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Wang JX, Luo Y, Limbu SM, Qian YC, Zhang YY, Li RX, Zhou WH, Qiao F, Chen LQ, Zhang ML, Du ZY. Inhibiting mitochondrial citrate shuttling induces hepatic triglyceride deposition in Nile tilapia (Oreochromis niloticus) through lipid anabolic remodeling. J Nutr Biochem 2024; 131:109678. [PMID: 38844080 DOI: 10.1016/j.jnutbio.2024.109678] [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: 10/08/2023] [Revised: 05/18/2024] [Accepted: 06/03/2024] [Indexed: 06/30/2024]
Abstract
The solute carrier family 25 member 1 (Slc25a1)-dependent mitochondrial citrate shuttle is responsible for exporting citrate from the mitochondria to the cytoplasm for supporting lipid biosynthesis and protein acetylation. Previous studies on Slc25a1 concentrated on pathological models. However, the importance of Slc25a1 in maintaining metabolic homeostasis under normal nutritional conditions remains poorly understood. Here, we investigated the mechanism of mitochondrial citrate shuttle in maintaining lipid metabolism homeostasis in male Nile tilapia (Oreochromis niloticus). To achieve the objective, we blocked the mitochondrial citrate shuttle by inhibiting Slc25a1 under normal nutritional conditions. Slc25a1 inhibition was established by feeding Nile tilapia with 250 mg/kg 1,2,3-benzenetricarboxylic acid hydrate for 6 weeks or intraperitoneal injecting them with dsRNA to knockdown slc25a1b for 7 days. The Nile tilapia with Slc25a1 inhibition exhibited an obesity-like phenotype accompanied by fat deposition, liver damage and hyperglycemia. Moreover, Slc25a1 inhibition decreased hepatic citrate-derived acetyl-CoA, but increased hepatic triglyceride levels. Furthermore, Slc25a1 inhibition replenished cytoplasmic acetyl-CoA through enhanced acetate pathway, which led to hepatic triglycerides accumulation. However, acetate-derived acetyl-CoA caused by hepatic Slc25a1 inhibition did not activate de novo lipogenesis, but rather modified protein acetylation. In addition, hepatic Slc25a1 inhibition enhanced fatty acids esterification through acetate-derived acetyl-CoA, which increased Lipin1 acetylation and its protein stability. Collectively, our results illustrate that inhibiting mitochondrial citrate shuttle triggers lipid anabolic remodeling and results in lipid accumulation, indicating the importance of mitochondrial citrate shuttle in maintaining lipid metabolism homeostasis.
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Affiliation(s)
- Jun-Xian Wang
- LANEH, Department of Zoology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuan Luo
- LANEH, Department of Zoology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Samwel Mchele Limbu
- Department of Aquaculture Technology, School of Aquatic Sciences and Fisheries Technology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Yu-Cheng Qian
- LANEH, Department of Zoology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yan-Yu Zhang
- LANEH, Department of Zoology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Rui-Xin Li
- LANEH, Department of Zoology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Wen-Hao Zhou
- LANEH, Department of Zoology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Fang Qiao
- LANEH, Department of Zoology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Li-Qiao Chen
- LANEH, Department of Zoology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Mei-Ling Zhang
- LANEH, Department of Zoology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhen-Yu Du
- LANEH, Department of Zoology, School of Life Sciences, East China Normal University, Shanghai, China.
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2
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Taniguchi T, Okahashi N, Matsuda F. 13C-metabolic flux analysis reveals metabolic rewiring in HL-60 neutrophil-like cells through differentiation and immune stimulation. Metab Eng Commun 2024; 18:e00239. [PMID: 38883865 PMCID: PMC11176794 DOI: 10.1016/j.mec.2024.e00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024] Open
Abstract
Neutrophils are innate immune cells and the first line of defense for the maintenance of homeostasis. However, our knowledge of the metabolic rewiring associated with their differentiation and immune stimulation is limited. Here, quantitative 13C-metabolic flux analysis was performed using HL-60 cells as the neutrophil model. A metabolic model for 13C-metabolic flux analysis of neutrophils was developed based on the accumulation of 13C in intracellular metabolites derived from 13C-labeled extracellular carbon sources and intracellular macromolecules. Aspartate and glutamate in the medium were identified as carbon sources that enter central carbon metabolism. Furthermore, the breakdown of macromolecules, estimated to be fatty acids and nucleic acids, was observed. Based on these results, a modified metabolic model was used for 13C-metabolic flux analysis of undifferentiated, differentiated, and lipopolysaccharide (LPS)-activated HL-60 cells. The glucose uptake rate and glycolytic flux decreased with differentiation, whereas the tricarboxylic acid (TCA) cycle flux remained constant. The addition of LPS to differentiated HL-60 cells activated the glucose uptake rate and pentose phosphate pathway (PPP) flux levels, resulting in an increased rate of total NADPH regeneration, which could be used to generate reactive oxygen species. The flux levels of fatty acid degradation and synthesis were also increased in LPS-activated HL-60 cells. Overall, this study highlights the quantitative metabolic alterations in multiple pathways via the differentiation and activation of HL-60 cells using 13C-metabolic flux analysis.
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Affiliation(s)
- Takeo Taniguchi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Kasprzyk-Pawelec A, Tan M, Rahhal R, McIntosh A, Fernandez H, Mosaoa R, Jiang L, Pearson GW, Glasgow E, Vockley J, Albanese C, Avantaggiati ML. Loss of the mitochondrial carrier, SLC25A1, during embryogenesis induces a unique senescence program controlled by p53. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.18.549409. [PMID: 37503155 PMCID: PMC10370133 DOI: 10.1101/2023.07.18.549409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Germline inactivating mutations of the SLC25A1 gene contribute to various human developmental disorders, including combined D/L-2-hydroxyglutaric aciduria (D/L-2HGA), a severe systemic syndrome characterized by the accumulation of both enantiomers of 2-hydroxyglutaric acid (2HG). The mechanisms by which SLC25A1 deficiency leads to this disease and the role of 2HG are unclear and no therapies exist. We now show that mice lacking both Slc25a1 alleles display a spectrum of alterations that resemble human D/L-2HGA. Mechanistically, SLC25A1 loss results in a proliferation defect and activates two distinct senescence pathways, oncogene-induced senescence (OIS) and mitochondrial dysfunction-induced senescence (MiDAS), both involving the p53 tumor suppressor and driven by two discernible signals: the accumulation of 2HG, inducing OIS, and mitochondrial dysfunction, triggering MiDAS. Inhibiting these senescence programs or blocking p53 activity reverses the growth defect caused by SLC25A1 dysfunction and restores proliferation. These findings reveal novel pathogenic roles of senescence in human disorders and suggest potential strategies to correct the molecular alterations caused by SLC25A1 loss.
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You X, Huang L, Huang O, Deng Y, Shi X. A comprehensive analysis of SLC25A1 expression and its oncogenic role in pan-cancer. Discov Oncol 2023; 14:207. [PMID: 37981593 PMCID: PMC10657916 DOI: 10.1007/s12672-023-00830-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023] Open
Abstract
OBJECTIVE The solute carrier family 25 member 1 (SLC25A1) is currently the only known human transporter for citrate in the mitochondrial membrane. However, its role in cancer development remains to be elucidated. We aim to analyze the expression profile, prognostic value, potential immunological significance, and effect on tumor growth of SLC25A1 at a pan-cancer level. METHODS Herein, the role of SLC25A1 in tumorigenesis and progression was investigated based on the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Genotype-Tissue Expression (GTEx), Clinical Proteomic Tumor Analysis Consortium (CPTAC), GeneMANIA, STRING and Cancer Dependency Map Project (DepMap) database via online websites or the R software. The protein expression levels were validated in tissue microarrays, and the effects on tumor cell lines were accessed through MTS and colony formation assays. RESULTS The expression of SLC25A1 increased in most cancers, and the upregulation of SLC25A1 in colon adenocarcinoma and lung adenocarcinoma was further confirmed by immunohistochemistry. Meanwhile, SLC25A1 was linked to clinical outcomes across multiple tumor types, particularly in lung adenocarcinoma, where its high expression predicted poor prognosis. Moreover, SLC25A1 was positively associated with MSI, TMB, and CD276 and tightly correlated with tumor-infiltrating immune cells. Furthermore, the knockout of SLC25A1 demonstrated inhibitory effects in most cancer cell lines in the DepMap project. Cellular experiments showed that SLC25A1 knockdown significantly reduced the proliferation of lung adenocarcinoma cells. CONCLUSIONS Our findings suggest the potential of SLC25A1 as a prognostic biomarker for cancers and a therapeutic target for precise antitumor strategy and cancer immunotherapy.
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Affiliation(s)
- Xin You
- Department of Oncology, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, Fujian, China
- Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, Fujian, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Lingling Huang
- Department of Oncology, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, Fujian, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Ouxiang Huang
- Department of Oncology, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, Fujian, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yujie Deng
- Department of Oncology, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, Fujian, China
- Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, Fujian, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xi Shi
- Department of Oncology, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, Fujian, China.
- Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, Fujian, China.
- Department of Oncology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
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Liang K, Wang Q, Qiu L, Gong X, Chen Z, Zhang H, Ding K, Liu Y, Wei J, Lin S, Fu S, Du H. Combined Inhibition of UBE2C and PLK1 Reduce Cell Proliferation and Arrest Cell Cycle by Affecting ACLY in Pan-Cancer. Int J Mol Sci 2023; 24:15658. [PMID: 37958642 PMCID: PMC10650476 DOI: 10.3390/ijms242115658] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Various studies have shown that the cell-cycle-related regulatory proteins UBE2C, PLK1, and BIRC5 promote cell proliferation and migration in different types of cancer. However, there is a lack of in-depth and systematic research on the mechanism of these three as therapeutic targets. In this study, we found a positive correlation between the expression of UBE2C and PLK1/BIRC5 in the Cancer Genome Atlas (TCGA) database, revealing a potential combination therapy candidate for pan-cancer. Quantitative real-time PCR (qRT-PCR), Western blotting (WB), cell phenotype detection, and RNA-seq techniques were used to evidence the effectiveness of the combination candidate. We found that combined interference of UBE2C with PLK1 and UBE2C with BIRC5 affected metabolic pathways by significantly downregulating the mRNA expression of IDH1 and ACLY, which was related to the synthesis of acetyl-CoA. By combining the PLK1 inhibitor volasertib and the ACLY inhibitor bempedoic acid, it showed a higher synergistic inhibition of cell viability and higher synergy scores in seven cell lines, compared with those of other combination treatments. Our study reveals the potential mechanisms through which cell-cycle-related genes regulate metabolism and proposes a potential combined targeted therapy for patients with higher PLK1 and ACLY expression in pan-cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (K.L.); (Q.W.); (L.Q.); (X.G.); (Z.C.); (H.Z.); (K.D.); (Y.L.); (J.W.); (S.L.); (S.F.)
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6
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Moiz B, Sriram G, Clyne AM. Interpreting metabolic complexity via isotope-assisted metabolic flux analysis. Trends Biochem Sci 2023; 48:553-567. [PMID: 36863894 PMCID: PMC10182253 DOI: 10.1016/j.tibs.2023.02.001] [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: 10/15/2022] [Revised: 01/22/2023] [Accepted: 02/03/2023] [Indexed: 03/04/2023]
Abstract
Isotope-assisted metabolic flux analysis (iMFA) is a powerful method to mathematically determine the metabolic fluxome from experimental isotope labeling data and a metabolic network model. While iMFA was originally developed for industrial biotechnological applications, it is increasingly used to analyze eukaryotic cell metabolism in physiological and pathological states. In this review, we explain how iMFA estimates the intracellular fluxome, including data and network model (inputs), the optimization-based data fitting (process), and the flux map (output). We then describe how iMFA enables analysis of metabolic complexities and discovery of metabolic pathways. Our goal is to expand the use of iMFA in metabolism research, which is essential to maximizing the impact of metabolic experiments and continuing to advance iMFA and biocomputational techniques.
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Affiliation(s)
- Bilal Moiz
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Alisa Morss Clyne
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA.
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7
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Zara V, Assalve G, Ferramosca A. Insights into the malfunctioning of the mitochondrial citrate carrier: Implications for cell pathology. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166758. [PMID: 37209873 DOI: 10.1016/j.bbadis.2023.166758] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023]
Abstract
The mitochondrial citrate carrier (CIC) is a member of the mitochondrial carrier family and is responsible for the transit of tricarboxylates and dicarboxylates across the inner membrane. By modulating the flux of these molecules, it represents the molecular link between catabolic and anabolic reactions that take place in distinct cellular sub-compartments. Therefore, this transport protein represents an important element of investigation both in physiology and in pathology. In this review we critically analyze the involvement of the mitochondrial CIC in several human pathologies, which can be divided into two subgroups, one characterized by a decrease and the other by an increase in the flux of citrate across the inner mitochondrial membrane. In particular, a decrease in the activity of the mitochondrial CIC is responsible for several congenital diseases of different severity, which are also characterized by the increase in urinary levels of L-2- and D-2-hydroxyglutaric acids. On the other hand, an increase in the activity of the mitochondrial CIC is involved, in various ways, in the onset of inflammation, autoimmune diseases, and cancer. Then, understanding the role of CIC and the mechanisms driving the flux of metabolic intermediates between mitochondria and cytosol would potentially allow for manipulation and control of metabolism in pathological conditions.
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Affiliation(s)
- Vincenzo Zara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, I-73100 Lecce, Italy
| | - Graziana Assalve
- Department of Biological and Environmental Sciences and Technologies, University of Salento, I-73100 Lecce, Italy
| | - Alessandra Ferramosca
- Department of Biological and Environmental Sciences and Technologies, University of Salento, I-73100 Lecce, Italy.
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8
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Lee G, Lee SM, Kim HU. A contribution of metabolic engineering to addressing medical problems: Metabolic flux analysis. Metab Eng 2023; 77:283-293. [PMID: 37075858 DOI: 10.1016/j.ymben.2023.04.008] [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: 02/04/2023] [Revised: 03/20/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
Metabolic engineering has served as a systematic discipline for industrial biotechnology as it has offered systematic tools and methods for strain development and bioprocess optimization. Because these metabolic engineering tools and methods are concerned with the biological network of a cell with emphasis on metabolic network, they have also been applied to a range of medical problems where better understanding of metabolism has also been perceived to be important. Metabolic flux analysis (MFA) is a unique systematic approach initially developed in the metabolic engineering community, and has proved its usefulness and potential when addressing a range of medical problems. In this regard, this review discusses the contribution of MFA to addressing medical problems. For this, we i) provide overview of the milestones of MFA, ii) define two main branches of MFA, namely constraint-based reconstruction and analysis (COBRA) and isotope-based MFA (iMFA), and iii) present successful examples of their medical applications, including characterizing the metabolism of diseased cells and pathogens, and identifying effective drug targets. Finally, synergistic interactions between metabolic engineering and biomedical sciences are discussed with respect to MFA.
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Affiliation(s)
- GaRyoung Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sang Mi Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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9
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Canciello A, Cerveró-Varona A, Peserico A, Mauro A, Russo V, Morrione A, Giordano A, Barboni B. "In medio stat virtus": Insights into hybrid E/M phenotype attitudes. Front Cell Dev Biol 2022; 10:1038841. [PMID: 36467417 PMCID: PMC9715750 DOI: 10.3389/fcell.2022.1038841] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/02/2022] [Indexed: 08/22/2023] Open
Abstract
Epithelial-mesenchymal plasticity (EMP) refers to the ability of cells to dynamically interconvert between epithelial (E) and mesenchymal (M) phenotypes, thus generating an array of hybrid E/M intermediates with mixed E and M features. Recent findings have demonstrated how these hybrid E/M rather than fully M cells play key roles in most of physiological and pathological processes involving EMT. To this regard, the onset of hybrid E/M state coincides with the highest stemness gene expression and is involved in differentiation of either normal and cancer stem cells. Moreover, hybrid E/M cells are responsible for wound healing and create a favorable immunosuppressive environment for tissue regeneration. Nevertheless, hybrid state is responsible of metastatic process and of the increasing of survival, apoptosis and therapy resistance in cancer cells. The present review aims to describe the main features and the emerging concepts regulating EMP and the formation of E/M hybrid intermediates by describing differences and similarities between cancer and normal hybrid stem cells. In particular, the comprehension of hybrid E/M cells biology will surely advance our understanding of their features and how they could be exploited to improve tissue regeneration and repair.
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Affiliation(s)
- Angelo Canciello
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Adrián Cerveró-Varona
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Alessia Peserico
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Annunziata Mauro
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Valentina Russo
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Andrea Morrione
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Antonio Giordano
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States
- Sbarro Health Research Organization (SHRO), Philadelphia, PA, United States
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Barbara Barboni
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
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10
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Moiz B, Li A, Padmanabhan S, Sriram G, Clyne AM. Isotope-Assisted Metabolic Flux Analysis: A Powerful Technique to Gain New Insights into the Human Metabolome in Health and Disease. Metabolites 2022; 12:1066. [PMID: 36355149 PMCID: PMC9694183 DOI: 10.3390/metabo12111066] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 04/28/2024] Open
Abstract
Cell metabolism represents the coordinated changes in genes, proteins, and metabolites that occur in health and disease. The metabolic fluxome, which includes both intracellular and extracellular metabolic reaction rates (fluxes), therefore provides a powerful, integrated description of cellular phenotype. However, intracellular fluxes cannot be directly measured. Instead, flux quantification requires sophisticated mathematical and computational analysis of data from isotope labeling experiments. In this review, we describe isotope-assisted metabolic flux analysis (iMFA), a rigorous computational approach to fluxome quantification that integrates metabolic network models and experimental data to generate quantitative metabolic flux maps. We highlight practical considerations for implementing iMFA in mammalian models, as well as iMFA applications in in vitro and in vivo studies of physiology and disease. Finally, we identify promising new frontiers in iMFA which may enable us to fully unlock the potential of iMFA in biomedical research.
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Affiliation(s)
- Bilal Moiz
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Andrew Li
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Surya Padmanabhan
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Alisa Morss Clyne
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
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11
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Wang Y, Liu L, Liu X, Tan X, Zhu Y, Luo N, Zhao G, Cui H, Wen J. SLC16A7 Promotes Triglyceride Deposition by De Novo Lipogenesis in Chicken Muscle Tissue. BIOLOGY 2022; 11:1547. [PMID: 36358250 PMCID: PMC9687483 DOI: 10.3390/biology11111547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/22/2022] [Accepted: 10/08/2022] [Indexed: 07/30/2023]
Abstract
Triglyceride (TG) content in chicken muscle tissue signifies intramuscular fat (IMF) content, which is important for improving meat quality. However, the genetic basis of TG deposition in chicken is still unclear. Using 520 chickens from an artificially selected line with significantly increased IMF content and a control line, a genome-wide association study (GWAS) with TG content reports a region of 802 Kb located in chromosome 1. The XP-EHH and gene expression analysis together reveal that the solute carrier family 16 member A7 (SLC16A7) gene is the key candidate gene associated with TG content in chicken muscle tissue. Furthermore, the weighted gene co-expression network analysis (WGCNA) confirmed the regulatory effects of SLC16A7 on promoting TG deposition by de novo lipogenesis (DNL). Functional verification of SLC16A7 in vitro also supports this view, and reveals that this effect mainly occurs in myocytes. Our data highlight a potential IMF deposition pathway by DNL, induced by SLC16A7 in chicken myocytes. These findings will improve the understanding of IMF regulation in chicken and guide the formulation of breeding strategies for high-quality chicken.
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Affiliation(s)
- Yongli Wang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lu Liu
- College of Animal Science and Technology, College of Veterinary Medicine of Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaojing Liu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaodong Tan
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuting Zhu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Na Luo
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huanxian Cui
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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12
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Metabolic reprogramming in the OPA1-deficient cells. Cell Mol Life Sci 2022; 79:517. [DOI: 10.1007/s00018-022-04542-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/12/2022] [Accepted: 08/31/2022] [Indexed: 11/03/2022]
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13
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Glioblastoma Stem-Like Cells (GSCs) with Mesenchymal Signature: Lipid Profiles of Mobile Lipids Obtained with MRS before and after Radio/Chemical Treatments. Biomolecules 2022; 12:biom12081051. [PMID: 36008944 PMCID: PMC9405836 DOI: 10.3390/biom12081051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/15/2022] [Accepted: 07/26/2022] [Indexed: 02/05/2023] Open
Abstract
Glioblastoma is the most common and lethal primary malignant brain tumor in adults. Glioblastoma stem cells (GSCs) promote and are responsible for glioblastoma intratumoral heterogeneity and therapy resistance, due to their two main features: self-renewal and differentiation. Lipids have important biological and physiological functions that are critical for understanding the regulation and control of stem cell fate; lipid metabolism and related unsaturation levels play a possible role as the target of therapeutics to overcome glioblastoma radioresistance. This paper aimed at an in-depth analysis of 13 GSC mesenchymal (MES) lines, two subclones, and a stabilized glioblastoma line (T98G) by magnetic resonance spectroscopy (MRS). Particularly, 2D MRS was used to investigate lipid unsaturation behavior during growth in culture and after treatment with etomoxir and photon beams. MES lines, although belonging to the same genetic and metabolic cluster, showed metabolic heterogeneity when observed by MRS, focusing on lipid signals. Nonetheless, the observed unsaturation level stability for two representative lines after stressful treatments suggests unusual robustness of the unsaturation levels for each line, as a peculiar and intrinsic characteristic of GSCs.
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14
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Accumulation of oncometabolite D-2-Hydroxyglutarate by SLC25A1 inhibition: A metabolic strategy for induction of HR-ness and radiosensitivity. Cell Death Dis 2022; 13:641. [PMID: 35869047 PMCID: PMC9307853 DOI: 10.1038/s41419-022-05098-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 01/21/2023]
Abstract
Oncogenic mutations in metabolic genes and associated oncometabolite accumulation support cancer progression but can also restrict cellular functions needed to cope with DNA damage. For example, gain-of-function mutations in isocitrate dehydrogenase (IDH) and the resulting accumulation of the oncometabolite D-2-hydroxyglutarate (D-2-HG) enhanced the sensitivity of cancer cells to inhibition of poly(ADP-ribose)-polymerase (PARP)1 and radiotherapy (RT). In our hand, inhibition of the mitochondrial citrate transport protein (SLC25A1) enhanced radiosensitivity of cancer cells and this was associated with increased levels of D-2-HG and a delayed repair of radiation-induced DNA damage. Here we aimed to explore the suggested contribution of D-2-HG-accumulation to disturbance of DNA repair, presumably homologous recombination (HR) repair, and enhanced radiosensitivity of cancer cells with impaired SLC25A1 function. Genetic and pharmacologic inhibition of SLC25A1 (SLC25A1i) increased D-2-HG-levels and sensitized lung cancer and glioblastoma cells to the cytotoxic action of ionizing radiation (IR). SLC25A1i-mediated radiosensitization was abrogated in MEFs with a HR-defect. D-2-HG-accumulation was associated with increased DNA damage and delayed resolution of IR-induced γH2AX and Rad51 foci. Combining SLC25A1i with PARP- or the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs)-inhibitors further potentiated IR-induced DNA damage, delayed DNA repair kinetics resulting in radiosensitization of cancer cells. Importantly, proof of concept experiments revealed that combining SLC25A1i with IR without and with PARPi also reduced tumor growth in the chorioallantoic membrane (CAM) model in vivo. Thereby SLC25A1i offers an innovative strategy for metabolic induction of context-dependent lethality approaches in combination with RT and clinically relevant inhibitors of complementary DNA repair pathways.
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15
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Abstract
In a recent issue of Nature, Arnold et al. report that the partitioning of citrate away from the oxidative steps of the tricarboxylic acid cycle and into the citrate-malate shuttle is essential for mouse embryonic stem cell differentiation. Their findings highlight a crucial role for metabolic regulation in developmental biology.
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Affiliation(s)
- Stanisław Deja
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter A Crawford
- Division of Molecular Medicine; Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Shawn C Burgess
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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16
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Zeng P, Lu W, Tian J, Qiao S, Li J, Glorieux C, Wen S, Zhang H, Li Y, Huang P. Reductive TCA cycle catalyzed by wild-type IDH2 promotes acute myeloid leukemia and is a metabolic vulnerability for potential targeted therapy. J Hematol Oncol 2022; 15:30. [PMID: 35313945 PMCID: PMC8935709 DOI: 10.1186/s13045-022-01245-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/03/2022] [Indexed: 12/20/2022] Open
Abstract
Background Isocitrate dehydrogenase-2 (IDH2) is a mitochondrial enzyme that catalyzes the metabolic conversion between isocitrate and alpha-ketoglutarate (α-KG) in the TCA cycle. IDH2 mutation is an oncogenic event in acute myeloid leukemia (AML) due to the generation of 2-hydroxyglutarate. However, the role of wild-type IDH2 in AML remains unknown, despite patients with it suffer worse clinical outcome than those harboring mutant type.
Methods IDH2 expression in AML cell lines and patient samples was evaluated by RT-qPCR, western blotting and database analyses. The role of wild-type IDH2 in AML cell survival and proliferation was tested using genetic knockdown and pharmacological inhibition in AML cells and animal models. LC–MS, GC–MS, isotope metabolic tracing, and molecular analyses were performed to reveal the underlying mechanisms. Results We found that wild-type IDH2 was overexpressed in AML and played a major role in promoting leukemia cell survival and proliferation in vitro and in vivo. Metabolomic analyses revealed an active IDH2-mediated reductive TCA cycle that promoted the conversion of α-KG to isocitrate/citrate to facilitate glutamine utilization for lipid synthesis in AML cells. Suppression of wild-type IDH2 by shRNA resulted in elevated α-KG and decreased isocitrate/citrate, leading to reduced lipid synthesis, a significant decrease in c-Myc downregulated by α-KG, and an inhibition of AML viability and proliferation. Importantly, pharmacological inhibition of IDH2 showed significant therapeutic effect in mice inoculated with AML cells with wt-IDH2 and induced a downregulation of C-MYC in vivo. Conclusions Wt-IDH2 is an essential molecule for AML cell survival and proliferation by promoting conversion of α-KG to isocitrate for lipid synthesis and by upregulating c-Myc expression and could be a potential therapeutic target in AML. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-022-01245-z.
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Affiliation(s)
- Peiting Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Wenhua Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jingyu Tian
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.,Metabolic Innovation Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shuang Qiao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jiangjiang Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Christophe Glorieux
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Shijun Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Hui Zhang
- Metabolic Innovation Center, Sun Yat-sen University, Guangzhou, 510080, China.,School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yiqing Li
- Department of Hematology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Peng Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China. .,Metabolic Innovation Center, Sun Yat-sen University, Guangzhou, 510080, China.
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17
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Patrício JS, Dias-Pedroso D, Carvalho RA, Viera HLA, Jones JG. A simple method for quantifying de novo lipogenesis rate and substrate selection in cell cultures by 13 C NMR isotopomer analysis of the crude lipid fraction. NMR IN BIOMEDICINE 2022; 35:e4648. [PMID: 34850989 DOI: 10.1002/nbm.4648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
PURPOSE De novo lipogenesis (DNL) is critical for cell growth and maintenance, and acetyl-CoA precursors can be derived from different substrates. We developed a 13 C NMR analysis of lipid extracts from cultured microglia cells administered with [U-13 C]glucose that informs overall lipogenic activity as well as the contribution of glucose to lipogenic acetyl-CoA. METHODS BV-2 microglial cell line cultured with glucose and glutamine was provided with [U-13 C]glucose and unlabeled glutamine for 24 h and studied in either the presence or absence of lipopolysaccharide (LPS). Cells were then extracted for lipids and the crude lipid fraction was analyzed by 13 C NMR. 13 C-isotopomer signals in the fatty acid ω - 1 and ω - 2 signals representing consecutive or non-consecutive enrichment of the fatty acid chain by [1,2-13 C2 ]acetyl-CoA were quantified and applied to a probabilistic model of acetyl-CoA precursor and fatty acid enrichment. RESULTS Glucose contributed 72 ± 2% of lipogenic acetyl-CoA while DNL from all sources accounted for 16 ± 2% of lipid turnover. With LPS, there was a significant decrease in glucose contribution (59 ± 4%, p < 0.05) while DNL was unchanged (11 ± 3%). CONCLUSIONS A simple 13 C NMR analysis of the crude lipid fractions of BV-2 cells administered with [U-13 C]glucose informs DNL activity and the contribution of glucose to the acetyl-CoA precursors. While DNL was preserved in the presence of LPS, there was redirection of lipogenic acetyl-CoA sources from glucose to other substrates. Thus, in the present article, we describe a novel and simple 13 C NMR analysis approach to disclose the overall lipogenic activity and substrate contribution to DNL, suitable for evaluating DNL rates in cell cultures.
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Affiliation(s)
- João S Patrício
- Center for Neurosciences and Cell Biology, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Daniela Dias-Pedroso
- CEDOC, Faculdade de Ciência Médicas/NOVA Medical School, Universidade Nova de Lisboa, Lisbon, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry/Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Rui A Carvalho
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
- Associated Laboratory for Green Chemistry-Clean Technologies and Processes, REQUIMTE, Faculty of Sciences and Technology, University of Porto, Oporto, Portugal
| | - Helena L A Viera
- CEDOC, Faculdade de Ciência Médicas/NOVA Medical School, Universidade Nova de Lisboa, Lisbon, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry/Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - John G Jones
- Center for Neurosciences and Cell Biology, University of Coimbra, Coimbra, Portugal
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18
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Chandris P, Giannouli CC, Panayotou G. Imaging Approaches for the Study of Metabolism in Real Time Using Genetically Encoded Reporters. Front Cell Dev Biol 2022; 9:725114. [PMID: 35118062 PMCID: PMC8804523 DOI: 10.3389/fcell.2021.725114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Metabolism comprises of two axes in order to serve homeostasis: anabolism and catabolism. Both axes are interbranched with the so-called bioenergetics aspect of metabolism. There is a plethora of analytical biochemical methods to monitor metabolites and reactions in lysates, yet there is a rising need to monitor, quantify and elucidate in real time the spatiotemporal orchestration of complex biochemical reactions in living systems and furthermore to analyze the metabolic effect of chemical compounds that are destined for the clinic. The ongoing technological burst in the field of imaging creates opportunities to establish new tools that will allow investigators to monitor dynamics of biochemical reactions and kinetics of metabolites at a resolution that ranges from subcellular organelle to whole system for some key metabolites. This article provides a mini review of available toolkits to achieve this goal but also presents a perspective on the open space that can be exploited to develop novel methodologies that will merge classic biochemistry of metabolism with advanced imaging. In other words, a perspective of "watching metabolism in real time."
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Affiliation(s)
- Panagiotis Chandris
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece
| | | | - George Panayotou
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece
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19
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Batchuluun B, Pinkosky SL, Steinberg GR. Lipogenesis inhibitors: therapeutic opportunities and challenges. Nat Rev Drug Discov 2022; 21:283-305. [PMID: 35031766 PMCID: PMC8758994 DOI: 10.1038/s41573-021-00367-2] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2021] [Indexed: 12/12/2022]
Abstract
Fatty acids are essential for survival, acting as bioenergetic substrates, structural components and signalling molecules. Given their vital role, cells have evolved mechanisms to generate fatty acids from alternative carbon sources, through a process known as de novo lipogenesis (DNL). Despite the importance of DNL, aberrant upregulation is associated with a wide variety of pathologies. Inhibiting core enzymes of DNL, including citrate/isocitrate carrier (CIC), ATP-citrate lyase (ACLY), acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS), represents an attractive therapeutic strategy. Despite challenges related to efficacy, selectivity and safety, several new classes of synthetic DNL inhibitors have entered clinical-stage development and may become the foundation for a new class of therapeutics. De novo lipogenesis (DNL) is vital for the maintenance of whole-body and cellular homeostasis, but aberrant upregulation of the pathway is associated with a broad range of conditions, including cardiovascular disease, metabolic disorders and cancers. Here, Steinberg and colleagues provide an overview of the physiological and pathological roles of the core DNL enzymes and assess strategies and agents currently in development to therapeutically target them.
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Affiliation(s)
- Battsetseg Batchuluun
- Centre for Metabolism, Obesity and Diabetes Research, Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | | | - Gregory R Steinberg
- Centre for Metabolism, Obesity and Diabetes Research, Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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20
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Cadoux-Hudson T, Schofield CJ, McCullagh JS. Isocitrate dehydrogenase gene variants in cancer and their clinical significance. Biochem Soc Trans 2021; 49:2561-2572. [PMID: 34854890 PMCID: PMC8786286 DOI: 10.1042/bst20210277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Human isocitrate dehydrogenase (IDH) genes encode for the IDH1, 2 & 3 isoenzymes which catalyse the formation of 2-oxoglutarate from isocitrate and are essential for normal mammalian metabolism. Although mutations in these genes in cancer were long thought to lead to a 'loss of function', combined genomic and metabolomic studies led to the discovery that a common IDH 1 mutation, present in low-grade glioma and acute myeloid leukaemia (AML), yields a variant (R132H) with a striking change of function leading to the production of (2R)-hydroxyglutarate (2HG) which consequently accumulates in large quantities both within and outside cells. Elevated 2HG is proposed to promote tumorigenesis, although the precise mechanism by which it does this remains uncertain. Inhibitors of R132H IDH1, and other subsequently identified cancer-linked 2HG producing IDH variants, are approved for clinical use in the treatment of chemotherapy-resistant AML, though resistance enabled by additional substitutions has emerged. In this review, we provide a current overview of cancer linked IDH mutations focussing on their distribution in different cancer types, the effects of substitution mutations on enzyme activity, the mode of action of recently developed inhibitors, and their relationship with emerging resistance-mediating double mutations.
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Affiliation(s)
- Thomas Cadoux-Hudson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - James S.O. McCullagh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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21
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Kumar A, Cordes T, Thalacker-Mercer AE, Pajor AM, Murphy AN, Metallo CM. NaCT/SLC13A5 facilitates citrate import and metabolism under nutrient-limited conditions. Cell Rep 2021; 36:109701. [PMID: 34525352 PMCID: PMC8500708 DOI: 10.1016/j.celrep.2021.109701] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/19/2021] [Accepted: 08/20/2021] [Indexed: 01/11/2023] Open
Abstract
Citrate lies at a critical node of metabolism, linking tricarboxylic acid metabolism and lipogenesis via acetyl-coenzyme A. Recent studies have observed that deficiency of the sodium-dependent citrate transporter (NaCT), encoded by SLC13A5, dysregulates hepatic metabolism and drives pediatric epilepsy. To examine how NaCT contributes to citrate metabolism in cells relevant to the pathophysiology of these diseases, we apply 13C isotope tracing to SLC13A5-deficient hepatocellular carcinoma (HCC) cells and primary rat cortical neurons. Exogenous citrate appreciably contributes to intermediary metabolism only under hypoxic conditions. In the absence of glutamine, citrate supplementation increases de novo lipogenesis and growth of HCC cells. Knockout of SLC13A5 in Huh7 cells compromises citrate uptake and catabolism. Citrate supplementation rescues Huh7 cell viability in response to glutamine deprivation or Zn2+ treatment, and NaCT deficiency mitigates these effects. Collectively, these findings demonstrate that NaCT-mediated citrate uptake is metabolically important under nutrient-limited conditions and may facilitate resistance to metal toxicity.
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Affiliation(s)
- Avi Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thekla Cordes
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anna E Thalacker-Mercer
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ana M Pajor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anne N Murphy
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA.
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22
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Chang L, Lu H, Chen H, Tang X, Zhao J, Zhang H, Chen YQ, Chen W. Lipid metabolism research in oleaginous fungus Mortierella alpina: Current progress and future prospects. Biotechnol Adv 2021; 54:107794. [PMID: 34245810 DOI: 10.1016/j.biotechadv.2021.107794] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 06/11/2021] [Accepted: 07/04/2021] [Indexed: 12/19/2022]
Abstract
The oleaginous fungus Mortierella alpina has distinct advantages in long-chain PUFAs production, and it is the only source for dietary arachidonic acid (ARA) certificated by FDA and European Commission. This review provides an overall introduction to M. alpina, including its major research methods, key factors governing lipid biosynthesis, metabolic engineering and omics studies. Currently, the research interests in M. alpina focus on improving lipid yield and fatty acid desaturation degree by enhancing fatty acid precursors and the reducing power NADPH, and genetic manipulation on PUFAs synthetic pathways is carried to optimise fatty acid composition. Besides, multi-omics studies have been applied to elucidate the global regulatory mechanism of lipogenesis in M. alpina. However, research challenges towards achieving a lipid cell factory lie in strain breeding and cost control due to the coenocytic mycelium, long fermentation period and insufficient conversion rate from carbon to lipid. We also proposed future research goals based on a multilevel regulating strategy: obtaining ideal chassis by directional evolution and high-throughput screening; rewiring central carbon metabolism and inhibiting competitive pathways by multi-gene manipulation system to enhance carbon to lipid conversion rate; optimisation of protein function based on post-translational modification; application of dynamic fermentation strategies suitable for different fermentation phases. By reviewing the comprehensive research progress of this oleaginous fungus, we aim to further comprehend the fungal lipid metabolism and provide reference information and guidelines for the exploration of microbial oils from the perspectives of fundamental research to industrial application.
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Affiliation(s)
- Lulu Chang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Hengqian Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China; Wuxi Translational Medicine Research Center, Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, Jiangsu 214122, PR China; Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
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23
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Comprehensive Plasma Metabolomic Profile of Patients with Advanced Neuroendocrine Tumors (NETs). Diagnostic and Biological Relevance. Cancers (Basel) 2021; 13:cancers13112634. [PMID: 34072010 PMCID: PMC8197817 DOI: 10.3390/cancers13112634] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Metabolic flexibility is one of the key hallmarks of cancer and metabolites are the final products of this adaptation, reflecting the aberrant changes of tumors. However, the metabolic plasticity of each cancer type is still unknown, and specifically to date, there are no data on metabolic profile in neuroendocrine tumors. The aim of our retrospective study was to assess the metabolomic profile of NET patients to understand metabolic deregulation in these tumors and identify novel biomarkers with clinical potential. We provided, for the first time, a comprehensive metabolic profile of NET patients and identifies a distinctive metabolic signature in plasma of potential clinical use, selecting a reduced set of metabolites of high diagnostic accuracy. We have identified 32 novel enriched metabolic pathways in NETs related with the TCA cycle, and with arginine, pyruvate or glutathione metabolism, which have distinct implications in oncogenesis and may open innovative avenues of clinical research. Abstract Purpose: High-throughput “-omic” technologies have enabled the detailed analysis of metabolic networks in several cancers, but NETs have not been explored to date. We aim to assess the metabolomic profile of NET patients to understand metabolic deregulation in these tumors and identify novel biomarkers with clinical potential. Methods: Plasma samples from 77 NETs and 68 controls were profiled by GC−MS, CE−MS and LC−MS untargeted metabolomics. OPLS-DA was performed to evaluate metabolomic differences. Related pathways were explored using Metaboanalyst 4.0. Finally, ROC and OPLS-DA analyses were performed to select metabolites with biomarker potential. Results: We identified 155 differential compounds between NETs and controls. We have detected an increase of bile acids, sugars, oxidized lipids and oxidized products from arachidonic acid and a decrease of carnitine levels in NETs. MPA/MSEA identified 32 enriched metabolic pathways in NETs related with the TCA cycle and amino acid metabolism. Finally, OPLS-DA and ROC analysis revealed 48 metabolites with diagnostic potential. Conclusions: This study provides, for the first time, a comprehensive metabolic profile of NET patients and identifies a distinctive metabolic signature in plasma of potential clinical use. A reduced set of metabolites of high diagnostic accuracy has been identified. Additionally, new enriched metabolic pathways annotated may open innovative avenues of clinical research.
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24
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Wang Z, Wang QA, Liu Y, Jiang L. Energy metabolism in brown adipose tissue. FEBS J 2021; 288:3647-3662. [PMID: 34028971 DOI: 10.1111/febs.16015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 12/14/2022]
Abstract
Brown adipose tissue (BAT) is well known to burn calories through uncoupled respiration, producing heat to maintain body temperature. This 'calorie wasting' feature makes BAT a special tissue, which can function as an 'energy sink' in mammals. While a combination of high energy intake and low energy expenditure is the leading cause of overweight and obesity in modern society, activating a safe 'energy sink' has been proposed as a promising obesity treatment strategy. Metabolically, lipids and glucose have been viewed as the major energy substrates in BAT, while succinate, lactate, branched-chain amino acids, and other metabolites can also serve as energy substrates for thermogenesis. Since the cataplerotic and anaplerotic reactions of these metabolites interconnect with each other, BAT relies on its dynamic, flexible, and complex metabolism to support its special function. In this review, we summarize how BAT orchestrates the metabolic utilization of various nutrients to support thermogenesis and contributes to whole-body metabolic homeostasis.
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Affiliation(s)
- Zhichao Wang
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, USA
| | - Qiong A Wang
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, USA.,Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Yong Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Institute for Advanced Studies, Wuhan University, China
| | - Lei Jiang
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, USA.,Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
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25
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Kiesel VA, Sheeley MP, Coleman MF, Cotul EK, Donkin SS, Hursting SD, Wendt MK, Teegarden D. Pyruvate carboxylase and cancer progression. Cancer Metab 2021; 9:20. [PMID: 33931119 PMCID: PMC8088034 DOI: 10.1186/s40170-021-00256-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/04/2021] [Indexed: 01/17/2023] Open
Abstract
Pyruvate carboxylase (PC) is a mitochondrial enzyme that catalyzes the ATP-dependent carboxylation of pyruvate to oxaloacetate (OAA), serving to replenish the tricarboxylic acid (TCA) cycle. In nonmalignant tissue, PC plays an essential role in controlling whole-body energetics through regulation of gluconeogenesis in the liver, synthesis of fatty acids in adipocytes, and insulin secretion in pancreatic β cells. In breast cancer, PC activity is linked to pulmonary metastasis, potentially by providing the ability to utilize glucose, fatty acids, and glutamine metabolism as needed under varying conditions as cells metastasize. PC enzymatic activity appears to be of particular importance in cancer cells that are unable to utilize glutamine for anaplerosis. Moreover, PC activity also plays a role in lipid metabolism and protection from oxidative stress in cancer cells. Thus, PC activity may be essential to link energy substrate utilization with cancer progression and to enable the metabolic flexibility necessary for cell resilience to changing and adverse conditions during the metastatic process.
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Affiliation(s)
- Violet A Kiesel
- Department of Nutrition Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Madeline P Sheeley
- Department of Nutrition Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Michael F Coleman
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Eylem Kulkoyluoglu Cotul
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
| | - Shawn S Donkin
- Department of Animal Science, Purdue University, West Lafayette, USA
| | - Stephen D Hursting
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Michael K Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
| | - Dorothy Teegarden
- Department of Nutrition Sciences, Purdue University, West Lafayette, IN, 47907, USA.
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26
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Zhang GF, Jensen MV, Gray SM, El K, Wang Y, Lu D, Becker TC, Campbell JE, Newgard CB. Reductive TCA cycle metabolism fuels glutamine- and glucose-stimulated insulin secretion. Cell Metab 2021; 33:804-817.e5. [PMID: 33321098 PMCID: PMC8115731 DOI: 10.1016/j.cmet.2020.11.020] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 11/06/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022]
Abstract
Metabolic fuels regulate insulin secretion by generating second messengers that drive insulin granule exocytosis, but the biochemical pathways involved are incompletely understood. Here we demonstrate that stimulation of rat insulinoma cells or primary rat islets with glucose or glutamine + 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (Gln + BCH) induces reductive, "counter-clockwise" tricarboxylic acid (TCA) cycle flux of glutamine to citrate. Molecular or pharmacologic suppression of isocitrate dehydrogenase-2 (IDH2), which catalyzes reductive carboxylation of 2-ketoglutarate to isocitrate, results in impairment of glucose- and Gln + BCH-stimulated reductive TCA cycle flux, lowering of NADPH levels, and inhibition of insulin secretion. Pharmacologic suppression of IDH2 also inhibits insulin secretion in living mice. Reductive TCA cycle flux has been proposed as a mechanism for generation of biomass in cancer cells. Here we demonstrate that reductive TCA cycle flux also produces stimulus-secretion coupling factors that regulate insulin secretion, including in non-dividing cells.
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Affiliation(s)
- Guo-Fang Zhang
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA; Department of Medicine, Endocrinology and Metabolism Division, Duke University Medical Center, Durham, NC 27701, USA
| | - Mette V Jensen
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Sarah M Gray
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Kimberley El
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - You Wang
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Danhong Lu
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Thomas C Becker
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA; Department of Medicine, Endocrinology and Metabolism Division, Duke University Medical Center, Durham, NC 27701, USA
| | - Jonathan E Campbell
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA; Department of Medicine, Endocrinology and Metabolism Division, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27701, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA; Department of Medicine, Endocrinology and Metabolism Division, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27701, USA.
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27
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Coleman PS, Parlo RA. Warburg's Ghost-Cancer's Self-Sustaining Phenotype: The Aberrant Carbon Flux in Cholesterol-Enriched Tumor Mitochondria via Deregulated Cholesterogenesis. Front Cell Dev Biol 2021; 9:626316. [PMID: 33777935 PMCID: PMC7994618 DOI: 10.3389/fcell.2021.626316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/29/2021] [Indexed: 01/08/2023] Open
Abstract
Interpreting connections between the multiple networks of cell metabolism is indispensable for understanding how cells maintain homeostasis or transform into the decontrolled proliferation phenotype of cancer. Situated at a critical metabolic intersection, citrate, derived via glycolysis, serves as either a combustible fuel for aerobic mitochondrial bioenergetics or as a continuously replenished cytosolic carbon source for lipid biosynthesis, an essentially anaerobic process. Therein lies the paradox: under what conditions do cells control the metabolic route by which they process citrate? The Warburg effect exposes essentially the same dilemma—why do cancer cells, despite an abundance of oxygen needed for energy-generating mitochondrial respiration with citrate as fuel, avoid catabolizing mitochondrial citrate and instead rely upon accelerated glycolysis to support their energy requirements? This review details the genesis and consequences of the metabolic paradigm of a “truncated” Krebs/TCA cycle. Abundant data are presented for substrate utilization and membrane cholesterol enrichment in tumors that are consistent with criteria of the Warburg effect. From healthy cellular homeostasis to the uncontrolled proliferation of tumors, metabolic alterations center upon the loss of regulation of the cholesterol biosynthetic pathway. Deregulated tumor cholesterogenesis at the HMGR locus, generating enhanced carbon flux through the cholesterol synthesis pathway, is an absolute prerequisite for DNA synthesis and cell division. Therefore, expedited citrate efflux from cholesterol-enriched tumor mitochondria via the CTP/SLC25A1 citrate transporter is fundamental for sustaining the constant demand for cytosolic citrate that fuels the elevated flow of carbons from acetyl-CoA through the deregulated pathway of cholesterol biosynthesis.
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Affiliation(s)
| | - Risa A Parlo
- Kingsborough Community College, Brooklyn, NY, United States
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28
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Liang L, Sun F, Wang H, Hu Z. Metabolomics, metabolic flux analysis and cancer pharmacology. Pharmacol Ther 2021; 224:107827. [PMID: 33662451 DOI: 10.1016/j.pharmthera.2021.107827] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Metabolic reprogramming is a hallmark of cancer and increasing evidence suggests that reprogrammed cell metabolism supports tumor initiation, progression, metastasis and drug resistance. Understanding metabolic dysregulation may provide therapeutic targets and facilitate drug research and development for cancer therapy. Metabolomics enables the high-throughput characterization of a large scale of small molecule metabolites in cells, tissues and biofluids, while metabolic flux analysis (MFA) tracks dynamic metabolic activities using stable isotope tracer methods. Recent advances in metabolomics and MFA technologies make them powerful tools for metabolic profiling and characterizing metabolic activities in health and disease, especially in cancer research. In this review, we introduce recent advances in metabolomics and MFA analytical technologies, and provide the first comprehensive summary of the most commonly used isotope tracing methods. In addition, we highlight how metabolomics and MFA are applied in cancer pharmacology studies particularly for discovering targetable metabolic vulnerabilities, understanding the mechanisms of drug action and drug resistance, exploring potential strategies with dietary intervention, identifying cancer biomarkers, as well as enabling precision treatment with pharmacometabolomics.
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Affiliation(s)
- Lingfan Liang
- School of Pharmaceutical Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Fei Sun
- School of Pharmaceutical Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Hongbo Wang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
| | - Zeping Hu
- School of Pharmaceutical Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China.
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29
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Barnabas GD, Lee JS, Shami T, Harel M, Beck L, Selitrennik M, Jerby-Arnon L, Erez N, Ruppin E, Geiger T. Serine Biosynthesis Is a Metabolic Vulnerability in IDH2-Driven Breast Cancer Progression. Cancer Res 2021; 81:1443-1456. [PMID: 33500247 DOI: 10.1158/0008-5472.can-19-3020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/27/2020] [Accepted: 01/19/2021] [Indexed: 11/16/2022]
Abstract
Cancer-specific metabolic phenotypes and their vulnerabilities represent a viable area of cancer research. In this study, we explored the association of breast cancer subtypes with different metabolic phenotypes and identified isocitrate dehydrogenase 2 (IDH2) as a key player in triple-negative breast cancer (TNBC) and HER2. Functional assays combined with mass spectrometry-based analyses revealed the oncogenic role of IDH2 in cell proliferation, anchorage-independent growth, glycolysis, mitochondrial respiration, and antioxidant defense. Genome-scale metabolic modeling identified phosphoglycerate dehydrogenase (PHGDH) and phosphoserine aminotransferase (PSAT1) as the synthetic dosage lethal (SDL) partners of IDH2. In agreement, CRISPR-Cas9 knockout of PHGDH and PSAT1 showed the essentiality of serine biosynthesis proteins in IDH2-high cells. The clinical significance of the SDL interaction was supported by patients with IDH2-high/PHGDH-low tumors, who exhibited longer survival than patients with IDH2-high/PHGDH-high tumors. Furthermore, PHGDH inhibitors were effective in treating IDH2-high cells in vitro and in vivo. Altogether, our study creates a new link between two known cancer regulators and emphasizes PHGDH as a promising target for TNBC with IDH2 overexpression. SIGNIFICANCE: These findings highlight the metabolic dependence of IDH2 on the serine biosynthesis pathway, adding an important layer to the connection between TCA cycle and glycolysis, which can be translated into novel targeted therapies.
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Affiliation(s)
- Georgina D Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joo Sang Lee
- Department of Artificial Intelligence & Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Suwon, Republic of Korea.,Cancer Data Science Lab, CCR, NCI, NIH, Maryland
| | - Tamar Shami
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Harel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lir Beck
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michael Selitrennik
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Livnat Jerby-Arnon
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Neta Erez
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eytan Ruppin
- Cancer Data Science Lab, CCR, NCI, NIH, Maryland
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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30
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The Mitochondrial Citrate Carrier SLC25A1/CIC and the Fundamental Role of Citrate in Cancer, Inflammation and Beyond. Biomolecules 2021; 11:biom11020141. [PMID: 33499062 PMCID: PMC7912299 DOI: 10.3390/biom11020141] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial citrate/isocitrate carrier, CIC, has been shown to play an important role in a growing list of human diseases. CIC belongs to a large family of nuclear-encoded mitochondrial transporters that serve the fundamental function of allowing the transit of ions and metabolites through the impermeable mitochondrial membrane. Citrate is central to mitochondrial metabolism and respiration and plays fundamental activities in the cytosol, serving as a metabolic substrate, an allosteric enzymatic regulator and, as the source of Acetyl-Coenzyme A, also as an epigenetic modifier. In this review, we highlight the complexity of the mechanisms of action of this transporter, describing its involvement in human diseases and the therapeutic opportunities for targeting its activity in several pathological conditions.
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31
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Audano M, Pedretti S, Ligorio S, Giavarini F, Caruso D, Mitro N. Investigating metabolism by mass spectrometry: From steady state to dynamic view. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4658. [PMID: 33084147 DOI: 10.1002/jms.4658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Metabolism is the set of life-sustaining reactions in organisms. These biochemical reactions are organized in metabolic pathways, in which one metabolite is converted through a series of steps catalyzed by enzymes in another chemical compound. Metabolic reactions are categorized as catabolic, the breaking down of metabolites to produce energy, and/or anabolic, the synthesis of compounds that consume energy. The balance between catabolism of the preferential fuel substrate and anabolism defines the overall metabolism of a cell or tissue. Metabolomics is a powerful tool to gain new insights contributing to the identification of complex molecular mechanisms in the field of biomedical research, both basic and translational. The enormous potential of this kind of analyses consists of two key aspects: (i) the possibility of performing so-called targeted and untargeted experiments through which it is feasible to verify or formulate a hypothesis, respectively, and (ii) the opportunity to run either steady-state analyses to have snapshots of the metabolome at a given time under different experimental conditions or dynamic analyses through the use of labeled tracers. In this review, we will highlight the most important practical (e.g., different sample extraction approaches) and conceptual steps to consider for metabolomic analysis, describing also the main application contexts in which it is used. In addition, we will provide some insights into the most innovative approaches and progress in the field of data analysis and processing, highlighting how this part is essential for the proper extrapolation and interpretation of data.
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Affiliation(s)
- Matteo Audano
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Simona Ligorio
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Flavio Giavarini
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Donatella Caruso
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Nico Mitro
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
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32
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Gao J, Guo Z, Cheng J, Sun B, Yang J, Li H, Wu S, Dong F, Yan X. Differential metabolic responses in breast cancer cell lines to acidosis and lactic acidosis revealed by stable isotope assisted metabolomics. Sci Rep 2020; 10:21967. [PMID: 33319827 PMCID: PMC7738541 DOI: 10.1038/s41598-020-78955-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/01/2020] [Indexed: 12/14/2022] Open
Abstract
Extracellular acidosis is considered as a hallmark of most human tumors, which plays an important role in promoting tumor malignant and aggressive phenotype in tumorigenesis. Acidosis and lactic acidosis can induce different responses in tumors. Previous studies have associated the response to lactic acidosis of tumors with good survival outcomes. In this study, we investigated the metabolomic changes in triple negative and luminal subtype breast cancer cell lines in response to acidosis and lactic acidosis. Our results showed that acidosis results in the reduction of cell viability and glycolysis in breast cancer cells, which is reversely correlated with the malignancy of cell lines. Under lactic acidosis, this reduction is reversed slightly. Untargeted metabolomic profiling revealed that glutaminolysis and fatty acid synthesis in cancer cells under acidosis are increased, while TCA cycle and glycolysis are decreased. Under lactic acidosis, the pentose phosphate pathway and acetate release are increased in MDA-MB-231 cells. The current results uncovered the different metabolic responses of breast cancer cells to acidosis and lactic acidosis, demonstrating the power of combined untargeted and stable isotope assisted metabolomics in comprehensive metabolomic analysis.
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Affiliation(s)
- Jiayue Gao
- National Center of Biomedical Analysis, No. 27 Taiping Road, Beijing, 100039, China
| | - Zhiying Guo
- National Center of Biomedical Analysis, No. 27 Taiping Road, Beijing, 100039, China.,Hepatal-Biliary-Pancreatic Center, Beijing Tsinghua Chang Gung Hospital, Beijing, 102218, China
| | - Jianhua Cheng
- National Center of Biomedical Analysis, No. 27 Taiping Road, Beijing, 100039, China
| | - Bo Sun
- National Center of Biomedical Analysis, No. 27 Taiping Road, Beijing, 100039, China
| | - Jie Yang
- National Center of Biomedical Analysis, No. 27 Taiping Road, Beijing, 100039, China
| | - Haijing Li
- National Center of Biomedical Analysis, No. 27 Taiping Road, Beijing, 100039, China
| | - Shengming Wu
- National Center of Biomedical Analysis, No. 27 Taiping Road, Beijing, 100039, China
| | - Fangting Dong
- National Center of Biomedical Analysis, No. 27 Taiping Road, Beijing, 100039, China.
| | - Xianzhong Yan
- National Center of Biomedical Analysis, No. 27 Taiping Road, Beijing, 100039, China.
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33
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Maniam S, Maniam S. Cancer Cell Metabolites: Updates on Current Tracing Methods. Chembiochem 2020; 21:3476-3488. [PMID: 32639076 DOI: 10.1002/cbic.202000290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/07/2020] [Indexed: 12/15/2022]
Abstract
Cancer is the second leading cause of death-1 in 6 deaths globally is due to cancer. Cancer metabolism is a complex and one of the most actively researched area in cancer biology. Metabolic reprogramming in cancer cells entails activities that involve several enzymes and metabolites to convert nutrient into building blocks that alter energy metabolism to fuel rapid cell division. Metabolic dependencies in cancer generate signature metabolites that have key regulatory roles in tumorigenesis. In this minireview, we highlight recent advances in the popular methods ingrained in biochemistry research such as stable and flux isotope analysis, as well as radioisotope labeling, which are valuable in elucidating cancer metabolites. These methods together with analytical tools such as chromatography, nuclear magnetic resonance spectroscopy and mass spectrometry have helped to bring about exploratory work in understanding the role of important as well as obscure metabolites in cancer cells. Information obtained from these analyses significantly contribute in the diagnosis and prognosis of tumors leading to potential therapeutic targets for cancer therapy.
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Affiliation(s)
- Subashani Maniam
- School of Applied Science, RMIT University, 240 La Trobe Street, Melbourne, VIC 3001, Australia
| | - Sandra Maniam
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
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34
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Advances into Understanding the Vital Role of the Mitochondrial Citrate Carrier (CIC) in Metabolic Diseases. Pharmacol Res 2020; 161:105132. [DOI: 10.1016/j.phrs.2020.105132] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/24/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023]
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35
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Wang Z, Ning T, Song A, Rutter J, Wang QA, Jiang L. Chronic cold exposure enhances glucose oxidation in brown adipose tissue. EMBO Rep 2020; 21:e50085. [PMID: 33043581 PMCID: PMC7645266 DOI: 10.15252/embr.202050085] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 09/02/2020] [Accepted: 09/10/2020] [Indexed: 01/20/2023] Open
Abstract
The cultured brown adipocytes can oxidize glucose in vitro, but it is still not fully clear whether brown adipose tissue (BAT) could completely oxidize glucose in vivo. Although positron emission tomography (PET) with 18F‐fluorodeoxyglucose (18F‐FDG) showed a high level of glucose uptake in the activated BAT, the non‐metabolizable 18F‐FDG cannot fully demonstrate intracellular glucose metabolism. Through in vivo [U‐13C]glucose tracing, here we show that chronic cold exposure dramatically activates glucose oxidation in BAT and the browning/beiging subcutaneous white adipose tissue (sWAT). Specifically, chronic cold exposure enhances glucose flux into the mitochondrial TCA cycle. Metabolic flux analysis models that β3‐adrenergic receptor (β3‐AR) agonist significantly enhances the flux of mitochondrial pyruvate uptake through mitochondrial pyruvate carrier (MPC) in the differentiated primary brown adipocytes. Furthermore, in vivo MPC inhibition blocks cold‐induced glucose oxidation and impairs body temperature maintenance in mice. Together, mitochondrial pyruvate uptake and oxidation serve an important energy source in the chronic cold exposure activated BAT and beige adipose tissue, which supports a role for glucose oxidation in brown fat thermogenesis.
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Affiliation(s)
- Zhichao Wang
- Department of Molecular & Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Tinglu Ning
- Department of Molecular & Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Anying Song
- Department of Molecular & Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Jared Rutter
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Qiong A Wang
- Department of Molecular & Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, USA.,Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Lei Jiang
- Department of Molecular & Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, USA.,Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
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36
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Wang M, Chen M, Niu W, Winston DD, Cheng W, Lei B. Injectable biodegradation-visual self-healing citrate hydrogel with high tissue penetration for microenvironment-responsive degradation and local tumor therapy. Biomaterials 2020; 261:120301. [PMID: 32871470 DOI: 10.1016/j.biomaterials.2020.120301] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/27/2020] [Accepted: 08/04/2020] [Indexed: 12/20/2022]
Abstract
Local tumor therapy through injectable biodegradable hydrogels with controlled drug release has attracted much attention recently, due to their easy operation, low side effect and efficiency. However, most of the reported therapeutic hydrogel system showed a lack of biodegradation tracking and tumor environment-responsive degradation/therapy. Herein, we developed a multifunctional injectable biodegradation-visual citric acid-based self-healing scaffolds with microenvironment-responsive degradation and drug release for safe and efficient skin tumor therapy (FPRC hydrogel). FPRC scaffolds possess multifunctional properties including thermosensitive, injectable, self-healing, photoluminescent and pH-responsive degradation/drug release. The FPRC scaffolds with strong red fluorescence which has good photostability, tissue penetration and biocompatibility can be tracked and monitored to evaluate the degradation of the scaffolds in vivo. Moreover, the FPRC scaffolds showed pH-responsive doxorubicin (DOX) release, efficiently killed the A375 cancer cell in vitro and suppressed the tumor growth in vivo. Compared to the free drug (DOX), the FPRC@DOX scaffolds displayed a significantly high therapeutic effect and less biotoxicity. This work provides an alternative strategy to design smart visual scaffolds for tumor therapy and regenerative medicine.
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Affiliation(s)
- Min Wang
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710000, China
| | - Mi Chen
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710000, China
| | - Wen Niu
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710000, China
| | - Dagogo Dorothy Winston
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710000, China
| | - Wei Cheng
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710000, China
| | - Bo Lei
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710000, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710054, China; National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710000, China; Instrument Analysis Center, Xi'an Jiaotong University, Xi'an, 710054, China.
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37
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Wang T, Wang L, Wang G, Zhuang Y. Leveraging and manufacturing in vitro multicellular spheroid-based tumor cell model as a preclinical tool for translating dysregulated tumor metabolism into clinical targets and biomarkers. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00325-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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38
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Chalermwat C, Thosapornvichai T, Wongkittichote P, Phillips JD, Cox JE, Jensen AN, Wattanasirichaigoon D, Jensen LT. Overexpression of the peroxin Pex34p suppresses impaired acetate utilization in yeast lacking the mitochondrial aspartate/glutamate carrier Agc1p. FEMS Yeast Res 2020; 19:5621492. [PMID: 31711143 DOI: 10.1093/femsyr/foz078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/10/2019] [Indexed: 12/19/2022] Open
Abstract
PEX34, encoding a peroxisomal protein implicated in regulating peroxisome numbers, was identified as a high copy suppressor, capable of bypassing impaired acetate utilization of agc1∆ yeast. However, improved growth of agc1∆ yeast on acetate is not mediated through peroxisome proliferation. Instead, stress to the endoplasmic reticulum and mitochondria from PEX34 overexpression appears to contribute to enhanced acetate utilization of agc1∆ yeast. The citrate/2-oxoglutarate carrier Yhm2p is required for PEX34 stimulated growth of agc1∆ yeast on acetate medium, suggesting that the suppressor effect is mediated through increased activity of a redox shuttle involving mitochondrial citrate export. Metabolomic analysis also revealed redirection of acetyl-coenzyme A (CoA) from synthetic reactions for amino acids in PEX34 overexpressing yeast. We propose a model in which increased formation of products from the glyoxylate shunt, together with enhanced utilization of acetyl-CoA, promotes the activity of an alternative mitochondrial redox shuttle, partially substituting for loss of yeast AGC1.
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Affiliation(s)
- Chalongchai Chalermwat
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400 Thailand
| | - Thitipa Thosapornvichai
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400 Thailand
| | - Parith Wongkittichote
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand.,Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - John D Phillips
- Department of Internal Medicine, Division of Hematology, University of Utah, 30 N 1900 E, Salt Lake City, UT 84132, USA
| | - James E Cox
- Metabolomics Core Research Facility, University of Utah, 15 N Medical Drive East, Salt Lake City, UT 84112, USA.,Department of Biochemistry, University of Utah, 15 N Medical Drive East, Salt Lake City, UT 84112, USA
| | - Amornrat N Jensen
- Department of Pathobiology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand
| | - Laran T Jensen
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400 Thailand
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Zhang C, Jiang J, Wang L, Zheng L, Xu J, Qi X, Huang H, Lu J, Li K, Wang H. Identification of Autophagy-Associated Biomarkers and Corresponding Regulatory Factors in the Progression of Colorectal Cancer. Front Genet 2020; 11:245. [PMID: 32265986 PMCID: PMC7100633 DOI: 10.3389/fgene.2020.00245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 02/28/2020] [Indexed: 12/30/2022] Open
Abstract
Autophagy is a self-degradation process that maintains homeostasis against stress in cells. Autophagy dysfunction plays a central role in the development of tumors, such as colorectal cancer (CRC). In this study, autophagy-related differentially expressed genes, their downstream functions, and upstream regulatory factors including RNA-binding proteins (RBP) involved in programmed cell death in the CRC were investigated. Transcription factors (TFs) and miRNAs have been shown to mainly regulate autophagy genes. Interestingly, we found that some of the RBP in the CRC, such as DDX17, SETDB1, and POLR3A, play an important regulatory role in maintaining autophagy at a basal level during growth by acting as TFs that regulate autophagy. Promoter methylations showed negative regulations on differentially expressed autophagy gene (DEAG), while copy number variations revealed a positive role in them. A proportional hazards regression analysis indicated that using autophagy-related prognostic signature can divide patients into high-risk and low-risk groups. Autophagy associated FDA-approved drugs were studied by a prognostic network. This would contribute to the identifications of new potential molecular therapeutic targets for CRC.
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Affiliation(s)
- Chunrui Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jing Jiang
- Obstetrics and Gynecology Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Liqiang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Liyu Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiankai Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiaolin Qi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education and College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Huiying Huang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jianping Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kongning Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education and College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Hong Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education and College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
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40
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Dai W, Wang G, Chwa J, Oh ME, Abeywardana T, Yang Y, Wang QA, Jiang L. Mitochondrial division inhibitor (mdivi-1) decreases oxidative metabolism in cancer. Br J Cancer 2020; 122:1288-1297. [PMID: 32147668 PMCID: PMC7188673 DOI: 10.1038/s41416-020-0778-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/31/2020] [Accepted: 02/18/2020] [Indexed: 12/22/2022] Open
Abstract
Background Previous studies suggested that mdivi-1 (mitochondrial division inhibitor), a putative inhibitor of dynamin-related protein (DRP1), decreased cancer cell proliferation through inducing mitochondrial fusion and altering oxygen consumption. However, the metabolic reprogramming underlying the DRP1 inhibition is still unclear in cancer cells. Methods To better understand the metabolic effect of DRP1 inhibition, [U-13C]glucose isotope tracing was employed to assess mdivi-1 effects in several cancer cell lines, DRP1-WT (wild-type) and DRP1-KO (knockout) H460 lung cancer cells and mouse embryonic fibroblasts (MEFs). Results Mitochondrial staining confirmed that mdivi-1 treatment and DRP1 deficiency induced mitochondrial fusion. Surprisingly, metabolic isotope tracing found that mdivi-1 decreased mitochondrial oxidative metabolism in the lung cancer cell lines H460, A549 and the colon cancer cell line HCT116. [U-13C]glucose tracing studies also showed that the TCA cycle intermediates had significantly lower enrichment in mdivi-1-treated cells. In comparison, DRP1-WT and DRP1-KO H460 cells had similar oxidative metabolism, which was decreased by mdivi-1 treatment. Furthermore, mdivi-1-mediated effects on oxidative metabolism were independent of mitochondrial fusion. Conclusions Our data suggest that, in cancer cells, mdivi-1, a putative inhibitor of DRP1, decreases oxidative metabolism to impair cell proliferation.
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Affiliation(s)
- Wenting Dai
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Guan Wang
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Jason Chwa
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Myung Eun Oh
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Tharindumala Abeywardana
- Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Yanzhong Yang
- Departments of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Qiong A Wang
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA.,Comprehensive Cancer Center, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Lei Jiang
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA. .,Comprehensive Cancer Center, City of Hope Medical Center, Duarte, CA, 91010, USA.
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Lin W, Wang Z, Huang M, Chu J, Zhuang Y, Zhang S. On stability analysis of cascaded linear time varying systems in dynamic isotope experiments. AIChE J 2020. [DOI: 10.1002/aic.16911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Weilu Lin
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology Shanghai China
| | - Zejian Wang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology Shanghai China
| | - Mingzhi Huang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology Shanghai China
| | - Ju Chu
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology Shanghai China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology Shanghai China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology Shanghai China
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42
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Tan M, Mosaoa R, Graham GT, Kasprzyk-Pawelec A, Gadre S, Parasido E, Catalina-Rodriguez O, Foley P, Giaccone G, Cheema A, Kallakury B, Albanese C, Yi C, Avantaggiati ML. Inhibition of the mitochondrial citrate carrier, Slc25a1, reverts steatosis, glucose intolerance, and inflammation in preclinical models of NAFLD/NASH. Cell Death Differ 2020; 27:2143-2157. [PMID: 31959914 PMCID: PMC7308387 DOI: 10.1038/s41418-020-0491-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/22/2019] [Accepted: 12/27/2019] [Indexed: 12/13/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) and its evolution to inflammatory steatohepatitis (NASH) are the most common causes of chronic liver damage and transplantation that are reaching epidemic proportions due to the upraising incidence of metabolic syndrome, obesity, and diabetes. Currently, there is no approved treatment for NASH. The mitochondrial citrate carrier, Slc25a1, has been proposed to play an important role in lipid metabolism, suggesting a potential role for this protein in the pathogenesis of this disease. Here, we show that Slc25a1 inhibition with a specific inhibitor compound, CTPI-2, halts salient alterations of NASH reverting steatosis, preventing the evolution to steatohepatitis, reducing inflammatory macrophage infiltration in the liver and adipose tissue, while starkly mitigating obesity induced by a high-fat diet. These effects are differentially recapitulated by a global ablation of one copy of the Slc25a1 gene or by a liver-targeted Slc25a1 knockout, which unravel dose-dependent and tissue-specific functions of this protein. Mechanistically, through citrate-dependent activities, Slc25a1 inhibition rewires the lipogenic program, blunts signaling from peroxisome proliferator-activated receptor gamma, a key regulator of glucose and lipid metabolism, and inhibits the expression of gluconeogenic genes. The combination of these activities leads not only to inhibition of lipid anabolic processes, but also to a normalization of hyperglycemia and glucose intolerance as well. In summary, our data show for the first time that Slc25a1 serves as an important player in the pathogenesis of fatty liver disease and thus, provides a potentially exploitable and novel therapeutic target.
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Affiliation(s)
- Mingjun Tan
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Rami Mosaoa
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA.,Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Garrett T Graham
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Anna Kasprzyk-Pawelec
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Shreyas Gadre
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Erika Parasido
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Olga Catalina-Rodriguez
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Patricia Foley
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Giuseppe Giaccone
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Amrita Cheema
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Bhaskar Kallakury
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Chris Albanese
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Chunling Yi
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA
| | - Maria Laura Avantaggiati
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, D.C., 20057, USA.
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Successful treatment of adult-onset type II citrullinemia with a low-carbohydrate diet and L-arginine after DNA analysis produced a definitive diagnosis. Clin J Gastroenterol 2020; 13:823-833. [PMID: 31898207 DOI: 10.1007/s12328-019-01083-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/12/2019] [Indexed: 10/25/2022]
Abstract
A 60-year-old male, who exhibited finger tremors, obnubilation, and hyperammonemia (409 μg/dL), was admitted to our hospital. Initially, we suspected that a portosystemic shunt had caused his hyperammonemia. However, his symptoms did not improve after balloon-occluded retrograde transvenous obliteration. He was subsequently found to have some peculiar eating habits, including a fondness for bean curd and peanuts, and an aversion to alcohol and sweets. Furthermore, marked citrullinemia (454.2 nmol/mL) was revealed, which led us to suspect adult-onset type II citrullinemia (CTLN2). DNA analysis of the patient and his mother, son, and daughter confirmed that he was homozygous for the c.852_855del mutation in the SLC25A13 gene, and his relatives were heterozygous for the c.852_855del mutation, which led to a definitive diagnosis. A low-carbohydrate diet and the administration of L-arginine ameliorated his symptoms. It is important to be aware that CTLN2 can occur in elderly patients. Thus, patients who exhibit symptoms of CTLN2 should be interviewed about their dietary habits and subjected to plasma amino acid analysis.In this report, we consider the metabolic disorders seen in citrin deficiency and the associated compensatory mechanisms in relation to the clinical features and treatment of CTLN2.
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44
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Serpa J. Metabolic Remodeling as a Way of Adapting to Tumor Microenvironment (TME), a Job of Several Holders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1219:1-34. [PMID: 32130691 DOI: 10.1007/978-3-030-34025-4_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The microenvironment depends and generates dependence on all the cells and structures that share the same niche, the biotope. The contemporaneous view of the tumor microenvironment (TME) agrees with this idea. The cells that make up the tumor, whether malignant or not, behave similarly to classes of elements within a living community. These elements inhabit, modify and benefit from all the facilities the microenvironment has to offer and that will contribute to the survival and growth of the tumor and the progression of the disease.The metabolic adaptation to microenvironment is a crucial process conducting to an established tumor able to grow locally, invade and metastasized. The metastatic cancer cells are reasonable more plastic than non-metastatic cancer cells, because the previous ones must survive in the microenvironment where the primary tumor develops and in addition, they must prosper in the microenvironment in the metastasized organ.The metabolic remodeling requires not only the adjustment of metabolic pathways per se but also the readjustment of signaling pathways that will receive and obey to the extracellular instructions, commanding the metabolic adaptation. Many diverse players are pivotal in cancer metabolic fitness from the initial signaling stimuli, going through the activation or repression of genes, until the phenotype display. The new phenotype will permit the import and consumption of organic compounds, useful for energy and biomass production, and the export of metabolic products that are useless or must be secreted for a further recycling or controlled uptake. In the metabolic network, three subsets of players are pivotal: (1) the organic compounds; (2) the transmembrane transporters, and (3) the enzymes.This chapter will present the "Pharaonic" intent of diagraming the interplay between these three elements in an attempt of simplifying and, at the same time, of showing the complex sight of cancer metabolism, addressing the orchestrating role of microenvironment and highlighting the influence of non-cancerous cells.
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Affiliation(s)
- Jacinta Serpa
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School | Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal.
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Lisbon, Portugal.
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Favara DM, Zois CE, Haider S, Pires E, Sheldon H, McCullagh J, Banham AH, Harris AL. ADGRL4/ELTD1 Silencing in Endothelial Cells Induces ACLY and SLC25A1 and Alters the Cellular Metabolic Profile. Metabolites 2019; 9:E287. [PMID: 31775252 PMCID: PMC6950702 DOI: 10.3390/metabo9120287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/29/2022] Open
Abstract
Adhesion G Protein-Coupled Receptor L4 (ADGRL4/ELTD1) is an endothelial cell adhesion G protein-coupled receptor (aGPCR) which regulates physiological and tumour angiogenesis, providing an attractive target for anti-cancer therapeutics. To date, ADGRL4/ELTD1's full role and mechanism of function within endothelial biology remains unknown, as do its ligand(s). In this study, ADGRL4/ELTD1 silencing, using two independent small interfering RNAs (siRNAs), was performed in human umbilical vein endothelial cells (HUVECS) followed by transcriptional profiling, target gene validation, and metabolomics using liquid chromatography-mass spectrometry in order to better characterise ADGRL4/ELTD1's role in endothelial cell biology. We show that ADGRL4/ELTD1 silencing induced expression of the cytoplasmic metabolic regulator ATP Citrate Lyase (ACLY) and the mitochondria-to-cytoplasm citrate transporter Solute Carrier Family 25 Member 1 (SLC25A1) but had no apparent effect on pathways downstream of ACLY (fatty acid and cholesterol synthesis or acetylation). Silencing induced KIT expression and affected the Notch signalling pathway, upregulating Delta Like Canonical Notch Ligand 4 (DLL4) and suppressing Jagged Canonical Notch Ligand 1 (JAG1) and Hes Family BHLH Transcription Factor 2 (HES2). The effect of ADGRL4/ELTD1 silencing on the cellular metabolic profile was modest but several metabolites were significantly affected. Cis-aconitic acid, uridine diphosphate (UDP)-glucoronate, fructose 2,6-diphosphate, uridine 5-diphosphate, and aspartic acid were all elevated as a result of silencing and phosphocreatine, N-acetylglutamic acid, taurine, deoxyadenosine triphosphate, and cytidine monophosphate were depleted. Metabolic pathway analysis implicated ADGRL4/ELTD1 in pyrimidine, amino acid, and sugar metabolism. In summary, this study shows that ADGRL4/ELTD1 impacts core components of endothelial metabolism and regulates genes involved in endothelial differentiation/homeostasis and Notch signalling.
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Affiliation(s)
- David M. Favara
- Balliol College, University of Oxford, Oxford OX1 3BJ, UK
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; (C.E.Z.); (S.H.); (H.S.)
| | - Christos E. Zois
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; (C.E.Z.); (S.H.); (H.S.)
| | - Syed Haider
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; (C.E.Z.); (S.H.); (H.S.)
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW7 3RP, UK
| | - Elisabete Pires
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; (E.P.); (J.M.)
| | - Helen Sheldon
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; (C.E.Z.); (S.H.); (H.S.)
| | - James McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; (E.P.); (J.M.)
| | - Alison H. Banham
- Nuffield Division of Clinical Laboratory Science, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK;
| | - Adrian L. Harris
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; (C.E.Z.); (S.H.); (H.S.)
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Sun J, Zhou Q, Hu X. Integrating multi-omics and regular analyses identifies the molecular responses of zebrafish brains to graphene oxide: Perspectives in environmental criteria. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 180:269-279. [PMID: 31100591 DOI: 10.1016/j.ecoenv.2019.05.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/29/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
With the broad application of nanoparticles, nanotoxicology has attracted substantial attention in environmental science. However, the methods for detecting few and targeted genes or proteins, even single omics approaches, may miss other responses, including the major responses induced by nanoparticles. To determine the actual toxicological mechanisms of zebrafish brains induced by graphene oxide (GO, a popular carbon-based nanomaterial applied in various fields) at nonlethal concentrations, multi-omics and regular analyses were combined. The biomolecule responses were remarkable, although GO was not obviously observed in brain tissues. The trends for gene and protein changes were the same and accounted for 3.53% and 5.36% of all changes in the genome and proteome, respectively, suggesting a limitation of single omics analysis. Transcriptomics and proteomics analyses indicated that GO affected the functions or pathways of the troponin complex, actin cytoskeleton, monosaccharide transmembrane transporter activity, oxidoreductase activity and focal adhesion. Both metabolomics and proteomics revealed mitochondrial dysfunction and disruption of the citric acid cycle. The integrated analysis of omics, transmission electron microscopy and immunostaining confirmed that GO induced energy disruptions and mitochondrial damage by downregulating tubulin. The combination of multi-omics and regular analyses provides insights into the actual and highly influential mechanisms underlying nanotoxicity.
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Affiliation(s)
- Jing Sun
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
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47
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Pang H, Jia W, Hu Z. Emerging Applications of Metabolomics in Clinical Pharmacology. Clin Pharmacol Ther 2019; 106:544-556. [DOI: 10.1002/cpt.1538] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/18/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Huanhuan Pang
- School of Pharmaceutical Sciences Tsinghua University Beijing China
| | - Wei Jia
- Cancer Biology Program University of Hawaii Cancer Center Honolulu Hawaii USA
| | - Zeping Hu
- School of Pharmaceutical Sciences Tsinghua University Beijing China
- Tsinghua‐Peking Joint Center for Life Sciences Tsinghua University Beijing China
- Beijing Frontier Research Center for Biological Structure Tsinghua University Beijing China
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48
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Lagziel S, Lee WD, Shlomi T. Studying metabolic flux adaptations in cancer through integrated experimental-computational approaches. BMC Biol 2019; 17:51. [PMID: 31272436 PMCID: PMC6609376 DOI: 10.1186/s12915-019-0669-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
| | | | - Tomer Shlomi
- Faculty of Computer Science, Technion, Haifa, Israel. .,Faculty of Biology, Technion, Haifa, Israel. .,Lokey Center for Life Science and Engineering, Technion, Haifa, Israel.
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49
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Engineering multifunctional bioactive citric acid-based nanovectors for intrinsical targeted tumor imaging and specific siRNA gene delivery in vitro/in vivo. Biomaterials 2019; 199:10-21. [DOI: 10.1016/j.biomaterials.2019.01.045] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/07/2019] [Accepted: 01/30/2019] [Indexed: 11/17/2022]
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50
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Quek LE, Turner N. Using the Human Genome-Scale Metabolic Model Recon 2 for Steady-State Flux Analysis of Cancer Cell Metabolism. Methods Mol Biol 2019; 1928:479-489. [PMID: 30725471 DOI: 10.1007/978-1-4939-9027-6_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Flux analysis is performed to infer intracellular metabolic activity using measured rates. By applying the highly curated human metabolic reconstruction Recon 2 as the reference model, the investigation of cancer cell metabolic fluxes can encompass the full metabolic potential of a human cell. But in its full form, Recon 2 is unsuitable for conventional metabolic flux analysis due to a large number of redundant elements. Here, we describe a procedure to reduce Recon 2 to an appropriate scale for cancer cell flux analysis such that calculated flux intervals are still informative, without compromising the opportunity to explore alternative pathways encoded in Recon 2 that may reveal novel metabolic features.
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Affiliation(s)
- Lake-Ee Quek
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia.
| | - Nigel Turner
- Department of Pharmacology, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia.
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