation(s)
- Carla Busquets-Hernández
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Silvia Ribó
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Esther Gratacós-Batlle
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Daniel Carbajo
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Alexandra Tsiotsia
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Juan B Blanco-Canosa
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde Glasgow UK
| | - Gemma Triola
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
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4
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Kundu A, Brinkley GJ, Nam H, Karki S, Kirkman R, Pandit M, Shim E, Widden H, Liu J, Heidarian Y, Mahmoudzadeh NH, Fitt AJ, Absher D, Ding HF, Crossman DK, Placzek WJ, Locasale JW, Rakheja D, McConathy JE, Ramachandran R, Bae S, Tennessen JM, Sudarshan S. l-2-Hydroxyglutarate remodeling of the epigenome and epitranscriptome creates a metabolic vulnerability in kidney cancer models. J Clin Invest 2024; 134:e171294. [PMID: 38743486 PMCID: PMC11213505 DOI: 10.1172/jci171294] [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: 04/17/2023] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
Tumor cells are known to undergo considerable metabolic reprogramming to meet their unique demands and drive tumor growth. At the same time, this reprogramming may come at a cost with resultant metabolic vulnerabilities. The small molecule l-2-hydroxyglutarate (l-2HG) is elevated in the most common histology of renal cancer. Similarly to other oncometabolites, l-2HG has the potential to profoundly impact gene expression. Here, we demonstrate that l-2HG remodels amino acid metabolism in renal cancer cells through combined effects on histone methylation and RNA N6-methyladenosine. The combined effects of l-2HG result in a metabolic liability that renders tumors cells reliant on exogenous serine to support proliferation, redox homeostasis, and tumor growth. In concert with these data, high-l-2HG kidney cancers demonstrate reduced expression of multiple serine biosynthetic enzymes. Collectively, our data indicate that high-l-2HG renal tumors could be specifically targeted by strategies that limit serine availability to tumors.
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Affiliation(s)
- Anirban Kundu
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Urology, University of Arizona, Tuscon, Arizona, USA
| | - Garrett J. Brinkley
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hyeyoung Nam
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Suman Karki
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Richard Kirkman
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Madhuparna Pandit
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - EunHee Shim
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hayley Widden
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yasaman Heidarian
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - Alexander J. Fitt
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - William J. Placzek
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jason W. Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Rekha Ramachandran
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sejong Bae
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Sunil Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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5
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Zhu Q, Combs ME, Bowles DE, Gross RT, Mendiola Pla M, Mack CP, Taylor JM. GRAF1 Acts as a Downstream Mediator of Parkin to Regulate Mitophagy in Cardiomyocytes. Cells 2024; 13:448. [PMID: 38474413 PMCID: PMC10930636 DOI: 10.3390/cells13050448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Cardiomyocytes rely on proper mitochondrial homeostasis to maintain contractility and achieve optimal cardiac performance. Mitochondrial homeostasis is controlled by mitochondrial fission, fusion, and mitochondrial autophagy (mitophagy). Mitophagy plays a particularly important role in promoting the degradation of dysfunctional mitochondria in terminally differentiated cells. However, the precise mechanisms by which this is achieved in cardiomyocytes remain opaque. Our study identifies GRAF1 as an important mediator in PINK1-Parkin pathway-dependent mitophagy. Depletion of GRAF1 (Arhgap26) in cardiomyocytes results in actin remodeling defects, suboptimal mitochondria clustering, and clearance. Mechanistically, GRAF1 promotes Parkin-LC3 complex formation and directs autophagosomes to damaged mitochondria. Herein, we found that these functions are regulated, at least in part, by the direct binding of GRAF1 to phosphoinositides (PI(3)P, PI(4)P, and PI(5)P) on autophagosomes. In addition, PINK1-dependent phosphorylation of Parkin promotes Parkin-GRAF1-LC3 complex formation, and PINK1-dependent phosphorylation of GRAF1 (on S668 and S671) facilitates the clustering and clearance of mitochondria. Herein, we developed new phosphor-specific antibodies to these sites and showed that these post-translational modifications are differentially modified in human hypertrophic cardiomyopathy and dilated cardiomyopathy. Furthermore, our metabolic studies using serum collected from isoproterenol-treated WT and GRAF1CKO mice revealed defects in mitophagy-dependent cardiomyocyte fuel flexibility that have widespread impacts on systemic metabolism. In summary, our study reveals that GRAF1 co-regulates actin and membrane dynamics to promote cardiomyocyte mitophagy and that dysregulation of GRAF1 post-translational modifications may underlie cardiac disease pathogenesis.
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Affiliation(s)
- Qiang Zhu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Q.Z.); (M.E.C.); (C.P.M.)
| | - Matthew E. Combs
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Q.Z.); (M.E.C.); (C.P.M.)
| | - Dawn E. Bowles
- Division of Surgical Sciences, Duke University Medical Center, Durham, NC 27710, USA; (D.E.B.); (R.T.G.); (M.M.P.)
| | - Ryan T. Gross
- Division of Surgical Sciences, Duke University Medical Center, Durham, NC 27710, USA; (D.E.B.); (R.T.G.); (M.M.P.)
| | - Michelle Mendiola Pla
- Division of Surgical Sciences, Duke University Medical Center, Durham, NC 27710, USA; (D.E.B.); (R.T.G.); (M.M.P.)
| | - Christopher P. Mack
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Q.Z.); (M.E.C.); (C.P.M.)
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joan M. Taylor
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Q.Z.); (M.E.C.); (C.P.M.)
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
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6
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Zhang R, Fang J, Xie X, Carrico C, Meyer JG, Wei L, Bons J, Rose J, Riley R, Kwok R, Ashok Kumaar PV, Zhang Y, He W, Nishida Y, Liu X, Locasale JW, Schilling B, Verdin E. Regulation of urea cycle by reversible high-stoichiometry lysine succinylation. Nat Metab 2024; 6:550-566. [PMID: 38448615 DOI: 10.1038/s42255-024-01005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
The post-translational modification lysine succinylation is implicated in the regulation of various metabolic pathways. However, its biological relevance remains uncertain due to methodological difficulties in determining high-impact succinylation sites. Here, using stable isotope labelling and data-independent acquisition mass spectrometry, we quantified lysine succinylation stoichiometries in mouse livers. Despite the low overall stoichiometry of lysine succinylation, several high-stoichiometry sites were identified, especially upon deletion of the desuccinylase SIRT5. In particular, multiple high-stoichiometry lysine sites identified in argininosuccinate synthase (ASS1), a key enzyme in the urea cycle, are regulated by SIRT5. Mutation of the high-stoichiometry lysine in ASS1 to succinyl-mimetic glutamic acid significantly decreased its enzymatic activity. Metabolomics profiling confirms that SIRT5 deficiency decreases urea cycle activity in liver. Importantly, SIRT5 deficiency compromises ammonia tolerance, which can be reversed by the overexpression of wild-type, but not succinyl-mimetic, ASS1. Therefore, lysine succinylation is functionally important in ammonia metabolism.
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Affiliation(s)
- Ran Zhang
- Buck Institute for Research on Aging, Novato, CA, USA
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jingqi Fang
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Xueshu Xie
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Chris Carrico
- Buck Institute for Research on Aging, Novato, CA, USA
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA
| | - Jesse G Meyer
- Buck Institute for Research on Aging, Novato, CA, USA
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lei Wei
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, CA, USA
| | | | - Ryan Kwok
- Buck Institute for Research on Aging, Novato, CA, USA
| | | | - Yini Zhang
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Wenjuan He
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA
| | - Yuya Nishida
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA
| | - Xiaojing Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | | | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, USA.
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA.
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7
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Singh M, Kiyuna LA, Odendaal C, Bakker BM, Harms AC, Hankemeier T. Development of targeted hydrophilic interaction liquid chromatography-tandem mass spectrometry method for acyl-Coenzyme A covering short- to long-chain species in a single analytical run. J Chromatogr A 2024; 1714:464524. [PMID: 38056390 DOI: 10.1016/j.chroma.2023.464524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/08/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023]
Abstract
Acyl-CoAs play a significant role in numerous physiological and metabolic processes making it important to assess their concentration levels for evaluating metabolic health. Considering the important role of acyl-CoAs, it is crucial to develop an analytical method that can analyze these compounds. Due to the structural variations of acyl-CoAs, multiple analytical methods are often required for comprehensive analysis of these compounds, which increases complexity and the analysis time. In this study, we have developed a method using a zwitterionic HILIC column that enables the coverage of free CoA and short- to long-chain acyl-CoA species in one analytical run. Initially, we developed the method using an LC-QTOF instrument for the identification of acyl-CoA species and optimizing their chromatography. Later, a targeted HILIC-MS/MS method was created in scheduled multiple reaction monitoring mode using a QTRAP MS detector. The performance of the method was evaluated based on various parameters such as linearity, precision, recovery and matrix effect. This method was applied to identify the difference in acyl-CoA profiles in HepG2 cells cultured in different conditions. Our findings revealed an increase in levels of acetyl-CoA, medium- and long-chain acyl-CoA while a decrease in the profiles of free CoA in the starved state, indicating a clear alteration in the fatty acid oxidation process.
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Affiliation(s)
- Madhulika Singh
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Ligia Akemi Kiyuna
- Laboratory of Paediatrics, University of Groningen, University Medical Centre Groningen, The Netherlands
| | - Christoff Odendaal
- Laboratory of Paediatrics, University of Groningen, University Medical Centre Groningen, The Netherlands
| | - Barbara M Bakker
- Laboratory of Paediatrics, University of Groningen, University Medical Centre Groningen, The Netherlands
| | - Amy C Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands.
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8
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Zhu Q, Combs ME, Liu J, Bai X, Wang WB, Herring LE, Liu J, Locasale JW, Bowles DE, Gross RT, Pla MM, Mack CP, Taylor JM. GRAF1 integrates PINK1-Parkin signaling and actin dynamics to mediate cardiac mitochondrial homeostasis. Nat Commun 2023; 14:8187. [PMID: 38081847 PMCID: PMC10713658 DOI: 10.1038/s41467-023-43889-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
The serine/threonine kinase, PINK1, and the E3 ubiquitin ligase, Parkin, are known to facilitate LC3-dependent autophagosomal encasement and lysosomal clearance of dysfunctional mitochondria, and defects in this process contribute to a variety of cardiometabolic and neurological diseases. Although recent evidence indicates that dynamic actin remodeling plays an important role in PINK1/Parkin-mediated mitochondrial autophagy (mitophagy), the underlying signaling mechanisms remain unknown. Here, we identify the RhoGAP GRAF1 (Arhgap26) as a PINK1 substrate that regulates mitophagy. GRAF1 promotes the release of damaged mitochondria from F-actin anchors, regulates mitochondrial-associated Arp2/3-mediated actin remodeling and facilitates Parkin-LC3 interactions to enhance mitochondria capture by autophagosomes. Graf1 phosphorylation on PINK1-dependent sites is dysregulated in human heart failure, and cardiomyocyte-restricted Graf1 depletion in mice blunts mitochondrial clearance and attenuates compensatory metabolic adaptations to stress. Overall, we identify GRAF1 as an enzyme that coordinates cytoskeletal and metabolic remodeling to promote cardioprotection.
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Affiliation(s)
- Qiang Zhu
- Department of Pathology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Matthew E Combs
- Department of Pathology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Xue Bai
- Department of Pathology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Wenbo B Wang
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Laura E Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jiandong Liu
- Department of Pathology, University of North Carolina, Chapel Hill, NC, 27599, USA
- McAllister Heart Institute University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Dawn E Bowles
- Division of Surgical Sciences, Duke University Medical Center, Durham, NC, 27710, USA
| | - Ryan T Gross
- Division of Surgical Sciences, Duke University Medical Center, Durham, NC, 27710, USA
| | - Michelle Mendiola Pla
- Division of Surgical Sciences, Duke University Medical Center, Durham, NC, 27710, USA
| | - Christopher P Mack
- Department of Pathology, University of North Carolina, Chapel Hill, NC, 27599, USA
- McAllister Heart Institute University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Joan M Taylor
- Department of Pathology, University of North Carolina, Chapel Hill, NC, 27599, USA.
- McAllister Heart Institute University of North Carolina, Chapel Hill, NC, 27599, USA.
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9
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Tokarska-Schlattner M, Zeaiter N, Cunin V, Attia S, Meunier C, Kay L, Achouri A, Hiriart-Bryant E, Couturier K, Tellier C, El Harras A, Elena-Herrmann B, Khochbin S, Le Gouellec A, Schlattner U. Multi-Method Quantification of Acetyl-Coenzyme A and Further Acyl-Coenzyme A Species in Normal and Ischemic Rat Liver. Int J Mol Sci 2023; 24:14957. [PMID: 37834405 PMCID: PMC10573920 DOI: 10.3390/ijms241914957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Thioesters of coenzyme A (CoA) carrying different acyl chains (acyl-CoAs) are central intermediates of many metabolic pathways and donor molecules for protein lysine acylation. Acyl-CoA species largely differ in terms of cellular concentrations and physico-chemical properties, rendering their analysis challenging. Here, we compare several approaches to quantify cellular acyl-CoA concentrations in normal and ischemic rat liver, using HPLC and LC-MS/MS for multi-acyl-CoA analysis, as well as NMR, fluorimetric and spectrophotometric techniques for the quantification of acetyl-CoAs. In particular, we describe a simple LC-MS/MS protocol that is suitable for the relative quantification of short and medium-chain acyl-CoA species. We show that ischemia induces specific changes in the short-chain acyl-CoA relative concentrations, while mild ischemia (1-2 min), although reducing succinyl-CoA, has little effects on acetyl-CoA, and even increases some acyl-CoA species upstream of the tricarboxylic acid cycle. In contrast, advanced ischemia (5-6 min) also reduces acetyl-CoA levels. Our approach provides the keys to accessing the acyl-CoA metabolome for a more in-depth analysis of metabolism, protein acylation and epigenetics.
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Affiliation(s)
- Malgorzata Tokarska-Schlattner
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Nour Zeaiter
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Valérie Cunin
- University Grenoble Alpes, CNRS UMR 5525, Laboratory TIMC—Translational Microbiology, Evolution, Engineering (TREE), Service de Biochimie, Biologie Moléculaire et Toxicologie Environnementale, CHU Grenoble-Alpes, 38058 Grenoble, France; (V.C.); (C.M.); (A.L.G.)
| | - Stéphane Attia
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Cécile Meunier
- University Grenoble Alpes, CNRS UMR 5525, Laboratory TIMC—Translational Microbiology, Evolution, Engineering (TREE), Service de Biochimie, Biologie Moléculaire et Toxicologie Environnementale, CHU Grenoble-Alpes, 38058 Grenoble, France; (V.C.); (C.M.); (A.L.G.)
| | - Laurence Kay
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Amel Achouri
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Edwige Hiriart-Bryant
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Karine Couturier
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Cindy Tellier
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Abderrafek El Harras
- University Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France; (A.E.H.); (B.E.-H.); (S.K.)
| | - Bénédicte Elena-Herrmann
- University Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France; (A.E.H.); (B.E.-H.); (S.K.)
| | - Saadi Khochbin
- University Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France; (A.E.H.); (B.E.-H.); (S.K.)
| | - Audrey Le Gouellec
- University Grenoble Alpes, CNRS UMR 5525, Laboratory TIMC—Translational Microbiology, Evolution, Engineering (TREE), Service de Biochimie, Biologie Moléculaire et Toxicologie Environnementale, CHU Grenoble-Alpes, 38058 Grenoble, France; (V.C.); (C.M.); (A.L.G.)
| | - Uwe Schlattner
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
- Institut Universitaire de France (IUF), 75231 Paris, France
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10
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Qiu S, Sheth V, Yan C, Liu J, Chacko BK, Li H, Crossman DK, Fortmann SD, Aryal S, Rennhack A, Grant MB, Welner RS, Paterson AJ, Wende AR, Darley-Usmar VM, Lu R, Locasale JW, Bhatia R. Metabolic adaptation to tyrosine kinase inhibition in leukemia stem cells. Blood 2023; 142:574-588. [PMID: 37192295 PMCID: PMC10447615 DOI: 10.1182/blood.2022018196] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/18/2023] Open
Abstract
Tyrosine kinase inhibitors (TKIs) are very effective in treating chronic myelogenous leukemia (CML), but primitive, quiescent leukemia stem cells persist as a barrier to the cure. We performed a comprehensive evaluation of metabolic adaptation to TKI treatment and its role in CML hematopoietic stem and progenitor cell persistence. Using a CML mouse model, we found that glycolysis, glutaminolysis, the tricarboxylic acid cycle, and oxidative phosphorylation (OXPHOS) were initially inhibited by TKI treatment in CML-committed progenitors but were restored with continued treatment, reflecting both selection and metabolic reprogramming of specific subpopulations. TKI treatment selectively enriched primitive CML stem cells with reduced metabolic gene expression. Persistent CML stem cells also showed metabolic adaptation to TKI treatment through altered substrate use and mitochondrial respiration maintenance. Evaluation of transcription factors underlying these changes helped detect increased HIF-1 protein levels and activity in TKI-treated stem cells. Treatment with an HIF-1 inhibitor in combination with TKI treatment depleted murine and human CML stem cells. HIF-1 inhibition increased mitochondrial activity and reactive oxygen species (ROS) levels, reduced quiescence, increased cycling, and reduced the self-renewal and regenerating potential of dormant CML stem cells. We, therefore, identified the HIF-1-mediated inhibition of OXPHOS and ROS and maintenance of CML stem cell dormancy and repopulating potential as a key mechanism of CML stem cell adaptation to TKI treatment. Our results identify a key metabolic dependency in CML stem cells persisting after TKI treatment that can be targeted to enhance their elimination.
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MESH Headings
- Mice
- Humans
- Animals
- Protein-Tyrosine Kinases/metabolism
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Reactive Oxygen Species/metabolism
- Neoplastic Stem Cells/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Drug Resistance, Neoplasm
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Affiliation(s)
- Shaowei Qiu
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, China
| | - Vipul Sheth
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL
| | - Chengcheng Yan
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC
| | - Balu K. Chacko
- Department of Pathology, Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL
| | - Hui Li
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL
| | - David K. Crossman
- Genomics Core Facility, University of Alabama at Birmingham, Birmingham, AL
| | - Seth D. Fortmann
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
- Medical Scientist Training Program, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Sajesan Aryal
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL
| | - Ashley Rennhack
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL
| | - Maria B. Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | - Robert S. Welner
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL
| | - Andrew J. Paterson
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL
| | - Adam R. Wende
- Department of Pathology, Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL
| | - Victor M. Darley-Usmar
- Department of Pathology, Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL
| | - Rui Lu
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL
| | - Jason W. Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC
| | - Ravi Bhatia
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL
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11
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Hinshaw DC, Benavides GA, Metge BJ, Swain CA, Kammerud SC, Alsheikh HA, Elhamamsy A, Chen D, Darley-Usmar V, Rathmell JC, Welner RS, Samant RS, Shevde LA. Hedgehog Signaling Regulates Treg to Th17 Conversion Through Metabolic Rewiring in Breast Cancer. Cancer Immunol Res 2023; 11:687-702. [PMID: 37058110 PMCID: PMC10159910 DOI: 10.1158/2326-6066.cir-22-0426] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/18/2022] [Accepted: 02/28/2023] [Indexed: 04/15/2023]
Abstract
The tumor immune microenvironment dynamically evolves to support tumor growth and progression. Immunosuppressive regulatory T cells (Treg) promote tumor growth and metastatic seeding in patients with breast cancer. Deregulation of plasticity between Treg and Th17 cells creates an immune regulatory framework that enables tumor progression. Here, we discovered a functional role for Hedgehog (Hh) signaling in promoting Treg differentiation and immunosuppressive activity, and when Hh activity was inhibited, Tregs adopted a Th17-like phenotype complemented by an enhanced inflammatory profile. Mechanistically, Hh signaling promoted O-GlcNAc modifications of critical Treg and Th17 transcription factors, Foxp3 and STAT3, respectively, that orchestrated this transition. Blocking Hh reprogramed Tregs metabolically, dampened their immunosuppressive activity, and supported their transdifferentiation into inflammatory Th17 cells that enhanced the recruitment of cytotoxic CD8+ T cells into tumors. Our results demonstrate a previously unknown role for Hh signaling in the regulation of Treg differentiation and activity and the switch between Tregs and Th17 cells in the tumor microenvironment.
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Affiliation(s)
- Dominique C. Hinshaw
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gloria A. Benavides
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brandon J. Metge
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Courtney A. Swain
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sarah C. Kammerud
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Heba A. Alsheikh
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amr Elhamamsy
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dongquan Chen
- Division of Preventive Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Victor Darley-Usmar
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey C. Rathmell
- Department of Pathology, Microbiology, and Immunology, VUMC, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Robert S. Welner
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rajeev S. Samant
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Birmingham VA Medical Center, Birmingham, AL, USA
| | - Lalita A. Shevde
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Senior author
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12
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Zhang R, Bons J, Scheidemantle G, Liu X, Bielska O, Carrico C, Rose J, Heckenbach I, Scheibye-Knudsen M, Schilling B, Verdin E. Histone malonylation is regulated by SIRT5 and KAT2A. iScience 2023; 26:106193. [PMID: 36879797 PMCID: PMC9985052 DOI: 10.1016/j.isci.2023.106193] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/18/2022] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
The posttranslational modification lysine malonylation is found in many proteins, including histones. However, it remains unclear whether histone malonylation is regulated or functionally relevant. Here, we report that availability of malonyl-co-enzyme A (malonyl-CoA), an endogenous malonyl donor, affects lysine malonylation, and that the deacylase SIRT5 selectively reduces malonylation of histones. To determine if histone malonylation is enzymatically catalyzed, we knocked down each of the 22 lysine acetyltransferases (KATs) to test their malonyltransferase potential. KAT2A knockdown in particular reduced histone malonylation levels. By mass spectrometry, H2B_K5 was highly malonylated and regulated by SIRT5 in mouse brain and liver. Acetyl-CoA carboxylase (ACC), the malonyl-CoA producing enzyme, was partly localized in the nucleolus, and histone malonylation increased nucleolar area and ribosomal RNA expression. Levels of global lysine malonylation and ACC expression were higher in older mouse brains than younger mice. These experiments highlight the role of histone malonylation in ribosomal gene expression.
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Affiliation(s)
- Ran Zhang
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Grace Scheidemantle
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Olga Bielska
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Chris Carrico
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Indra Heckenbach
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Nørregade 10, Copenhagen, Denmark
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Nørregade 10, Copenhagen, Denmark
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
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13
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Yang Y, Reid MA, Hanse EA, Li H, Li Y, Ruiz BI, Fan Q, Kong M. SAPS3 subunit of protein phosphatase 6 is an AMPK inhibitor and controls metabolic homeostasis upon dietary challenge in male mice. Nat Commun 2023; 14:1368. [PMID: 36914647 PMCID: PMC10011557 DOI: 10.1038/s41467-023-36809-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/17/2023] [Indexed: 03/16/2023] Open
Abstract
Inhibition of AMPK is tightly associated with metabolic perturbations upon over nutrition, yet the molecular mechanisms underlying are not clear. Here, we demonstrate the serine/threonine-protein phosphatase 6 regulatory subunit 3, SAPS3, is a negative regulator of AMPK. SAPS3 is induced under high fat diet (HFD) and recruits the PP6 catalytic subunit to deactivate phosphorylated-AMPK, thereby inhibiting AMPK-controlled metabolic pathways. Either whole-body or liver-specific deletion of SAPS3 protects male mice against HFD-induced detrimental consequences and reverses HFD-induced metabolic and transcriptional alterations while loss of SAPS3 has no effects on mice under balanced diets. Furthermore, genetic inhibition of AMPK is sufficient to block the protective phenotype in SAPS3 knockout mice under HFD. Together, our results reveal that SAPS3 is a negative regulator of AMPK and suppression of SAPS3 functions as a guardian when metabolism is perturbed and represents a potential therapeutic strategy to treat metabolic syndromes.
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Affiliation(s)
- Ying Yang
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Michael A Reid
- Department of Cancer Biology, Beckman Research Institute of City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Eric A Hanse
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Haiqing Li
- Integrative Genomics Core, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Yuanding Li
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Bryan I Ruiz
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Qi Fan
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Mei Kong
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA.
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14
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Xue L, Schnacke P, Frei MS, Koch B, Hiblot J, Wombacher R, Fabritz S, Johnsson K. Probing coenzyme A homeostasis with semisynthetic biosensors. Nat Chem Biol 2023; 19:346-355. [PMID: 36316571 PMCID: PMC9974488 DOI: 10.1038/s41589-022-01172-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/13/2022] [Indexed: 11/07/2022]
Abstract
Coenzyme A (CoA) is one of the central cofactors of metabolism, yet a method for measuring its concentration in living cells is missing. Here we introduce the first biosensor for measuring CoA levels in different organelles of mammalian cells. The semisynthetic biosensor is generated through the specific labeling of an engineered GFP-HaloTag fusion protein with a fluorescent ligand. Its readout is based on CoA-dependent changes in Förster resonance energy transfer efficiency between GFP and the fluorescent ligand. Using this biosensor, we probe the role of numerous proteins involved in CoA biosynthesis and transport in mammalian cells. On the basis of these studies, we propose a cellular map of CoA biosynthesis that suggests how pools of cytosolic and mitochondrial CoA are maintained.
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Affiliation(s)
- Lin Xue
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
- MOE Key Laboratory for Cellular Dynamics, Hefei National Center for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, China.
| | - Paul Schnacke
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Richard Wombacher
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Sebastian Fabritz
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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15
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Meyers AK, Wang Z, Han W, Zhao Q, Zabalawi M, Duan L, Liu J, Zhang Q, Manne RK, Lorenzo F, Quinn MA, Song Q, Fan D, Lin HK, Furdui CM, Locasale JW, McCall CE, Zhu X. Pyruvate dehydrogenase kinase supports macrophage NLRP3 inflammasome activation during acute inflammation. Cell Rep 2023; 42:111941. [PMID: 36640341 PMCID: PMC10117036 DOI: 10.1016/j.celrep.2022.111941] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 08/02/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Activating the macrophage NLRP3 inflammasome can promote excessive inflammation with severe cell and tissue damage and organ dysfunction. Here, we show that pharmacological or genetic inhibition of pyruvate dehydrogenase kinase (PDHK) significantly attenuates NLRP3 inflammasome activation in murine and human macrophages and septic mice by lowering caspase-1 cleavage and interleukin-1β (IL-1β) secretion. Inhibiting PDHK reverses NLRP3 inflammasome-induced metabolic reprogramming, enhances autophagy, promotes mitochondrial fusion over fission, preserves crista ultrastructure, and attenuates mitochondrial reactive oxygen species (ROS) production. The suppressive effect of PDHK inhibition on the NLRP3 inflammasome is independent of its canonical role as a pyruvate dehydrogenase regulator. Our study suggestsa non-canonical role of mitochondrial PDHK in promoting mitochondrial stress and supporting NLRP3 inflammasome activation during acute inflammation.
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Affiliation(s)
- Allison K Meyers
- Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Zhan Wang
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Wenzheng Han
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Department of Cardiology, Huadong Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Qingxia Zhao
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Manal Zabalawi
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Likun Duan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Qianyi Zhang
- Department of Biology, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Rajesh K Manne
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Felipe Lorenzo
- Section on Endocrinology and Metabolism, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Matthew A Quinn
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Qianqian Song
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Daping Fan
- Department of Cell Biology and Anatomy, University of South Carolina School of Medicine, Columbia, SC 29209, USA
| | - Hui-Kuan Lin
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Cristina M Furdui
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Charles E McCall
- Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Xuewei Zhu
- Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
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16
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Filonenko V, Gout I. Discovery and functional characterisation of protein CoAlation and the antioxidant function of coenzyme A. BBA ADVANCES 2023; 3:100075. [PMID: 37082257 PMCID: PMC10074942 DOI: 10.1016/j.bbadva.2023.100075] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Coenzyme A (CoA) is an essential cofactor in all living cells which plays critical role in cellular metabolism, the regulation of gene expression and the biosynthesis of major cellular constituents. Recently, CoA was found to function as a major antioxidant in both prokaryotic and eukaryotic cells. This unconventional function of CoA is mediated by a novel post-translational modification, termed protein CoAlation. This review will highlight the history of this discovery, current knowledge, and future directions on studying molecular mechanisms of protein CoAlation and whether the antioxidant function of CoA is associated with pathologies, such as neurodegeneration and cancer.
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Affiliation(s)
- Valeriy Filonenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
- Corresponding authors.
| | - Ivan Gout
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
- Corresponding authors.
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17
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James AM, Norman AAI, Houghton JW, Prag HA, Logan A, Antrobus R, Hartley RC, Murphy MP. Native chemical ligation approach to sensitively probe tissue acyl-CoA pools. Cell Chem Biol 2022; 29:1232-1244.e5. [PMID: 35868236 DOI: 10.1016/j.chembiol.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/29/2022] [Accepted: 04/18/2022] [Indexed: 11/16/2022]
Abstract
During metabolism, carboxylic acids are often activated by conjugation to the thiol of coenzyme A (CoA). The resulting acyl-CoAs comprise a group of ∼100 thioester-containing metabolites that could modify protein behavior through non-enzymatic N-acylation of lysine residues. However, the importance of many potential acyl modifications remains unclear because antibody-based methods to detect them are unavailable and the in vivo concentrations of their respective acyl-CoAs are poorly characterized. Here, we develop cysteine-triphenylphosphonium (CysTPP), a mass spectrometry probe that uses "native chemical ligation" to sensitively detect the major acyl-CoAs present in vivo through irreversible modification of its amine via a thioester intermediate. Using CysTPP, we show that longer-chain (C13-C22) acyl-CoAs often constitute ∼60% of the acyl-CoA pool in rat tissues. These hydrophobic longer-chain fatty acyl-CoAs have the potential to non-enzymatically modify protein residues.
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Affiliation(s)
- Andrew M James
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
| | - Abigail A I Norman
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Jack W Houghton
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Hiran A Prag
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Angela Logan
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Robin Antrobus
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Richard C Hartley
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Michael P Murphy
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
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18
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Duan L, Cooper DE, Scheidemantle G, Locasale JW, Kirsch DG, Liu X. 13C tracer analysis suggests extensive recycling of endogenous CO 2 in vivo. Cancer Metab 2022; 10:11. [PMID: 35799202 PMCID: PMC9264524 DOI: 10.1186/s40170-022-00287-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/16/2022] [Indexed: 12/11/2022] Open
Abstract
Background 13C tracer analysis is increasingly used to monitor cellular metabolism in vivo and in intact cells, but data interpretation is still the key element to unveil the complexity of metabolic activities. The distinct 13C labeling patterns (e.g., M + 1 species in vivo but not in vitro) of metabolites from [U-13C]-glucose or [U-13C]-glutamine tracing in vivo and in vitro have been previously reported by multiple groups. However, the reason for the difference in the M + 1 species between in vivo and in vitro experiments remains poorly understood. Methods We have performed [U-13C]-glucose and [U-13C]-glutamine tracing in sarcoma-bearing mice (in vivo) and in cancer cell lines (in vitro). 13C enrichment of metabolites in cultured cells and tissues was determined by LC coupled with high-resolution mass spectrometry (LC-HRMS). All p-values are obtained from the Student’s t-test two-tailed using GraphPad Prism 8 unless otherwise noted. Results We observed distinct enrichment patterns of tricarboxylic acid cycle intermediates in vivo and in vitro. As expected, citrate M + 2 or M + 4 was the dominant mass isotopologue in vitro. However, citrate M + 1 was unexpectedly the dominant isotopologue in mice receiving [U-13C]-glucose or [U-13C]-glutamine infusion, but not in cultured cells. Our results are consistent with a model where the difference in M + 1 species is due to the different sources of CO2 in vivo and in vitro, which was largely overlooked in the past. In addition, a time course study shows the generation of high abundance citrate M + 1 in plasma of mice as early as few minutes after [U-13C]-glucose infusion. Conclusions Altogether, our results show that recycling of endogenous CO2 is substantial in vivo. The production and recycling of 13CO2 from the decarboxylation of [U-13C]-glucose or [U-13C]-glutamine is negligible in vitro partially due to dilution by the exogenous HCO3−/CO2 source, but in vivo incorporation of endogenous 13CO2 into M + 1 metabolites is substantial and should be considered. These findings provide a new paradigm to understand carbon atom transformations in vivo and should be taken into account when developing mathematical models to better reflect carbon flux. Supplementary Information The online version contains supplementary material available at 10.1186/s40170-022-00287-8.
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Affiliation(s)
- Likun Duan
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, 27695, USA
| | - Daniel E Cooper
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC, 27708, USA
| | - Grace Scheidemantle
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, 27695, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, 27708, USA
| | - David G Kirsch
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC, 27708, USA.,Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, 27708, USA
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, 27695, USA.
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19
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Pearce RW, Kodger JV, Sandlers YI. A liquid chromatography tandem mass spectrometry method for a semiquantitative screening of cellular acyl-CoA. Anal Biochem 2022; 640:114430. [PMID: 34688603 DOI: 10.1016/j.ab.2021.114430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/28/2021] [Accepted: 10/17/2021] [Indexed: 01/10/2023]
Abstract
This study describes LC-ESI-MS/MS method that covers the analysis of various cellular acyl-CoA in a single injection. The method is based on a quick extraction step eliminating LLE/SPE clean up. Method performance characteristics were determined after spiking acyl-CoA standards in different concentrations into a surrogate matrix. The extensive matrix effect for most acyl-CoA except for palmitoyl-CoA was compensated by using isotopically labeled internal standard and matrix-matched calibration. As a result of the high matrix effect, the accuracy for palmitoyl-CoA at the low concentration deviated from the target range of ±20%. The developed method was applied to identify twenty-one cellular acyl-CoA in SK-HEP-1 cells and screening for alterations in acyl-CoA levels post Mito Q antioxidant intervention.
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Affiliation(s)
- Ryan W Pearce
- Cleveland State University, Department of Chemistry, United States
| | - Jillian V Kodger
- Cleveland State University, Department of Chemistry, United States
| | - Yana I Sandlers
- Cleveland State University, Department of Chemistry, United States.
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20
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Keshet U, Kind T, Lu X, Devi S, Fiehn O. Acyl-CoA Identification in Mouse Liver Samples Using the In Silico CoA-Blast Tandem Mass Spectral Library. Anal Chem 2022; 94:2732-2739. [PMID: 35119811 DOI: 10.1021/acs.analchem.1c03272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acyl-coenzyme A derivatives (acyl-CoAs) are core molecules in the fatty acid and energy metabolism across all species. However, in vivo, many other carboxylic acids can form xenobiotic acyl-CoA esters, including drugs. More than 2467 acyl-CoAs are known from the published literature. In addition, more than 300 acyl-CoAs are covered in pathway databases, but as of October 2020, only 53 experimental acyl-CoA tandem mass spectra are present in NIST20 and MoNA libraries to enable annotation of the mass spectra in untargeted metabolomics studies. The experimental spectra originated from low-resolution ion trap and triple quadrupole mass spectrometers as well as high-resolution quadrupole-time of flight and orbital ion trap instruments at various collision energies. We used MassFrontier software and the literature to annotate fragment ions to generate fragmentation rules and intensities for the different instruments and collision energies. These rules were then applied to 1562 unique species based on [M+H]+ and [M-H]- precursor ions to generate two mass spectra per instrument platform and collision energy, amassing an in silico library of 10,934 accurate mass MS/MS spectra that are freely available at github.com/urikeshet/CoA-Blast. The spectra can be imported into a commercial or freely available mass spectral search tool. We used the libraries to annotate 23 acyl-CoA esters in mouse liver, including 8 novel species.
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Affiliation(s)
- Uri Keshet
- University of California Davis, Genome Center-Metabolomics, Davis, California 95616, United States
| | - Tobias Kind
- University of California Davis, Genome Center-Metabolomics, Davis, California 95616, United States
| | - Xinchen Lu
- University of California Davis, Genome Center-Metabolomics, Davis, California 95616, United States.,College of Environmental Sciences and Engineering, Peking University, Beijing 100871, P. R. China
| | - Sarita Devi
- University of California Davis, Genome Center-Metabolomics, Davis, California 95616, United States.,St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore 560034, India
| | - Oliver Fiehn
- University of California Davis, Genome Center-Metabolomics, Davis, California 95616, United States
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21
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Park SY, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S. Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite. Cell 2022; 185:513-529.e21. [PMID: 35120663 PMCID: PMC8896310 DOI: 10.1016/j.cell.2022.01.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/07/2021] [Accepted: 01/05/2022] [Indexed: 02/05/2023]
Abstract
The human gut microbiota resides within a diverse chemical environment challenging our ability to understand the forces shaping this ecosystem. Here, we reveal that fitness of the Bacteroidales, the dominant order of bacteria in the human gut, is an emergent property of glycans and one specific metabolite, butyrate. Distinct sugars serve as strain-variable fitness switches activating context-dependent inhibitory functions of butyrate. Differential fitness effects of butyrate within the Bacteroides are mediated by species-level variation in Acyl-CoA thioesterase activity and nucleotide polymorphisms regulating an Acyl-CoA transferase. Using in vivo multi-omic profiles, we demonstrate Bacteroides fitness in the human gut is associated together, but not independently, with Acyl-CoA transferase expression and butyrate. Our data reveal that each strain of the Bacteroides exists within a unique fitness landscape based on the interaction of chemical components unpredictable by the effect of each part alone mediated by flexibility in the core genome.
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Affiliation(s)
- Sun-Yang Park
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Chitong Rao
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Katharine Z Coyte
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Gavin A Kuziel
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Yancong Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wentao Huang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seth Rakoff-Nahoum
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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22
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Bhatt DP, Mills CA, Anderson KA, Henriques BJ, Lucas TG, Francisco S, Liu J, Ilkayeva OR, Adams AE, Kulkarni SR, Backos DS, Major MB, Grimsrud PA, Gomes CM, Hirschey MD. Deglutarylation of glutaryl-CoA dehydrogenase by deacylating enzyme SIRT5 promotes lysine oxidation in mice. J Biol Chem 2022; 298:101723. [PMID: 35157847 PMCID: PMC8969154 DOI: 10.1016/j.jbc.2022.101723] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022] Open
Abstract
A wide range of protein acyl modifications has been identified on enzymes across various metabolic processes; however, the impact of these modifications remains poorly understood. Protein glutarylation is a recently identified modification that can be nonenzymatically driven by glutaryl-CoA. In mammalian systems, this unique metabolite is only produced in the lysine and tryptophan oxidative pathways. To better understand the biology of protein glutarylation, we studied the relationship between enzymes within the lysine/tryptophan catabolic pathways, protein glutarylation, and regulation by the deglutarylating enzyme sirtuin 5 (SIRT5). Here, we identify glutarylation on the lysine oxidation pathway enzyme glutaryl-CoA dehydrogenase (GCDH) and show increased GCDH glutarylation when glutaryl-CoA production is stimulated by lysine catabolism. Our data reveal that glutarylation of GCDH impacts its function, ultimately decreasing lysine oxidation. We also demonstrate the ability of SIRT5 to deglutarylate GCDH, restoring its enzymatic activity. Finally, metabolomic and bioinformatic analyses indicate an expanded role for SIRT5 in regulating amino acid metabolism. Together, these data support a feedback loop model within the lysine/tryptophan oxidation pathway in which glutaryl-CoA is produced, in turn inhibiting GCDH function via glutaryl modification of GCDH lysine residues and can be relieved by SIRT5 deacylation activity.
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23
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Ma X, Wu J, Li Y, Liang X, Casper D, Ding W, Wang X, Shi A, Shi X, Ma L, Eer H, Lang X. Transcriptome and metabolome analyses reveal muscle changes in Tan sheep (Ovis aries) at different ages. Livest Sci 2022. [DOI: 10.1016/j.livsci.2021.104781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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24
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Sekiya M, Kainoh K, Sugasawa T, Yoshino R, Hirokawa T, Tokiwa H, Nakano S, Nagatoishi S, Tsumoto K, Takeuchi Y, Miyamoto T, Matsuzaka T, Shimano H. The transcriptional corepressor CtBP2 serves as a metabolite sensor orchestrating hepatic glucose and lipid homeostasis. Nat Commun 2021; 12:6315. [PMID: 34728642 PMCID: PMC8563733 DOI: 10.1038/s41467-021-26638-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/15/2021] [Indexed: 01/19/2023] Open
Abstract
Biological systems to sense and respond to metabolic perturbations are critical for the maintenance of cellular homeostasis. Here we describe a hepatic system in this context orchestrated by the transcriptional corepressor C-terminal binding protein 2 (CtBP2) that harbors metabolite-sensing capabilities. The repressor activity of CtBP2 is reciprocally regulated by NADH and acyl-CoAs. CtBP2 represses Forkhead box O1 (FoxO1)-mediated hepatic gluconeogenesis directly as well as Sterol Regulatory Element-Binding Protein 1 (SREBP1)-mediated lipogenesis indirectly. The activity of CtBP2 is markedly defective in obese liver reflecting the metabolic perturbations. Thus, liver-specific CtBP2 deletion promotes hepatic gluconeogenesis and accelerates the progression of steatohepatitis. Conversely, activation of CtBP2 ameliorates diabetes and hepatic steatosis in obesity. The structure-function relationships revealed in this study identify a critical structural domain called Rossmann fold, a metabolite-sensing pocket, that is susceptible to metabolic liabilities and potentially targetable for developing therapeutic approaches.
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Affiliation(s)
- Motohiro Sekiya
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Kenta Kainoh
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Takehito Sugasawa
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Ryunosuke Yoshino
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo, 171-8501, Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshinori Takeuchi
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Takafumi Miyamoto
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Takashi Matsuzaka
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Hitoshi Shimano
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
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25
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Liang Y, Tang Z, Jiang Y, Ai C, Peng J, Liu Y, Chen J, Xin X, Lei B, Zhang J, Cai Z. Lipid metabolism disorders associated with dioxin exposure in a cohort of Chinese male workers revealed by a comprehensive lipidomics study. ENVIRONMENT INTERNATIONAL 2021; 155:106665. [PMID: 34098336 DOI: 10.1016/j.envint.2021.106665] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/23/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Dioxins, environmentally stable and ubiquitous, have been found to induce metabolic changes especially in lipids and be related to multiple diseases. However, limited study is available on lipid alternations related to human exposure to dioxins. This study aims to explore the serum lipidomic characterization and to understand the underlying mechanisms of adverse health risks associated with dioxin exposure. A lipidomic study integrating nontargeted lipidomics, and targeted free fatty acid (FFA) and acyl-coenzyme A (acyl-CoA) analyses were conducted to investigate the 94 serum samples from two groups of male workers with remarkably different dioxin concentrations. The obtained results exhibited distinct lipidomic signatures between the high and low exposed groups. A total of 37 lipids were identified with the significant changes. The results revealed that dioxin exposure caused accumulations of triglyceride (TG), ceramide (Cer) and sphingoid (So), remodeling of glycerophospholipid (GP), imbalanced FFA metabolism, as well as upregulation of platelet-activating factor (PAF). These findings implied the associations between dioxin exposure and potential adverse health risks including inflammation, apoptosis, cardiovascular diseases (CVDs), and liver diseases. This study is the first to explain the associations between dioxin exposure and health effects at the level of lipid metabolism.
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Affiliation(s)
- Yanshan Liang
- Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region
| | - Zhi Tang
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China; Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yousheng Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Chunyan Ai
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Jinling Peng
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Yuan Liu
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Jinru Chen
- Songgang Preventive Health Center of Baoan District, Shenzhen, 518105, China
| | - Xiong Xin
- Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai, China
| | - Bo Lei
- Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai, China
| | - Jianqing Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China.
| | - Zongwei Cai
- Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region.
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26
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Hinshaw DC, Hanna A, Lama-Sherpa T, Metge B, Kammerud SC, Benavides GA, Kumar A, Alsheikh HA, Mota M, Chen D, Ballinger SW, Rathmell JC, Ponnazhagan S, Darley-Usmar V, Samant RS, Shevde LA. Hedgehog signaling regulates metabolism and polarization of mammary tumor-associated macrophages. Cancer Res 2021; 81:5425-5437. [PMID: 34289986 DOI: 10.1158/0008-5472.can-20-1723] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 05/03/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022]
Abstract
Elevated infiltration of immunosuppressive alternatively polarized (M2) macrophages is associated with poor prognosis in cancer patients. The tumor microenvironment remarkably orchestrates molecular mechanisms that program these macrophages. Here we identify a novel role for oncogenic Hedgehog (Hh) signaling in programming signature metabolic circuitries that regulate alternative polarization of tumor-associated macrophages. Two immunocompetent orthotopic mouse models of mammary tumors were used to test the effect of inhibiting Hh signaling on tumor-associated macrophages. Treatment with the pharmacological Hh inhibitor Vismodegib induced a significant shift in the profile of tumor-infiltrating macrophages. Mass spectrometry-based metabolomic analysis showed Hh inhibition induced significant alterations in metabolic processes, including metabolic sensing, mitochondrial adaptations, and lipid metabolism. In particular, inhibition of Hh in M2 macrophages reduced flux through the UDP-GlcNAc biosynthesis pathway. Consequently, O-GlcNAc-modification of STAT6 decreased, mitigating the immune suppressive program of M2 macrophages, and the metabolically demanding M2 macrophages shifted their metabolism and bioenergetics from fatty acid oxidation to glycolysis. M2 macrophages enriched from Vismodegib-treated mammary tumors showed characteristically decreased O-GlcNAcylation and altered mitochondrial dynamics. These Hh-inhibited macrophages are reminiscent of inflammatory (M1) macrophages, phenotypically characterized by fragmented mitochondria. This is the first report highlighting the relevance of Hh signaling in controlling a complex metabolic network in immune cells. These data describe a novel immunometabolic function of Hh signaling that can be clinically exploited.
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Affiliation(s)
| | | | | | | | | | | | - Atul Kumar
- Department of Pathology, University of Alabama at Birmingham
| | | | - Mateus Mota
- Department of Pathology, University of Alabama at Birmingham
| | - Dongquan Chen
- Division of Preventive Medicine, University of Alabama at Birmingham
| | | | - Jeffrey C Rathmell
- Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | | | | | | | - Lalita A Shevde
- Department of Pathology, University of Alabama at Birmingham
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27
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Ye Q, Zeng X, Wang S, Zeng X, Yang G, Ye C, Cai S, Chen M, Li S, Qiao S. Butyrate drives the acetylation of histone H3K9 to activate steroidogenesis through PPARγ and PGC1α pathways in ovarian granulosa cells. FASEB J 2021; 35:e21316. [PMID: 33433947 DOI: 10.1096/fj.202000444r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 11/26/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022]
Abstract
Maintaining ovarian steroidogenesis is of critical importance, considering that steroid hormones are required for successful establishment and maintenance of pregnancy and proper development of embryos and fetuses. Investigating the mechanism that butyrate modulates the ovarian steroidogenesis is beneficial for understanding the impact of lipid nutrition on steroidogenesis. Herein, we identified that butyrate improved estradiol and progesterone synthesis in rat primary ovarian granulosa cells and human granulosa KGN cells and discovered the related mechanism. Our data indicated that butyrate was sensed by GPR41 and GPR43 in ovarian granulosa cells. Butyrate primarily upregulated the acetylation of histone H3K9 (H3K9ac). Chromatin immune-precipitation and sequencing (ChIP-seq) data of H3K9ac revealed the influenced pathways involving in the mitochondrial function (including cellular metabolism and steroidogenesis) and cellular antioxidant capacity. Additionally, increasing H3K9ac by butyrate further stimulated the PPARγ/CD36/StAR pathways to increase ovarian steroidogenesis and activated PGC1α to enhance mitochondrial dynamics and alleviate oxidative damage. The improvement in antioxidant capacity and mitochondrial dynamics by butyrate enhanced ovarian steroidogenesis. Collectively, butyrate triggers histone H3K9ac to activate steroidogenesis through PPARγ and PGC1α pathways in ovarian granulosa cells.
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Affiliation(s)
- Qianhong Ye
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing, P.R. China.,Beijing Key Laboratory of Biofeed Additives, Beijing, P.R. China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing, P.R. China.,Beijing Key Laboratory of Biofeed Additives, Beijing, P.R. China
| | - Shuai Wang
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing, P.R. China.,Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Xiangzhou Zeng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing, P.R. China.,Beijing Key Laboratory of Biofeed Additives, Beijing, P.R. China
| | - Guangxin Yang
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing, P.R. China.,Beijing Key Laboratory of Biofeed Additives, Beijing, P.R. China
| | - Changchuan Ye
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing, P.R. China.,Beijing Key Laboratory of Biofeed Additives, Beijing, P.R. China
| | - Shuang Cai
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing, P.R. China.,Beijing Key Laboratory of Biofeed Additives, Beijing, P.R. China
| | - Meixia Chen
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing, P.R. China.,Beijing Key Laboratory of Biofeed Additives, Beijing, P.R. China
| | - Siyu Li
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing, P.R. China.,Beijing Key Laboratory of Biofeed Additives, Beijing, P.R. China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing, P.R. China.,Beijing Key Laboratory of Biofeed Additives, Beijing, P.R. China
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Trabjerg MS, Andersen DC, Huntjens P, Oklinski KE, Bolther L, Hald JL, Baisgaard AE, Mørk K, Warming N, Kullab UB, Kroese LJ, Pritchard CEJ, Huijbers IJ, Nieland JDV. Downregulating carnitine palmitoyl transferase 1 affects disease progression in the SOD1 G93A mouse model of ALS. Commun Biol 2021; 4:509. [PMID: 33931719 PMCID: PMC8087699 DOI: 10.1038/s42003-021-02034-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/26/2021] [Indexed: 02/03/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron disease characterized by death of motor neurons. The etiology and pathogenesis remains elusive despite decades of intensive research. Herein, we report that dysregulated metabolism plays a central role in the SOD1 G93A mouse model mimicking ALS. Specifically, we report that the activity of carnitine palmitoyl transferase 1 (CPT1) lipid metabolism is associated with disease progression. Downregulation of CPT1 activity by pharmacological and genetic methods results in amelioration of disease symptoms, inflammation, oxidative stress and mitochondrial function, whereas upregulation by high-fat diet or corticosterone results in a more aggressive disease progression. Finally, we show that downregulating CPT1 shifts the gut microbiota communities towards a protective phenotype in SOD1 G93A mice. These findings reveal that metabolism, and specifically CPT1 lipid metabolism plays a central role in the SOD1 G93A mouse model and shows that CPT1 might be a therapeutic target in ALS.
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Affiliation(s)
| | | | - Pam Huntjens
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | | - Luise Bolther
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Jonas Laugård Hald
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | | - Kasper Mørk
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Nikolaj Warming
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Ulla Bismark Kullab
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Lona John Kroese
- Mouse Clinic for Cancer and Aging Research, Transgenic Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Colin Eliot Jason Pritchard
- Mouse Clinic for Cancer and Aging Research, Transgenic Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ivo Johan Huijbers
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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29
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Cakić N, Kopke B, Rabus R, Wilkes H. Suspect screening and targeted analysis of acyl coenzyme A thioesters in bacterial cultures using a high-resolution tribrid mass spectrometer. Anal Bioanal Chem 2021; 413:3599-3610. [PMID: 33881564 PMCID: PMC8141488 DOI: 10.1007/s00216-021-03318-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/14/2021] [Accepted: 03/30/2021] [Indexed: 11/20/2022]
Abstract
Analysis of acyl coenzyme A thioesters (acyl-CoAs) is crucial in the investigation of a wide range of biochemical reactions and paves the way to fully understand the concerned metabolic pathways and their superimposed networks. We developed two methods for suspect screening of acyl-CoAs in bacterial cultures using a high-resolution Orbitrap Fusion tribrid mass spectrometer. The methods rely on specific fragmentation patterns of the target compounds, which originate from the coenzyme A moiety. They make use of the formation of the adenosine 3′,5′-diphosphate key fragment (m/z 428.0365) and the neutral loss of the adenosine 3′-phosphate-5′-diphosphate moiety (506.9952) as preselection criteria for the detection of acyl-CoAs. These characteristic ions are generated either by an optimised in-source fragmentation in a full scan Orbitrap measurement or by optimised HCD fragmentation. Additionally, five different filters are included in the design of method. Finally, data-dependent MS/MS experiments on specifically preselected precursor ions are performed. The utility of the methods is demonstrated by analysing cultures of the denitrifying betaproteobacterium “Aromatoleum” sp. strain HxN1 anaerobically grown with hexanoate. We detected 35 acyl-CoAs in total and identified 24 of them by comparison with reference standards, including all 9 acyl-CoA intermediates expected to occur in the degradation pathway of hexanoate. The identification of additional acyl-CoAs provides insight into further metabolic processes occurring in this bacterium. The sensitivity of the method described allows detecting acyl-CoAs present in biological samples in highly variable abundances. Graphical abstract ![]()
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Affiliation(s)
- Nevenka Cakić
- Organic Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany.
| | - Bernd Kopke
- Organic Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Ralf Rabus
- General & Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Heinz Wilkes
- Organic Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
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30
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Metabolic supervision by PPIP5K, an inositol pyrophosphate kinase/phosphatase, controls proliferation of the HCT116 tumor cell line. Proc Natl Acad Sci U S A 2021; 118:2020187118. [PMID: 33649228 PMCID: PMC7958180 DOI: 10.1073/pnas.2020187118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Identification of common patterns of cancer metabolic reprogramming could assist the development of new therapeutic strategies. Recent attention in this field has focused on identifying and targeting signal transduction pathways that interface directly with major metabolic control processes. In the current study we demonstrate the importance of signaling by the diphosphoinositol pentakisphosphate kinases (PPIP5Ks) to the metabolism and proliferation of the HCT116 colonic tumor cell line. We observed reciprocal cross talk between PPIP5K catalytic activity and glucose metabolism, and we show that CRISPR-mediated PPIP5K deletion suppresses HCT116 cell proliferation in glucose-limited culture conditions that mimic the tumor cell microenvironment. We conducted detailed, global metabolomic analyses of wild-type and PPIP5K knockout (KO) cells by measuring both steady-state metabolite levels and by performing isotope tracing experiments. We attribute the growth-impaired phenotype to a specific reduction in the supply of precursor material for de novo nucleotide biosynthesis from the one carbon serine/glycine pathway and the pentose phosphate pathway. We identify two enzymatic control points that are inhibited in the PPIP5K KO cells: serine hydroxymethyltransferase and phosphoribosyl pyrophosphate synthetase, a known downstream target of AMP-regulated protein kinase, which we show is noncanonically activated independently of adenine nucleotide status. Finally, we show the proliferative defect in PPIP5K KO cells can be significantly rescued either by addition of inosine monophosphate or a nucleoside mixture or by stable expression of PPIP5K activity. Overall, our data describe multiple, far-reaching metabolic consequences for metabolic supervision by PPIP5Ks in a tumor cell line.
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31
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Mason JA, Cockfield JA, Pape DJ, Meissner H, Sokolowski MT, White TC, Valentín López JC, Liu J, Liu X, Martínez-Reyes I, Chandel NS, Locasale JW, Schafer ZT. SGK1 signaling promotes glucose metabolism and survival in extracellular matrix detached cells. Cell Rep 2021; 34:108821. [PMID: 33730592 DOI: 10.1016/j.celrep.2021.108821] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 12/30/2020] [Accepted: 02/12/2021] [Indexed: 12/29/2022] Open
Abstract
Loss of integrin-mediated attachment to extracellular matrix (ECM) proteins can trigger a variety of cellular changes that affect cell viability. Foremost among these is the activation of anoikis, caspase-mediated cell death induced by ECM detachment. In addition, loss of ECM attachment causes profound alterations in cellular metabolism, which can lead to anoikis-independent cell death. Here, we describe a surprising role for serum and glucocorticoid kinase-1 (SGK1) in the promotion of energy production when cells are detached. Our data demonstrate that SGK1 activation is necessary and sufficient for ATP generation during ECM detachment and anchorage-independent growth. More specifically, SGK1 promotes a substantial elevation in glucose uptake because of elevated GLUT1 transcription. In addition, carbon flux into the pentose phosphate pathway (PPP) is necessary to accommodate elevated glucose uptake and PPP-mediated glyceraldehyde-3-phosphate (G3P) is necessary for ATP production. Thus, our data show SGK1 as master regulator of glucose metabolism and cell survival during ECM-detached conditions.
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Affiliation(s)
- Joshua A Mason
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jordan A Cockfield
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Daniel J Pape
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hannah Meissner
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael T Sokolowski
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Taylor C White
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - José C Valentín López
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Juan Liu
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaojing Liu
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Navdeep S Chandel
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jason W Locasale
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Zachary T Schafer
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
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32
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Itaconate Alters Succinate and Coenzyme A Metabolism via Inhibition of Mitochondrial Complex II and Methylmalonyl-CoA Mutase. Metabolites 2021; 11:metabo11020117. [PMID: 33670656 PMCID: PMC7922098 DOI: 10.3390/metabo11020117] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 12/29/2022] Open
Abstract
Itaconate is a small molecule metabolite that is endogenously produced by cis-aconitate decarboxylase-1 (ACOD1) in mammalian cells and influences numerous cellular processes. The metabolic consequences of itaconate in cells are diverse and contribute to its regulatory function. Here, we have applied isotope tracing and mass spectrometry approaches to explore how itaconate impacts various metabolic pathways in cultured cells. Itaconate is a competitive and reversible inhibitor of Complex II/succinate dehydrogenase (SDH) that alters tricarboxylic acid (TCA) cycle metabolism leading to succinate accumulation. Upon activation with coenzyme A (CoA), itaconyl-CoA inhibits adenosylcobalamin-mediated methylmalonyl-CoA (MUT) activity and, thus, indirectly impacts branched-chain amino acid (BCAA) metabolism and fatty acid diversity. Itaconate, therefore, alters the balance of CoA species in mitochondria through its impacts on TCA, amino acid, vitamin B12, and CoA metabolism. Our results highlight the diverse metabolic pathways regulated by itaconate and provide a roadmap to link these metabolites to potential downstream biological functions.
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Arias-Alvarado A, Aghayev M, Ilchenko S, Rachdaoui N, Lepp J, Tsai TH, Zhang GF, Previs S, Kasumov T. Measuring acetyl-CoA and acetylated histone turnover in vivo: Effect of a high fat diet. Anal Biochem 2020; 615:114067. [PMID: 33340539 DOI: 10.1016/j.ab.2020.114067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 11/24/2022]
Abstract
Cellular availability of acetyl-CoA, a central intermediate of metabolism, regulates histone acetylation. The impact of a high-fat diet (HFD) on the turnover rates of acetyl-CoA and acetylated histones is unknown. We developed a method for simultaneous measurement of acetyl-CoA and acetylated histones kinetics using a single 2H2O tracer, and used it to examine effect of HFD-induced perturbations on hepatic histone acetylation in LDLR-/- mice, a mouse model of non-alcoholic fatty liver disease (NAFLD). Mice were given 2H2O in the drinking water and the kinetics of hepatic acetyl-CoA, histones, and acetylated histones were quantified based on their 2H-labeling. Consumption of a high fat Western-diet (WD) for twelve weeks led to decreased acetylation of hepatic histones (p< 0.05), as compared to a control diet. These changes were associated with 1.5-3-fold increased turnover rates of histones without any change in acetyl-CoA flux. Acetylation significantly reduced the stability of histones and the turnover rates of acetylated peptides were correlated with the number of acetyl groups in neighboring lysine sites. We conclude that 2H2O-method can be used to study metabolically controlled histone acetylation and acetylated histone turnover in vivo.
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Affiliation(s)
- Andrea Arias-Alvarado
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Mirjavid Aghayev
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Serguei Ilchenko
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Nadia Rachdaoui
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Josephine Lepp
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Tsung-Heng Tsai
- Department of Mathematical Sciences, Kent State University, Kent, OH, 44242, USA
| | - Guo-Fang Zhang
- Division of Division of Endocrinology, Metabolism and Nutrition, Duke Molecular Physiology Institute, And Department of Medicine, Duke University, Durham, NC, 27701, USA
| | - Stephen Previs
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA; Departments of Gastroenterology, Hepatology and Nutrition, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.
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34
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You SK, Ko YJ, Shin SK, Hwang DH, Kang DH, Park HM, Han SO. Enhanced CO 2 fixation and lipid production of Chlorella vulgaris through the carbonic anhydrase complex. BIORESOURCE TECHNOLOGY 2020; 318:124072. [PMID: 32911368 DOI: 10.1016/j.biortech.2020.124072] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/27/2020] [Accepted: 08/30/2020] [Indexed: 06/11/2023]
Abstract
Photosynthesis of C. vulgaris shows slow growth and low lipid production due to the low solubility of CO2, and it is thus necessary to increase the dissolved inorganic carbon source to solve this problem. In this study, carbonic anhydrase (CA) was fused with dockerin to form a CA complex by cohesion-dockerin interaction. The CA complex was displayed on the surface of C. vulgaris by a cellulose binding module. The CA complex increased activity and stability compared to those of a single enzyme. Additionally, C. vulgaris showed an average of 1.6-fold rapid growth during log phase through the influence of the CA complex. The bicarbonate produced by the CA complex increased the lipid production about 1.7-fold (23.3%), compared to 13.6% for the control group. The present results suggest that the CA complex successfully enhances the CO2 fixation, which should be an essential study for 4th generation biofuels.
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Affiliation(s)
- Seung Kyou You
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Young Jin Ko
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sang Kyu Shin
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Dong-Hyeuk Hwang
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Dae Hee Kang
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Hyeon Min Park
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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35
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Brinkley G, Nam H, Shim E, Kirkman R, Kundu A, Karki S, Heidarian Y, Tennessen JM, Liu J, Locasale JW, Guo T, Wei S, Gordetsky J, Johnson-Pais TL, Absher D, Rakheja D, Challa AK, Sudarshan S. Teleological role of L-2-hydroxyglutarate dehydrogenase in the kidney. Dis Model Mech 2020; 13:dmm045898. [PMID: 32928875 PMCID: PMC7710027 DOI: 10.1242/dmm.045898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
L-2-hydroxyglutarate (L-2HG) is an oncometabolite found elevated in renal tumors. However, this molecule might have physiological roles that extend beyond its association with cancer, as L-2HG levels are elevated in response to hypoxia and during Drosophila larval development. L-2HG is known to be metabolized by L-2HG dehydrogenase (L2HGDH), and loss of L2HGDH leads to elevated L-2HG levels. Despite L2HGDH being highly expressed in the kidney, its role in renal metabolism has not been explored. Here, we report our findings utilizing a novel CRISPR/Cas9 murine knockout model, with a specific focus on the role of L2HGDH in the kidney. Histologically, L2hgdh knockout kidneys have no demonstrable histologic abnormalities. However, GC-MS metabolomics demonstrates significantly reduced levels of the TCA cycle intermediate succinate in multiple tissues. Isotope labeling studies with [U-13C] glucose demonstrate that restoration of L2HGDH in renal cancer cells (which lowers L-2HG) leads to enhanced incorporation of label into TCA cycle intermediates. Subsequent biochemical studies demonstrate that L-2HG can inhibit the TCA cycle enzyme α-ketoglutarate dehydrogenase. Bioinformatic analysis of mRNA expression data from renal tumors demonstrates that L2HGDH is co-expressed with genes encoding TCA cycle enzymes as well as the gene encoding the transcription factor PGC-1α, which is known to regulate mitochondrial metabolism. Restoration of PGC-1α in renal tumor cells results in increased L2HGDH expression with a concomitant reduction in L-2HG levels. Collectively, our analyses provide new insight into the physiological role of L2HGDH as well as mechanisms that promote L-2HG accumulation in disease states.
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Affiliation(s)
- Garrett Brinkley
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hyeyoung Nam
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Eunhee Shim
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Richard Kirkman
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Anirban Kundu
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Suman Karki
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yasaman Heidarian
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jason M Tennessen
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Tao Guo
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shi Wei
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jennifer Gordetsky
- Departments of Pathology and Urology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anil K Challa
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sunil Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Birmingham VA Medical Center, Birmingham, AL 35233, USA
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36
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SUCLA2 mutations cause global protein succinylation contributing to the pathomechanism of a hereditary mitochondrial disease. Nat Commun 2020; 11:5927. [PMID: 33230181 PMCID: PMC7684291 DOI: 10.1038/s41467-020-19743-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage. Succinyl-CoA ligase (SCL) deficiency causes a mitochondrial encephalomyopathy of unknown pathomechanism. Here, we show that succinyl-CoA accumulates in cells derived from patients with recessive mutations in the tricarboxylic acid cycle (TCA) gene succinyl-CoA ligase subunit-β (SUCLA2), causing global protein hyper-succinylation. Using mass spectrometry, we quantify nearly 1,000 protein succinylation sites on 366 proteins from patient-derived fibroblasts and myotubes. Interestingly, hyper-succinylated proteins are distributed across cellular compartments, and many are known targets of the (NAD+)-dependent desuccinylase SIRT5. To test the contribution of hyper-succinylation to disease progression, we develop a zebrafish model of the SCL deficiency and find that SIRT5 gain-of-function reduces global protein succinylation and improves survival. Thus, increased succinyl-CoA levels contribute to the pathology of SCL deficiency through post-translational modifications. The pathomechanism of succinyl-CoA ligase (SCL) deficiency, a hereditary mitochondrial disease, is not fully understood. Here, the authors show that increased succinyl-CoA levels contribute to SCL pathology by causing global protein hyper-succinylation.
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37
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Yu Y, Le HH, Curtis BJ, Wrobel CJJ, Zhang B, Maxwell DN, Pan JY, Schroeder FC. An Untargeted Approach for Revealing Electrophilic Metabolites. ACS Chem Biol 2020; 15:3030-3037. [PMID: 33074644 DOI: 10.1021/acschembio.0c00706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactive electrophilic intermediates such as coenzyme A esters play central roles in metabolism but are difficult to detect with conventional strategies. Here, we introduce hydroxylamine-based stable isotope labeling to convert reactive electrophilic intermediates into stable derivatives that are easily detectable via LC-MS. In the model system Caenorhabditis elegans, parallel treatment with 14NH2OH and 15NH2OH revealed >1000 labeled metabolites, e.g., derived from peptide, fatty acid, and ascaroside pheromone biosyntheses. Results from NH2OH treatment of a pheromone biosynthesis mutant, acox-1.1, suggested upregulation of thioesterase activity, which was confirmed by gene expression analysis. The upregulated thioesterase contributes to the biosynthesis of a specific subset of ascarosides, determining the balance of dispersal and attractive signals. These results demonstrate the utility of NH2OH labeling for investigating complex biosynthetic networks. Initial results with Aspergillus and human cell lines indicate applicability toward uncovering reactive metabolomes in diverse living systems.
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Affiliation(s)
- Yan Yu
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Henry H. Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian J. Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Chester J. J. Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Bingsen Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Danielle N. Maxwell
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Judy Y. Pan
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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38
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Lam SM, Zhou T, Li J, Zhang S, Chua GH, Li B, Shui G. A robust, integrated platform for comprehensive analyses of acyl-coenzyme As and acyl-carnitines revealed chain length-dependent disparity in fatty acyl metabolic fates across Drosophila development. Sci Bull (Beijing) 2020; 65:1840-1848. [PMID: 36659124 DOI: 10.1016/j.scib.2020.07.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/02/2020] [Accepted: 06/15/2020] [Indexed: 01/21/2023]
Abstract
Acyl-coenzyme A thioesters (acyl-CoAs) denote a key class of intermediary metabolites that lies at the hub of major metabolic pathways. The great diversity in polarity between short- and long-chain acyl-CoAs makes it technically challenging to cover an inclusive range of acyl-CoAs within a single method. Levels of acyl-carnitines, which function to convey fatty acyls into mitochondria matrix for β-oxidation, indicate the efficiency of mitochondrial import and utilization of corresponding acyl-CoAs. Herein, we report a robust, integrated platform to allow simultaneous quantitation of endogenous acyl-CoAs and acyl-carnitines. Using this method, we monitored changes in intermediary lipid profiles across Drosophila development under control (ND) and high-fat diet (HFD). We observed specific accumulations of medium-chain (C8-C12) and long-chain (≥C16) acyl-carnitines distinct to L3 larval and pupal stages, respectively. These observations suggested development-specific, chain length-dependent disparity in metabolic fates of acyl-CoAs across Drosophila development, which was validated by deploying the same platform to monitor isotope incorporation introduced from labelled 12:0 and 16:0 fatty acids into extra- and intra-mitochondrial acyl-CoA pools. We found that pupal mitochondria preferentially import and oxidise C12:0-CoAs (accumulated as C12:0-carnitines in L3 stage) over C16:0-CoAs. Preferential oxidation of medium-chain acyl-CoAs limits mitochondrial utilization of long-chain acyl-CoAs (C16-C18), leading to pupal-specific accumulation of long-chain acyl-carnitines mediated by enhanced CPT1-6A activity. HFD skewed C16:0-CoAs towards catabolism over anabolism in pupa, thereby adversely affecting overall development. Our developed platform emphasizes the importance of integrating biological knowledge in the design of pathway-oriented platforms to derive maximal physiological insights from analysis of complex biological systems.
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Affiliation(s)
- Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianxing Zhou
- LipidALL Technologies Company Limited, Changzhou 213022, China
| | - Jie Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaohua Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gek Huey Chua
- LipidALL Technologies Company Limited, Changzhou 213022, China
| | - Bowen Li
- LipidALL Technologies Company Limited, Changzhou 213022, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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From a "Metabolomics fashion" to a sound application of metabolomics in research on human nutrition. Eur J Clin Nutr 2020; 74:1619-1629. [PMID: 33087891 DOI: 10.1038/s41430-020-00781-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/02/2020] [Accepted: 10/02/2020] [Indexed: 12/28/2022]
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40
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Trefely S, Lovell CD, Snyder NW, Wellen KE. Compartmentalised acyl-CoA metabolism and roles in chromatin regulation. Mol Metab 2020; 38:100941. [PMID: 32199817 PMCID: PMC7300382 DOI: 10.1016/j.molmet.2020.01.005] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Many metabolites serve as important signalling molecules to adjust cellular activities and functions based on nutrient availability. Links between acetyl-CoA metabolism, histone lysine acetylation, and gene expression have been documented and studied over the past decade. In recent years, several additional acyl modifications to histone lysine residues have been identified, which depend on acyl-coenzyme A thioesters (acyl-CoAs) as acyl donors. Acyl-CoAs are intermediates of multiple distinct metabolic pathways, and substantial evidence has emerged that histone acylation is metabolically sensitive. Nevertheless, the metabolic sources of acyl-CoAs used for chromatin modification in most cases remain poorly understood. Elucidating how these diverse chemical modifications are coupled to and regulated by cellular metabolism is important in deciphering their functional significance. SCOPE OF REVIEW In this article, we review the metabolic pathways that produce acyl-CoAs, as well as emerging evidence for functional roles of diverse acyl-CoAs in chromatin regulation. Because acetyl-CoA has been extensively reviewed elsewhere, we will focus on four other acyl-CoA metabolites integral to major metabolic pathways that are also known to modify histones: succinyl-CoA, propionyl-CoA, crotonoyl-CoA, and butyryl-CoA. We also briefly mention several other acyl-CoA species, which present opportunities for further research; malonyl-CoA, glutaryl-CoA, 3-hydroxybutyryl-CoA, 2-hydroxyisobutyryl-CoA, and lactyl-CoA. Each acyl-CoA species has distinct roles in metabolism, indicating the potential to report shifts in the metabolic status of the cell. For each metabolite, we consider the metabolic pathways in which it participates and the nutrient sources from which it is derived, the compartmentalisation of its metabolism, and the factors reported to influence its abundance and potential nuclear availability. We also highlight reported biological functions of these metabolically-linked acylation marks. Finally, we aim to illuminate key questions in acyl-CoA metabolism as they relate to the control of chromatin modification. MAJOR CONCLUSIONS A majority of acyl-CoA species are annotated to mitochondrial metabolic processes. Since acyl-CoAs are not known to be directly transported across mitochondrial membranes, they must be synthesized outside of mitochondria and potentially within the nucleus to participate in chromatin regulation. Thus, subcellular metabolic compartmentalisation likely plays a key role in the regulation of histone acylation. Metabolite tracing in combination with targeting of relevant enzymes and transporters will help to map the metabolic pathways that connect acyl-CoA metabolism to chromatin modification. The specific function of each acyl-CoA may be determined in part by biochemical properties that affect its propensity for enzymatic versus non-enzymatic protein modification, as well as the various enzymes that can add, remove and bind each modification. Further, competitive and inhibitory effects of different acyl-CoA species on these enzymes make determining the relative abundance of acyl-CoA species in specific contexts important to understand the regulation of chromatin acylation. An improved and more nuanced understanding of metabolic regulation of chromatin and its roles in physiological and disease-related processes will emerge as these questions are answered.
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Affiliation(s)
- Sophie Trefely
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Metabolic Disease Research, Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Claudia D Lovell
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Ishak Gabra MB, Yang Y, Li H, Senapati P, Hanse EA, Lowman XH, Tran TQ, Zhang L, Doan LT, Xu X, Schones DE, Fruman DA, Kong M. Dietary glutamine supplementation suppresses epigenetically-activated oncogenic pathways to inhibit melanoma tumour growth. Nat Commun 2020; 11:3326. [PMID: 32620791 PMCID: PMC7335172 DOI: 10.1038/s41467-020-17181-w] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/15/2020] [Indexed: 12/14/2022] Open
Abstract
Tumour cells adapt to nutrient deprivation in vivo, yet strategies targeting the nutrient poor microenvironment remain unexplored. In melanoma, tumour cells often experience low glutamine levels, which promote cell dedifferentiation. Here, we show that dietary glutamine supplementation significantly inhibits melanoma tumour growth, prolongs survival in a transgenic melanoma mouse model, and increases sensitivity to a BRAF inhibitor. Metabolomic analysis reveals that dietary uptake of glutamine effectively increases the concentration of glutamine in tumours and its downstream metabolite, αKG, without increasing biosynthetic intermediates necessary for cell proliferation. Mechanistically, we find that glutamine supplementation uniformly alters the transcriptome in tumours. Our data further demonstrate that increase in intra-tumoural αKG concentration drives hypomethylation of H3K4me3, thereby suppressing epigenetically-activated oncogenic pathways in melanoma. Therefore, our findings provide evidence that glutamine supplementation can serve as a potential dietary intervention to block melanoma tumour growth and sensitize tumours to targeted therapy via epigenetic reprogramming.
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Affiliation(s)
- Mari B Ishak Gabra
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Ying Yang
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Haiqing Li
- Center for Informatics, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Department of Computational & Quantitative Medicine, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Parijat Senapati
- Department of Diabetes and Metabolic Disease, Beckman Research Institute of City of Hope Cancer Center, Duarte, CA, 91010, USA
| | - Eric A Hanse
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Xazmin H Lowman
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Thai Q Tran
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Lishi Zhang
- Institute for Clinical and Translational Science, University of California, Irvine, CA, 92687, USA
| | - Linda T Doan
- UCI Health Dermatology Center, Irvine, CA, 92697, USA
| | - Xiangdong Xu
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dustin E Schones
- Department of Diabetes and Metabolic Disease, Beckman Research Institute of City of Hope Cancer Center, Duarte, CA, 91010, USA
| | - David A Fruman
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Mei Kong
- Department of Molecular Biology and Biochemistry; School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA.
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Diehl KL, Muir TW. Chromatin as a key consumer in the metabolite economy. Nat Chem Biol 2020; 16:620-629. [PMID: 32444835 DOI: 10.1038/s41589-020-0517-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/05/2020] [Indexed: 12/31/2022]
Abstract
In eukaryotes, chromatin remodeling and post-translational modifications (PTMs) shape the local chromatin landscape to establish permissive and repressive regions within the genome, orchestrating transcription, replication, and DNA repair in concert with other epigenetic mechanisms. Though cellular nutrient signaling encompasses a huge number of pathways, recent attention has turned to the hypothesis that the metabolic state of the cell is communicated to the genome through the type and concentration of metabolites in the nucleus that are cofactors for chromatin-modifying enzymes. Importantly, both epigenetic and metabolic dysregulation are hallmarks of a range of diseases, and this metabolism-chromatin axis may yield a well of new therapeutic targets. In this Perspective, we highlight emerging themes in the inter-regulation of the genome and metabolism via chromatin, including nonenzymatic histone modifications arising from chemically reactive metabolites, the expansion of PTM diversity from cofactor-promiscuous chromatin-modifying enzymes, and evidence for the existence and importance of subnucleocytoplasmic metabolite pools.
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Affiliation(s)
- Katharine L Diehl
- Department of Chemistry, Princeton University, Princeton, NJ, USA. .,Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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43
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Wei J, Li X, Xiang L, Song Y, Liu Y, Jiang Y, Cai Z. Metabolomics and lipidomics study unveils the impact of polybrominated diphenyl ether-47 on breast cancer mice. JOURNAL OF HAZARDOUS MATERIALS 2020; 390:121451. [PMID: 31796364 DOI: 10.1016/j.jhazmat.2019.121451] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/01/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
Polybrominated diphenyl ether-47 (BDE-47) is a congener of polybrominated diphenyl ethers (PBDEs) and relates to different health risks. However, in vivo study of the association between BDE-47 and breast cancer was scarce. In this study, we performed in vivo exposure of BDE-47 to breast cancer nude mice and conducted mass spectrometry-based metabolomics and lipidomics analysis to investigate the metabolic changes in mice. Results showed that the tumor sizes were positively associated with the dosage of BDE-47. Metabolomics and lipidomics profiling analysis indicated that BDE-47 induced significant alterations of metabolic pathways in livers, including glutathione metabolism, ascorbate and aldarate metabolism, and lipids metabolism, etc. The upregulations of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs) suggested the membrane remodeling, and the downregulations of Lyso-PCs and Lyso-PEs might be associated with the tumor growth. Targeted metabolomics analysis revealed that BDE-47 inhibited fatty acid β-oxidation (FAO) and induced incomplete FAO. The inhibition of FAO and downregulation of PPARγ would contribute to inflammation, which could promote tumor growth. In addition, BDE-47 elevated the expression of the cytokines TNFRSF12A, TNF-α, IL-1β and IL-6, and lowered the cytokines SOCS3 and the nuclear receptor PPARα. The changes of cytokines and receptor may contribute to the tumor growth of mice.
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Affiliation(s)
- Juntong Wei
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Xiaona Li
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Li Xiang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Yuanyuan Song
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region, China; State Key Laboratory of Chemical Oncogenomics, Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong, China
| | - Yuanchen Liu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Yuyang Jiang
- State Key Laboratory of Chemical Oncogenomics, Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region, China.
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Gao S, Liu H, Chang H, Zhang Z, Hu J, Tao S, Wan Y. Visualized Metabolic Disorder and Its Chemical Inducer in Wild Crucian Carp from Taihu Lake, China. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3343-3352. [PMID: 32091217 DOI: 10.1021/acs.est.0c00099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A variety of anthropogenic chemicals can disrupt the equilibrium of intrinsic biological metabolites in organisms, leading to metabolic disorders and an increased risk of metabolic syndromes. However, exposure to pollutants that induce metabolic disorders in wildlife as a cause of adverse effects is unknown. In this study, approximately 3108 compounds, including 11 groups of metabolites and 388 pollutants, were simultaneously identified in the blood of wild crucian carp (Carassius auratus) captured in three bays of Taihu Lake, China. A visualized network linking thousands of co-regulated metabolites was automatically produced for the screened signals. This comprehensive view of the differences in blood metabolite profiles in carp from the north and south bays showed that triglycerides (TGs) were the intrinsic molecules most affected by differing environmental pollution in each bay. The regional differences in metabolite profiles were linked to exposure to screened perfluorinated compounds that displayed corresponding regional differences in concentrations and effects on TGs in in vivo exposure tests. Perfluoroundecanoic acid (PFUnDA) was the key pollutant responsible for the variation in blood TGs in wild crucian carp, and exposure to PFUnDA resulted in extremely high biological activity on lipid deposition in the liver tissues of crucian carp at environmental levels.
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Affiliation(s)
- Shixiong Gao
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hang Liu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hong Chang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Sciences & Engineering, Beijing Forestry University, Beijing 100083, China
| | - Zhaobin Zhang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Jianying Hu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shu Tao
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yi Wan
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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45
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Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing. Nat Cell Biol 2020; 22:310-320. [PMID: 32144411 DOI: 10.1038/s41556-020-0477-0] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 02/04/2020] [Indexed: 12/24/2022]
Abstract
Although metastasis remains the cause of most cancer-related mortality, mechanisms governing seeding in distal tissues are poorly understood. Here, we establish a robust method for the identification of global transcriptomic changes in rare metastatic cells during seeding using single-cell RNA sequencing and patient-derived-xenograft models of breast cancer. We find that both primary tumours and micrometastases display transcriptional heterogeneity but micrometastases harbour a distinct transcriptome program conserved across patient-derived-xenograft models that is highly predictive of poor survival of patients. Pathway analysis revealed mitochondrial oxidative phosphorylation as the top pathway upregulated in micrometastases, in contrast to higher levels of glycolytic enzymes in primary tumour cells, which we corroborated by flow cytometric and metabolomic analyses. Pharmacological inhibition of oxidative phosphorylation dramatically attenuated metastatic seeding in the lungs, which demonstrates the functional importance of oxidative phosphorylation in metastasis and highlights its potential as a therapeutic target to prevent metastatic spread in patients with breast cancer.
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46
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Schöttl T, Pachl F, Giesbertz P, Daniel H, Kuster B, Fromme T, Klingenspor M. Proteomic and Metabolite Profiling Reveals Profound Structural and Metabolic Reorganization of Adipocyte Mitochondria in Obesity. Obesity (Silver Spring) 2020; 28:590-600. [PMID: 32034895 DOI: 10.1002/oby.22737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Previous studies have revealed decreased mitochondrial respiration in adipocytes of obese mice. This study aimed to identify the molecular underpinnings of altered mitochondrial metabolism in adipocytes. METHODS Untargeted proteomics of mitochondria isolated from adipocytes and metabolite profiling of adipose tissues were conducted in diet-induced obese (DIO) and lean mice. Subcutaneous and intra-abdominal adipose tissues were studied to depict depot-specific alterations. RESULTS In subcutaneous adipocytes of DIO mice, changes in proteins related to mitochondrial structure and function were observed. Mitochondrial proteins of the inner and outer membrane were strongly reduced, whereas proteins of key matrix metabolic pathways were increased in the obese versus lean state, as further substantiated by metabolite profiling. A pronounced decrease in the oxidative phosphorylation (OXPHOS) enzymatic equipment and cristae density of the inner membrane was identified. In intra-abdominal adipocytes, similar systematic downregulation of the OXPHOS machinery in obesity occurred, but there was no regulation of outer membrane or matrix proteins. CONCLUSIONS Protein components of the OXPHOS machinery are systematically downregulated in adipose tissues of DIO mice compared with lean mice. Loss of the mitochondrial OXPHOS capacity in adipocytes may aggravate the development of metabolic disease.
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Affiliation(s)
- Theresa Schöttl
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- EKFZ-Else Kröner Fresenius Zentrum for Nutritional Medicine, Technical Universtiy of Munich, Freising, Germany
- ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Fiona Pachl
- ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Pieter Giesbertz
- Chair of Nutritional Physiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Hannelore Daniel
- Chair of Nutritional Physiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Tobias Fromme
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- EKFZ-Else Kröner Fresenius Zentrum for Nutritional Medicine, Technical Universtiy of Munich, Freising, Germany
- ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- EKFZ-Else Kröner Fresenius Zentrum for Nutritional Medicine, Technical Universtiy of Munich, Freising, Germany
- ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
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47
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Assiri MA, Ali HR, Marentette JO, Yun Y, Liu J, Hirschey MD, Saba LM, Harris PS, Fritz KS. Investigating RNA expression profiles altered by nicotinamide mononucleotide therapy in a chronic model of alcoholic liver disease. Hum Genomics 2019; 13:65. [PMID: 31823815 PMCID: PMC6902345 DOI: 10.1186/s40246-019-0251-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/19/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Chronic alcohol consumption is a significant cause of liver disease worldwide. Several biochemical mechanisms have been linked to the initiation and progression of alcoholic liver disease (ALD) such as oxidative stress, inflammation, and metabolic dysregulation, including the disruption of NAD+/NADH. Indeed, an ethanol-mediated reduction in hepatic NAD+ levels is thought to be one factor underlying ethanol-induced steatosis, oxidative stress, steatohepatitis, insulin resistance, and inhibition of gluconeogenesis. Therefore, we applied a NAD+ boosting supplement to investigate alterations in the pathogenesis of early-stage ALD. METHODS To examine the impact of NAD+ therapy on the early stages of ALD, we utilized nicotinamide mononucleotide (NMN) at 500 mg/kg intraperitoneal injection every other day, for the duration of a Lieber-DeCarli 6-week chronic ethanol model in mice. Numerous strategies were employed to characterize the effect of NMN therapy, including the integration of RNA-seq, immunoblotting, and metabolomics analysis. RESULTS Our findings reveal that NMN therapy increased hepatic NAD+ levels, prevented an ethanol-induced increase in plasma ALT and AST, and changed the expression of 25% of the genes that were modulated by ethanol metabolism. These genes were associated with a number of pathways including the MAPK pathway. Interestingly, our analysis revealed that NMN treatment normalized Erk1/2 signaling and prevented an induction of Atf3 overexpression. CONCLUSIONS These findings reveal previously unreported mechanisms by which NMN supplementation alters hepatic gene expression and protein pathways to impact ethanol hepatotoxicity in an early-stage murine model of ALD. Overall, our data suggest further research is needed to fully characterize treatment paradigms and biochemical implications of NAD+-based interventions.
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Affiliation(s)
- Mohammed A Assiri
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hadi R Ali
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - John O Marentette
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Youngho Yun
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Matthew D Hirschey
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC, 27710, USA
| | - Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Peter S Harris
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kristofer S Fritz
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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48
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Galmozzi A, Kok BP, Kim AS, Montenegro-Burke JR, Lee JY, Spreafico R, Mosure S, Albert V, Cintron-Colon R, Godio C, Webb WR, Conti B, Solt LA, Kojetin D, Parker CG, Peluso JJ, Pru JK, Siuzdak G, Cravatt BF, Saez E. PGRMC2 is an intracellular haem chaperone critical for adipocyte function. Nature 2019; 576:138-142. [PMID: 31748741 PMCID: PMC6895438 DOI: 10.1038/s41586-019-1774-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 10/01/2019] [Indexed: 12/16/2022]
Abstract
Heme is an essential prosthetic group of numerous proteins and a central signaling molecule in many physiologic processes1,2. The chemical reactivity of heme requires that a network of intracellular chaperone proteins exist to avert the cytotoxic effects of free heme, but the constituents of such trafficking pathways are unknown3,4. Heme synthesis is completed in mitochondria, with ferrochelatase (FECH) adding iron to protoporphyrin IX. How this vital but highly reactive metabolite is delivered from mitochondria to hemoproteins throughout the cell remains poorly defined3,4. Here, we show that PGRMC2 is required for delivery of labile, or signaling heme, to the nucleus. Deletion of PGMRC2 in brown fat, which has a high demand for heme, reduced labile heme in the nucleus and increased stability of the heme-responsive transcriptional repressors Rev-Erbα and BACH1. Ensuing alterations in gene expression spawn severe mitochondrial defects that rendered adipose-specific PGRMC2-null mice unable to activate adaptive thermogenesis and prone to greater metabolic deterioration when fed a high-fat diet. In contrast, obese-diabetic mice treated with a small-molecule PGRMC2 activator showed substantial improvement of diabetic features. These studies uncover a role for PGRMC2 in intracellular heme transport, reveal the impact of adipose tissue heme dynamics on physiology, and suggest that modulation of PGRMC2 may revert obesity-linked defects in adipocytes.
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Affiliation(s)
- Andrea Galmozzi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Bernard P Kok
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Arthur S Kim
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Jae Y Lee
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biology, University of California, Los Angeles, CA, USA
| | - Sarah Mosure
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA
| | - Verena Albert
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Rigo Cintron-Colon
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Cristina Godio
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - William R Webb
- Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA
| | - Bruno Conti
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura A Solt
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Douglas Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - John J Peluso
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - James K Pru
- Center for Reproductive Biology, Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Gary Siuzdak
- Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Enrique Saez
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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49
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Gao X, Sanderson SM, Dai Z, Reid MA, Cooper DE, Lu M, Richie JP, Ciccarella A, Calcagnotto A, Mikhael PG, Mentch SJ, Liu J, Ables G, Kirsch DG, Hsu DS, Nichenametla SN, Locasale JW. Dietary methionine influences therapy in mouse cancer models and alters human metabolism. Nature 2019; 572:397-401. [PMID: 31367041 PMCID: PMC6951023 DOI: 10.1038/s41586-019-1437-3] [Citation(s) in RCA: 383] [Impact Index Per Article: 76.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 06/26/2019] [Indexed: 02/07/2023]
Abstract
Nutrition exerts considerable effects on health, and dietary interventions are commonly used to treat diseases of metabolic aetiology. Although cancer has a substantial metabolic component1, the principles that define whether nutrition may be used to influence outcomes of cancer are unclear2. Nevertheless, it is established that targeting metabolic pathways with pharmacological agents or radiation can sometimes lead to controlled therapeutic outcomes. By contrast, whether specific dietary interventions can influence the metabolic pathways that are targeted in standard cancer therapies is not known. Here we show that dietary restriction of the essential amino acid methionine-the reduction of which has anti-ageing and anti-obesogenic properties-influences cancer outcome, through controlled and reproducible changes to one-carbon metabolism. This pathway metabolizes methionine and is the target of a variety of cancer interventions that involve chemotherapy and radiation. Methionine restriction produced therapeutic responses in two patient-derived xenograft models of chemotherapy-resistant RAS-driven colorectal cancer, and in a mouse model of autochthonous soft-tissue sarcoma driven by a G12D mutation in KRAS and knockout of p53 (KrasG12D/+;Trp53-/-) that is resistant to radiation. Metabolomics revealed that the therapeutic mechanisms operate via tumour-cell-autonomous effects on flux through one-carbon metabolism that affects redox and nucleotide metabolism-and thus interact with the antimetabolite or radiation intervention. In a controlled and tolerated feeding study in humans, methionine restriction resulted in effects on systemic metabolism that were similar to those obtained in mice. These findings provide evidence that a targeted dietary manipulation can specifically affect tumour-cell metabolism to mediate broad aspects of cancer outcome.
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Affiliation(s)
- Xia Gao
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Sydney M Sanderson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Ziwei Dai
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Michael A Reid
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Daniel E Cooper
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Min Lu
- Center for Genomics and Computational Biology, Duke University, Durham, NC, USA
- Department of Medical Oncology, Duke University Medical Center, Durham, NC, USA
| | - John P Richie
- Department of Public Health Sciences, Penn State University College of Medicine, Hershey, PA, USA
| | - Amy Ciccarella
- Penn State University Clinical Research Center, State College, PA, USA
| | - Ana Calcagnotto
- Department of Public Health Sciences, Penn State University College of Medicine, Hershey, PA, USA
| | - Peter G Mikhael
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Samantha J Mentch
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Gene Ables
- Orentreich Foundation for the Advancement of Science, Cold Spring, NY, USA
| | - David G Kirsch
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - David S Hsu
- Center for Genomics and Computational Biology, Duke University, Durham, NC, USA
- Department of Medical Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
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O’Kane PT, Dudley QM, McMillan AK, Jewett MC, Mrksich M. High-throughput mapping of CoA metabolites by SAMDI-MS to optimize the cell-free biosynthesis of HMG-CoA. SCIENCE ADVANCES 2019; 5:eaaw9180. [PMID: 31183410 PMCID: PMC6551189 DOI: 10.1126/sciadv.aaw9180] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/02/2019] [Indexed: 05/30/2023]
Abstract
Metabolic engineering uses enzymes to produce small molecules with industrial, pharmaceutical, and energy applications. However, efforts to optimize enzymatic pathways for commercial production are limited by the throughput of assays for quantifying metabolic intermediates and end products. We developed a multiplexed method for profiling CoA-dependent pathways that uses a cysteine-terminated peptide to covalently capture CoA-bound metabolites. Captured metabolites are then rapidly separated from the complex mixture by immobilization onto arrays of self-assembled monolayers and directly quantified by SAMDI mass spectrometry. We demonstrate the throughput of the assay by characterizing the cell-free synthesis of HMG-CoA, a key intermediate in the biosynthesis of isoprenoids, collecting over 10,000 individual spectra to map more than 800 unique reaction conditions. We anticipate that our rapid and robust analytical method will accelerate efforts to engineer metabolic pathways.
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Affiliation(s)
- Patrick T. O’Kane
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Quentin M. Dudley
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Aislinn K. McMillan
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Michael C. Jewett
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Milan Mrksich
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
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