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Zhang X, Reichetzeder C, Liu Y, Hocher JG, Hasan AA, Lin G, Kleuser B, Hu L, Hocher B. Parental sex-dependent effects of either maternal or paternal eNOS deficiency on the offspring's phenotype without transmission of the parental eNOS deficiency to the offspring. Front Physiol 2023; 14:1306178. [PMID: 38169827 PMCID: PMC10758467 DOI: 10.3389/fphys.2023.1306178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Background: Preclinical animal studies and clinical studies indicate that both maternal as well as paternal genetic alterations/gene defects might affect the phenotype of the next-generation without transmissions of the affected gene. Currently, the question of whether the same genetic defect present in the mother or father leads to a similar phenotype in the offspring remains insufficiently elucidated. Methods: In this head-to-head study, we crossbred female and male mice with heterozygous endothelial eNOS knockout (eNOS+/-) with male and female wild-type (wt) mice, respectively. Subsequently, we compared the phenotype of the resulting wt offspring with that of wt offspring born to parents with no eNOS deficiency. Results: Wt female offspring of mothers with heterozygous eNOS showed elevated liver fat accumulation, while wt male offspring of fathers with heterozygous eNOS exhibited increased fasting insulin, heightened insulin levels after a glucose load, and elevated liver glycogen content. By quantitative mass-spectrometry it was shown that concentrations of six serum metabolites (lysoPhosphatidylcholine acyl C20:3, phosphatidylcholine diacyl C36:2, phosphatidylcholine diacyl C38:1, phosphatidylcholine acyl-alkyl C34:1, phosphatidylcholine acyl-alkyl C36:3, and phosphatidylcholine acyl-alkyl C42:5 (PC ae C42:5) as well as four liver carbon metabolites (fructose 6-phosphate, fructose 1,6-bisphosphate, glucose 6-phosphate and fumarate) were different between wt offspring with eNOS+/- mothers and wt offspring with eNOS+/- fathers. Importantly, fumarate was inversely correlated with the liver fat accumulation in female offspring with eNOS+/- mothers and increased liver glycogen in offspring of both sexes with eNOS+/- fathers. The qRT-PCR results revealed that the gene expression patterns were different between wt offspring with eNOS+/- mothers and those offspring with eNOS+/- fathers. Different gene expression patterns were correlated with different observed phenotypic changes in male/female offspring born to mothers or fathers with a heterozygous eNOS genotype. Conclusion: The identical parental genetic alteration (heterozygous eNOS deficiency), without being passed on to the offspring, results in distinct metabolic, liver phenotype, and gene expression pattern variations depending on whether the genetic alteration originated from the father or the mother.
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Affiliation(s)
- Xiaoli Zhang
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | | | - Yvonne Liu
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
- Medical Faculty of Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Johann-Georg Hocher
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
- Second Medical Faculty, Charles University Prague, Prague, Czechia
| | - Ahmed A. Hasan
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Ge Lin
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Burkhard Kleuser
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Liang Hu
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Berthold Hocher
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- IMD Berlin, Institute of Medical Diagnostics, Berlin, Germany
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Patil N, Howe O, Cahill P, Byrne HJ. Monitoring and modelling the dynamics of the cellular glycolysis pathway: A review and future perspectives. Mol Metab 2022; 66:101635. [PMID: 36379354 PMCID: PMC9703637 DOI: 10.1016/j.molmet.2022.101635] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/28/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The dynamics of the cellular glycolysis pathway underpin cellular function and dysfunction, and therefore ultimately health, disease, diagnostic and therapeutic strategies. Evolving our understanding of this fundamental process and its dynamics remains critical. SCOPE OF REVIEW This paper reviews the medical relevance of glycolytic pathway in depth and explores the current state of the art for monitoring and modelling the dynamics of the process. The future perspectives of label free, vibrational microspectroscopic techniques to overcome the limitations of the current approaches are considered. MAJOR CONCLUSIONS Vibrational microspectroscopic techniques can potentially operate in the niche area of limitations of other omics technologies for non-destructive, real-time, in vivo label-free monitoring of glycolysis dynamics at a cellular and subcellular level.
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Affiliation(s)
- Nitin Patil
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland; School of Physics and Optometric & Clinical Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland.
| | - Orla Howe
- School of Biological and Health Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland
| | - Paul Cahill
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Hugh J Byrne
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland
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CD147 a direct target of miR-146a supports energy metabolism and promotes tumor growth in ALK+ ALCL. Leukemia 2022; 36:2050-2063. [PMID: 35676454 PMCID: PMC9343252 DOI: 10.1038/s41375-022-01617-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 11/30/2022]
Abstract
We recently reported that miR-146a is differentially expressed in ALK+ and ALK− anaplastic large cell lymphoma (ALCL). In this study, the downstream targets of miR-146a in ALK+ ALCL were investigated by transcriptome analysis, identifying CD147 as potential target gene. Because CD147 is differentially expressed in ALK+ ALCL versus ALK− ALCL and normal T cells, this gene emerged as a strong candidate for the pathogenesis of this tumor. Here we demonstrate that CD147 is a direct target of miR-146 and contributes to the survival and proliferation of ALK+ ALCL cells in vitro and to the engraftment and tumor growth in vivo in an ALK+ ALCL-xenotransplant mouse model. CD147 knockdown in ALK+ ALCL cells resulted in loss of monocarboxylate transporter 1 (MCT1) expression, reduced glucose consumption and tumor growth retardation, as demonstrated by [18F]FDG-PET/MRI analysis. Investigation of metabolism in vitro and in vivo supported these findings, revealing reduced aerobic glycolysis and increased basal respiration in CD147 knockdown. In conclusion, our findings indicate that CD147 is of vital importance for ALK+ ALCL to maintain the high energy demand of rapid cell proliferation, promoting lactate export, and tumor growth. Furthermore, CD147 has the potential to serve as a novel therapeutic target in ALK+ ALCL, and warrants further investigation.
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Lapin A, Perfahl H, Jain HV, Reuss M. Integrating a dynamic central metabolism model of cancer cells with a hybrid 3D multiscale model for vascular hepatocellular carcinoma growth. Sci Rep 2022; 12:12373. [PMID: 35858953 PMCID: PMC9300625 DOI: 10.1038/s41598-022-15767-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
We develop here a novel modelling approach with the aim of closing the conceptual gap between tumour-level metabolic processes and the metabolic processes occurring in individual cancer cells. In particular, the metabolism in hepatocellular carcinoma derived cell lines (HEPG2 cells) has been well characterized but implementations of multiscale models integrating this known metabolism have not been previously reported. We therefore extend a previously published multiscale model of vascular tumour growth, and integrate it with an experimentally verified network of central metabolism in HEPG2 cells. This resultant combined model links spatially heterogeneous vascular tumour growth with known metabolic networks within tumour cells and accounts for blood flow, angiogenesis, vascular remodelling and nutrient/growth factor transport within a growing tumour, as well as the movement of, and interactions between normal and cancer cells. Model simulations report for the first time, predictions of spatially resolved time courses of core metabolites in HEPG2 cells. These simulations can be performed at a sufficient scale to incorporate clinically relevant features of different tumour systems using reasonable computational resources. Our results predict larger than expected temporal and spatial heterogeneity in the intracellular concentrations of glucose, oxygen, lactate pyruvate, f16bp and Acetyl-CoA. The integrated multiscale model developed here provides an ideal quantitative framework in which to study the relationship between dosage, timing, and scheduling of anti-neoplastic agents and the physiological effects of tumour metabolism at the cellular level. Such models, therefore, have the potential to inform treatment decisions when drug response is dependent on the metabolic state of individual cancer cells.
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Affiliation(s)
- Alexey Lapin
- Stuttgart Research Center Systems Biology, University Stuttgart, Stuttgart, Germany.,Institute of Chemical Process Engineering, University Stuttgart, Stuttgart, Germany
| | - Holger Perfahl
- Stuttgart Research Center Systems Biology, University Stuttgart, Stuttgart, Germany
| | - Harsh Vardhan Jain
- Department of Mathematics and Statistics, University of Minnesota Duluth, Duluth, MN, USA
| | - Matthias Reuss
- Stuttgart Research Center Systems Biology, University Stuttgart, Stuttgart, Germany.
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5
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Ghallab A, Myllys M, Friebel A, Duda J, Edlund K, Halilbasic E, Vucur M, Hobloss Z, Brackhagen L, Begher-Tibbe B, Hassan R, Burke M, Genc E, Frohwein LJ, Hofmann U, Holland CH, González D, Keller M, Seddek AL, Abbas T, Mohammed ESI, Teufel A, Itzel T, Metzler S, Marchan R, Cadenas C, Watzl C, Nitsche MA, Kappenberg F, Luedde T, Longerich T, Rahnenführer J, Hoehme S, Trauner M, Hengstler JG. Spatio-Temporal Multiscale Analysis of Western Diet-Fed Mice Reveals a Translationally Relevant Sequence of Events during NAFLD Progression. Cells 2021; 10:cells10102516. [PMID: 34685496 PMCID: PMC8533774 DOI: 10.3390/cells10102516] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 12/12/2022] Open
Abstract
Mouse models of non-alcoholic fatty liver disease (NAFLD) are required to define therapeutic targets, but detailed time-resolved studies to establish a sequence of events are lacking. Here, we fed male C57Bl/6N mice a Western or standard diet over 48 weeks. Multiscale time-resolved characterization was performed using RNA-seq, histopathology, immunohistochemistry, intravital imaging, and blood chemistry; the results were compared to human disease. Acetaminophen toxicity and ammonia metabolism were additionally analyzed as functional readouts. We identified a sequence of eight key events: formation of lipid droplets; inflammatory foci; lipogranulomas; zonal reorganization; cell death and replacement proliferation; ductular reaction; fibrogenesis; and hepatocellular cancer. Functional changes included resistance to acetaminophen and altered nitrogen metabolism. The transcriptomic landscape was characterized by two large clusters of monotonously increasing or decreasing genes, and a smaller number of 'rest-and-jump genes' that initially remained unaltered but became differentially expressed only at week 12 or later. Approximately 30% of the genes altered in human NAFLD are also altered in the present mouse model and an increasing overlap with genes altered in human HCC occurred at weeks 30-48. In conclusion, the observed sequence of events recapitulates many features of human disease and offers a basis for the identification of therapeutic targets.
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Affiliation(s)
- Ahmed Ghallab
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt;
- Correspondence: (A.G.); (J.G.H.); Tel.: +49-0231-1084-356 (A.G.); +49-0231-1084-348 (J.G.H.)
| | - Maiju Myllys
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Adrian Friebel
- Institute of Computer Science & Saxonian Incubator for Clinical Research (SIKT), University of Leipzig, Haertelstr. 16-18, 04107 Leipzig, Germany; (A.F.); (S.H.)
| | - Julia Duda
- Department of Statistics, TU Dortmund University, 44227 Dortmund, Germany; (J.D.); (F.K.); (J.R.)
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Emina Halilbasic
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (E.H.); (M.T.)
| | - Mihael Vucur
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty at Heinrich-Heine-University, University Hospital Duesseldorf, 40225 Dusseldorf, Germany; (M.V.); (T.L.)
| | - Zaynab Hobloss
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Lisa Brackhagen
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Brigitte Begher-Tibbe
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Reham Hassan
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt;
| | - Michael Burke
- MRI Unit, Leibniz Research Centre for Working Environment and Human Factors, Department of Psychology and Neurosciences, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.B.); (E.G.)
| | - Erhan Genc
- MRI Unit, Leibniz Research Centre for Working Environment and Human Factors, Department of Psychology and Neurosciences, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.B.); (E.G.)
| | | | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, University of Tübingen, Auerbachstr. 112, 70376 Stuttgart, Germany;
| | - Christian H. Holland
- Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine, Bioquant—Im Neuenheimer Feld 267, 69120 Heidelberg, Germany;
| | - Daniela González
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Magdalena Keller
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Abdel-latif Seddek
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt;
| | - Tahany Abbas
- Histology Department, Faculty of Medicine, South Valley University, Qena 83523, Egypt;
| | - Elsayed S. I. Mohammed
- Department of Histology and Cytology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt;
| | - Andreas Teufel
- Department of Medicine I, University Hospital, 93053 Regensburg, Germany; (A.T.); (T.I.)
| | - Timo Itzel
- Department of Medicine I, University Hospital, 93053 Regensburg, Germany; (A.T.); (T.I.)
| | - Sarah Metzler
- Leibniz Research Centre for Working Environment and Human Factors, Department of Immunology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (S.M.); (C.W.)
| | - Rosemarie Marchan
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Cristina Cadenas
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Carsten Watzl
- Leibniz Research Centre for Working Environment and Human Factors, Department of Immunology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (S.M.); (C.W.)
| | - Michael A. Nitsche
- Leibniz Research Centre for Working Environment and Human Factors, Department of Psychology and Neurosciences, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany;
| | - Franziska Kappenberg
- Department of Statistics, TU Dortmund University, 44227 Dortmund, Germany; (J.D.); (F.K.); (J.R.)
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty at Heinrich-Heine-University, University Hospital Duesseldorf, 40225 Dusseldorf, Germany; (M.V.); (T.L.)
| | - Thomas Longerich
- Translational Gastrointestinal Pathology, Institute of Pathology, University Hospital Heidelberg, D-69120 Heidelberg, Germany;
| | - Jörg Rahnenführer
- Department of Statistics, TU Dortmund University, 44227 Dortmund, Germany; (J.D.); (F.K.); (J.R.)
| | - Stefan Hoehme
- Institute of Computer Science & Saxonian Incubator for Clinical Research (SIKT), University of Leipzig, Haertelstr. 16-18, 04107 Leipzig, Germany; (A.F.); (S.H.)
| | - Michael Trauner
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (E.H.); (M.T.)
| | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
- Correspondence: (A.G.); (J.G.H.); Tel.: +49-0231-1084-356 (A.G.); +49-0231-1084-348 (J.G.H.)
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Sex-dependent dynamics of metabolism in primary mouse hepatocytes. Arch Toxicol 2021; 95:3001-3013. [PMID: 34241659 PMCID: PMC8380230 DOI: 10.1007/s00204-021-03118-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022]
Abstract
The liver is one of the most sexually dimorphic organs. The hepatic metabolic pathways that are subject to sexual dimorphism include xenobiotic, amino acid and lipid metabolism. Non-alcoholic fatty liver disease and hepatocellular carcinoma are among diseases with sex-dependent prevalence, progression and outcome. Although male and female livers differ in their abilities to metabolize foreign compounds, including drugs, sex-dependent treatment and pharmacological dynamics are rarely applied in all relevant cases. Therefore, it is important to consider hepatic sexual dimorphism when developing new treatment strategies and to understand the underlying mechanisms in model systems. We isolated primary hepatocytes from male and female C57BL6/N mice and examined the sex-dependent transcriptome, proteome and extracellular metabolome parameters in the course of culturing them for 96 h. The sex-specific gene expression of the general xenobiotic pathway altered and the female-specific expression of Cyp2b13 and Cyp2b9 was significantly reduced during culture. Sex-dependent differences of several signaling pathways increased, including genes related to serotonin and melatonin degradation. Furthermore, the ratios of male and female gene expression were inversed for other pathways, such as amino acid degradation, beta-oxidation, androgen signaling and hepatic steatosis. Because the primary hepatocytes were cultivated without the influence of known regulators of sexual dimorphism, these results suggest currently unknown modulatory mechanisms of sexual dimorphism in vitro. The large sex-dependent differences in the regulation and dynamics of drug metabolism observed during cultivation can have an immense influence on the evaluation of pharmacodynamic processes when conducting initial preclinical trials to investigate potential new drugs.
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Morio B, Panthu B, Bassot A, Rieusset J. Role of mitochondria in liver metabolic health and diseases. Cell Calcium 2020; 94:102336. [PMID: 33387847 DOI: 10.1016/j.ceca.2020.102336] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023]
Abstract
The liver is a major organ that coordinates the metabolic flexibility of the whole body, which is characterized by the ability to adapt dynamically in response to fluctuations in energy needs and supplies. In this context, hepatocyte mitochondria are key partners in fine-tuning metabolic flexibility. Here we review the metabolic and signalling pathways carried by mitochondria in the liver, the major pathways that regulate mitochondrial function and how they function in health and metabolic disorders associated to obesity, i.e. insulin resistance, non-alcoholic steatosis and steatohepatitis and hepatocellular carcinoma. Finally, strategies targeting mitochondria to counteract liver disorders are discussed.
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Affiliation(s)
- Béatrice Morio
- CarMeN Laboratory, INSERM U1060, INRA U1397, Lyon, France
| | | | - Arthur Bassot
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G2H7, Canada
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8
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Kolbe E, Aleithe S, Rennert C, Spormann L, Ott F, Meierhofer D, Gajowski R, Stöpel C, Hoehme S, Kücken M, Brusch L, Seifert M, von Schoenfels W, Schafmayer C, Brosch M, Hofmann U, Damm G, Seehofer D, Hampe J, Gebhardt R, Matz-Soja M. Mutual Zonated Interactions of Wnt and Hh Signaling Are Orchestrating the Metabolism of the Adult Liver in Mice and Human. Cell Rep 2020; 29:4553-4567.e7. [PMID: 31875560 DOI: 10.1016/j.celrep.2019.11.104] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/14/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
The Hedgehog (Hh) and Wnt/β-Catenin (Wnt) cascades are morphogen pathways whose pronounced influence on adult liver metabolism has been identified in recent years. How both pathways communicate and control liver metabolic functions are largely unknown. Detecting core components of Wnt and Hh signaling and mathematical modeling showed that both pathways in healthy liver act largely complementary to each other in the pericentral (Wnt) and the periportal zone (Hh) and communicate mainly by mutual repression. The Wnt/Hh module inversely controls the spatiotemporal operation of various liver metabolic pathways, as revealed by transcriptome, proteome, and metabolome analyses. Shifting the balance to Wnt (activation) or Hh (inhibition) causes pericentralization and periportalization of liver functions, respectively. Thus, homeostasis of the Wnt/Hh module is essential for maintaining proper liver metabolism and to avoid the development of certain metabolic diseases. With caution due to minor species-specific differences, these conclusions may hold for human liver as well.
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Affiliation(s)
- Erik Kolbe
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Susanne Aleithe
- Department of Neurology, Leipzig University, Leipzig 04103, Germany
| | - Christiane Rennert
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany; Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig 04103, Germany
| | - Luise Spormann
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Fritzi Ott
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Faculty, Berlin 14195, Germany
| | - Robert Gajowski
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Faculty, Berlin 14195, Germany
| | - Claus Stöpel
- Institute for Computer Science, Leipzig University, Leipzig 04103, Germany
| | - Stefan Hoehme
- Institute for Computer Science, Leipzig University, Leipzig 04103, Germany
| | - Michael Kücken
- Center for Information Services and High Performance Computing, Technische Universität Dresden, Dresden 01069, Germany
| | - Lutz Brusch
- Center for Information Services and High Performance Computing, Technische Universität Dresden, Dresden 01069, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden 01307, Germany
| | - Witigo von Schoenfels
- Department of General Surgery and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Clemens Schafmayer
- Department of General Surgery and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Mario Brosch
- Medical Department 1, University Hospital Dresden, Technical University Dresden, Dresden 01069, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, University of Tübingen, Stuttgart 70376, Germany
| | - Georg Damm
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig 04103, Germany
| | - Daniel Seehofer
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig 04103, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, Technical University Dresden, Dresden 01069, Germany
| | - Rolf Gebhardt
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Madlen Matz-Soja
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany.
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9
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Hebing L, Tran F, Brandt H, Engell S. Robust Optimizing Control of Fermentation Processes Based on a Set of Structurally Different Process Models. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.9b05504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Florian Tran
- io-consultants GmbH & Co. KG, Speyerer Straße 14, 69115 Heidelberg, Germany
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10
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Heller S, Maurer GD, Wanka C, Hofmann U, Luger AL, Bruns I, Steinbach JP, Rieger J. Gene Suppression of Transketolase-Like Protein 1 (TKTL1) Sensitizes Glioma Cells to Hypoxia and Ionizing Radiation. Int J Mol Sci 2018; 19:ijms19082168. [PMID: 30044385 PMCID: PMC6121283 DOI: 10.3390/ijms19082168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/18/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022] Open
Abstract
In several tumor entities, transketolase-like protein 1 (TKTL1) has been suggested to promote the nonoxidative part of the pentose phosphate pathway (PPP) and thereby to contribute to a malignant phenotype. However, its role in glioma biology has only been sparsely documented. In the present in vitro study using LNT-229 glioma cells, we analyzed the impact of TKTL1 gene suppression on basic metabolic parameters and on survival following oxygen restriction and ionizing radiation. TKTL1 was induced by hypoxia and by hypoxia-inducible factor-1α (HIF-1α). Knockdown of TKTL1 via shRNA increased the cells’ demand for glucose, decreased flux through the PPP and promoted cell death under hypoxic conditions. Following irradiation, suppression of TKTL1 expression resulted in elevated levels of reactive oxygen species (ROS) and reduced clonogenic survival. In summary, our results indicate a role of TKTL1 in the adaptation of tumor cells to oxygen deprivation and in the acquisition of radioresistance. Further studies are necessary to examine whether strategies that antagonize TKTL1 function will be able to restore the sensitivity of glioma cells towards irradiation and antiangiogenic therapies in the more complex in vivo environment.
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Affiliation(s)
- Sonja Heller
- Dr. Senckenberg Institute of Neurooncology and University Cancer Center (UCT), University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany.
| | - Gabriele D Maurer
- Dr. Senckenberg Institute of Neurooncology and University Cancer Center (UCT), University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany.
| | - Christina Wanka
- Dr. Senckenberg Institute of Neurooncology and University Cancer Center (UCT), University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany.
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Eberhard Karls University, 72074 Tuebingen, Germany.
| | - Anna-Luisa Luger
- Dr. Senckenberg Institute of Neurooncology and University Cancer Center (UCT), University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany.
| | - Ines Bruns
- Dr. Senckenberg Institute of Neurooncology and University Cancer Center (UCT), University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany.
| | - Joachim P Steinbach
- Dr. Senckenberg Institute of Neurooncology and University Cancer Center (UCT), University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany.
| | - Johannes Rieger
- Dr. Senckenberg Institute of Neurooncology and University Cancer Center (UCT), University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany.
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, University Hospital Tuebingen, Eberhard Karls University, 72076 Tuebingen, Germany.
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11
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Carrola J, Pinto RJB, Nasirpour M, Freire CSR, Gil AM, Santos C, Oliveira H, Duarte IF. NMR Metabolomics Reveals Metabolism-Mediated Protective Effects in Liver (HepG2) Cells Exposed to Subtoxic Levels of Silver Nanoparticles. J Proteome Res 2018; 17:1636-1646. [DOI: 10.1021/acs.jproteome.7b00905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Joana Carrola
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ricardo J. B. Pinto
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Maryam Nasirpour
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carmen S. R. Freire
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ana M. Gil
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Conceição Santos
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Helena Oliveira
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
- CESAM & Laboratory of Biotechnology and Cytomics, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Iola F. Duarte
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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12
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Thiepold AL, Lorenz NI, Foltyn M, Engel AL, Divé I, Urban H, Heller S, Bruns I, Hofmann U, Dröse S, Harter PN, Mittelbronn M, Steinbach JP, Ronellenfitsch MW. Mammalian target of rapamycin complex 1 activation sensitizes human glioma cells to hypoxia-induced cell death. Brain 2017; 140:2623-2638. [PMID: 28969371 DOI: 10.1093/brain/awx196] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/21/2017] [Indexed: 11/13/2022] Open
Abstract
Glioblastomas are characterized by fast uncontrolled growth leading to hypoxic areas and necrosis. Signalling from EGFR via mammalian target of rapamycin complex 1 (mTORC1) is a major driver of cell growth and proliferation and one of the most commonly altered signalling pathways in glioblastomas. Therefore, epidermal growth factor receptor and mTORC1 signalling are plausible therapeutic targets and clinical trials with inhibitors are in progress. However, we have previously shown that epidermal growth factor receptor and mTORC1 inhibition triggers metabolic changes leading to adverse effects under the conditions of the tumour microenvironment by protecting from hypoxia-induced cell death. We hypothesized that conversely mTORC1 activation sensitizes glioma cells to hypoxia-induced cell death. As a model for mTORC1 activation we used gene suppression of its physiological inhibitor TSC2 (TSC2sh). TSC2sh glioma cells showed increased sensitivity to hypoxia-induced cell death that was accompanied by an earlier ATP depletion and an increase in reactive oxygen species. There was no difference in extracellular glucose consumption but an altered intracellular metabolic profile with an increase of intermediates of the pentose phosphate pathway. Mechanistically, mTORC1 upregulated the first and rate limiting enzyme of the pentose phosphate pathway, G6PD. Furthermore, an increase in oxygen consumption in TSC2sh cells was detected. This appeared to be due to higher transcription rates of genes involved in mitochondrial respiratory function including PPARGC1A and PPARGC1B (also known as PGC-1α and -β). The finding that mTORC1 activation causes an increase in oxygen consumption and renders malignant glioma cells susceptible to hypoxia and nutrient deprivation could help identify glioblastoma patient cohorts more likely to benefit from hypoxia-inducing therapies such as the VEGFA-targeting antibody bevacizumab in future clinical evaluations.
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Affiliation(s)
- Anna-Luisa Thiepold
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
| | - Nadja I Lorenz
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
| | - Martha Foltyn
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
| | - Anna L Engel
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
| | - Iris Divé
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
| | - Hans Urban
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
| | - Sonja Heller
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
| | - Ines Bruns
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart and University of Tübingen, Germany
| | - Stefan Dröse
- Department of Anaesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Patrick N Harter
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany.,Institute of Neurology (Edinger-Institute), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Michel Mittelbronn
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany.,Institute of Neurology (Edinger-Institute), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Joachim P Steinbach
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
| | - Michael W Ronellenfitsch
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
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13
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Control analysis of the impact of allosteric regulation mechanism in a Escherichia coli kinetic model: Application to serine production. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Hocher B, Haumann H, Rahnenführer J, Reichetzeder C, Kalk P, Pfab T, Tsuprykov O, Winter S, Hofmann U, Li J, Püschel GP, Lang F, Schuppan D, Schwab M, Schaeffeler E. Maternal eNOS deficiency determines a fatty liver phenotype of the offspring in a sex dependent manner. Epigenetics 2016; 11:539-52. [PMID: 27175980 PMCID: PMC4939931 DOI: 10.1080/15592294.2016.1184800] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Maternal environmental factors can impact on the phenotype of the offspring via the induction of epigenetic adaptive mechanisms. The advanced fetal programming hypothesis proposes that maternal genetic variants may influence the offspring's phenotype indirectly via epigenetic modification, despite the absence of a primary genetic defect. To test this hypothesis, heterozygous female eNOS knockout mice and wild type mice were bred with male wild type mice. We then assessed the impact of maternal eNOS deficiency on the liver phenotype of wild type offspring. Birth weight of male wild type offspring born to female heterozygous eNOS knockout mice was reduced compared to offspring of wild type mice. Moreover, the offspring displayed a sex specific liver phenotype, with an increased liver weight, due to steatosis. This was accompanied by sex specific differences in expression and DNA methylation of distinct genes. Liver global DNA methylation was significantly enhanced in both male and female offspring. Also, hepatic parameters of carbohydrate metabolism were reduced in male and female offspring. In addition, male mice displayed reductions in various amino acids in the liver. Maternal genetic alterations, such as partial deletion of the eNOS gene, can affect liver metabolism of wild type offspring without transmission of the intrinsic defect. This occurs in a sex specific way, with more detrimental effects in females. This finding demonstrates that a maternal genetic defect can epigenetically alter the phenotype of the offspring, without inheritance of the defect itself. Importantly, these acquired epigenetic phenotypic changes can persist into adulthood.
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Affiliation(s)
- Berthold Hocher
- a Department of Basic Medicine , Medical College of Hunan Normal University , Changsha , China.,b Institute of Nutritional Science, University of Potsdam , Nuthetal , Germany.,c IFLb, Laboratoriumsmedizin Berlin GmbH , Berlin , Germany
| | - Hannah Haumann
- d Department of Internal Medicine IV/Nephrology (UKBF) , Charité Campus Benjamin Franklin , Berlin , Germany.,e Center for Cardiovascular Research, Charité Campus Mitte , Berlin , Germany
| | - Jan Rahnenführer
- b Institute of Nutritional Science, University of Potsdam , Nuthetal , Germany
| | | | - Philipp Kalk
- d Department of Internal Medicine IV/Nephrology (UKBF) , Charité Campus Benjamin Franklin , Berlin , Germany.,e Center for Cardiovascular Research, Charité Campus Mitte , Berlin , Germany
| | - Thiemo Pfab
- d Department of Internal Medicine IV/Nephrology (UKBF) , Charité Campus Benjamin Franklin , Berlin , Germany.,f Diaverum Deutschland , Potsdam , Germany
| | - Oleg Tsuprykov
- b Institute of Nutritional Science, University of Potsdam , Nuthetal , Germany.,e Center for Cardiovascular Research, Charité Campus Mitte , Berlin , Germany
| | - Stefan Winter
- g Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology , Stuttgart , Germany.,h University of Tübingen , Tübingen , Germany
| | - Ute Hofmann
- g Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology , Stuttgart , Germany.,h University of Tübingen , Tübingen , Germany
| | - Jian Li
- a Department of Basic Medicine , Medical College of Hunan Normal University , Changsha , China
| | - Gerhard P Püschel
- b Institute of Nutritional Science, University of Potsdam , Nuthetal , Germany
| | - Florian Lang
- i Institute of Physiology, University of Tübingen , Tübingen , Germany
| | - Detlef Schuppan
- j Institute of Translational Immunology, University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany.,k Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston , MA , USA
| | - Matthias Schwab
- g Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology , Stuttgart , Germany.,l Department of Clinical Pharmacology , University Hospital Tübingen , Tübingen , Germany.,m Department of Pharmacy and Biochemistry , University Tübingen , Tübingen , Germany
| | - Elke Schaeffeler
- g Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology , Stuttgart , Germany.,h University of Tübingen , Tübingen , Germany
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15
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RNAi in murine hepatocytes: the agony of choice--a study of the influence of lipid-based transfection reagents on hepatocyte metabolism. Arch Toxicol 2015; 89:1579-88. [PMID: 26233687 DOI: 10.1007/s00204-015-1571-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/15/2015] [Indexed: 10/23/2022]
Abstract
Primary hepatocyte cell cultures are widely used for studying hepatic diseases with alterations in hepatic glucose and lipid metabolism, such as diabetes and non-alcoholic fatty liver disease. Therefore, small interfering RNAs (siRNAs) provide a potent and specific tool to elucidate the signaling pathways and gene functions involved in these pathologies. Although RNA interference (RNAi) in vitro is frequently used in these investigations, the metabolic alterations elucidated by different siRNA delivery strategies have hardly been investigated in transfected hepatocytes. To elucidate the influence of the most commonly used lipid-based transfection reagents on cultured primary hepatocytes, we studied the cytotoxic effects and transfection efficiencies of INTERFERin(®), Lipofectamine(®)RNAiMAX, and HiPerFect(®). All of these transfection agents displayed low cytotoxicity (5.6-9.0 ± 1.3-3.4%), normal cell viability, and high transfection efficiency (fold change 0.08-0.13 ± 0.03-0.05), and they also favored the satisfactory down-regulation of target gene expression. However, when effects on the metabolome and lipidome were studied, considerable differences were observed among the transfection reagents. Cellular triacylglycerides levels were either up- or down-regulated [maximum fold change: INTERFERin(®) (48 h) 2.55 ± 0.34, HiPerFect(®) (24 h) 0.79 ± 0.08, Lipofectamine(®)RNAiMAX (48 h) 1.48 ± 0.21], and mRNA levels of genes associated with lipid metabolism were differentially affected. Likewise, metabolic functions such as amino acid utilization from were perturbed (alanine, arginine, glycine, ornithine, and pyruvate). In conclusion, these findings demonstrate that the choice of non-viral siRNA delivery agent is critical in hepatocytes. This should be remembered, especially if RNA silencing is used for studying hepatic lipid homeostasis and its regulation.
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16
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Rehberg M, Ritter JB, Reichl U. Glycolysis is governed by growth regime and simple enzyme regulation in adherent MDCK cells. PLoS Comput Biol 2014; 10:e1003885. [PMID: 25329309 PMCID: PMC4211564 DOI: 10.1371/journal.pcbi.1003885] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 08/31/2014] [Indexed: 11/18/2022] Open
Abstract
Due to its vital importance in the supply of cellular pathways with energy and precursors, glycolysis has been studied for several decades regarding its capacity and regulation. For a systems-level understanding of the Madin-Darby canine kidney (MDCK) cell metabolism, we couple a segregated cell growth model published earlier with a structured model of glycolysis, which is based on relatively simple kinetics for enzymatic reactions of glycolysis, to explain the pathway dynamics under various cultivation conditions. The structured model takes into account in vitro enzyme activities, and links glycolysis with pentose phosphate pathway and glycogenesis. Using a single parameterization, metabolite pool dynamics during cell cultivation, glucose limitation and glucose pulse experiments can be consistently reproduced by considering the cultivation history of the cells. Growth phase-dependent glucose uptake together with cell-specific volume changes generate high intracellular metabolite pools and flux rates to satisfy the cellular demand during growth. Under glucose limitation, the coordinated control of glycolytic enzymes re-adjusts the glycolytic flux to prevent the depletion of glycolytic intermediates. Finally, the model's predictive power supports the design of more efficient bioprocesses. Glycolysis generates biomass precursors and energy from sugars and is therefore a key element in the metabolism of mammalian cells. Changes in its activity greatly affect cellular function which is often recognized as metabolic disease but also as opportunity for the design of efficient bioprocesses. Metabolic research discovered that continuously growing mammalian cells often exhibit a high glycolytic activity but also delivered seemingly endless facets in the pathway operation. The latter call for a systems-level understanding regarding capacity and regulation for a broad range of cultivation conditions. In this work, we couple a cell growth model to a simple kinetic description of glycolysis to consistently explain intracellular metabolite pool dynamics of the Madin-Darby canine kidney cell line over a variety of experiments and time scales while considering the growth status and cultivation history of the cells. We argue that the many different dynamics in glycolysis result from an interplay between a growth-dependent sugar uptake together with simple intrinsic enzyme regulation.
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Affiliation(s)
- Markus Rehberg
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- * E-mail:
| | - Joachim B. Ritter
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Otto von Guericke University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany
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17
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Costa RS, Veríssimo A, Vinga S. KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. BMC SYSTEMS BIOLOGY 2014; 8:85. [PMID: 25115331 PMCID: PMC4236735 DOI: 10.1186/s12918-014-0085-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/11/2014] [Indexed: 01/03/2023]
Abstract
BACKGROUND The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of KiMoSys development. DESCRIPTION KiMoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data.KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research. CONCLUSIONS KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects.The web application implemented using Ruby on Rails framework is freely available for web access at http://kimosys.org, along with its full documentation.
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Affiliation(s)
- Rafael S Costa
- Instituto de Engenharia de Sistemas e Computadores, Investigacão e Desenvolvimento (INESC-ID), R Alves Redol 9, Lisboa, 1000-029, Portugal
- Center for Intelligent Systems, LAETA,IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, Lisboa, 1049-001, Portugal
| | - André Veríssimo
- Center for Intelligent Systems, LAETA,IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, Lisboa, 1049-001, Portugal
| | - Susana Vinga
- Center for Intelligent Systems, LAETA,IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, Lisboa, 1049-001, Portugal
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18
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Abstract
Organisms have to continuously adapt to changing environmental conditions or undergo developmental transitions. To meet the accompanying change in metabolic demands, the molecular mechanisms of adaptation involve concerted interactions which ultimately induce a modification of the metabolic state, which is characterized by reaction fluxes and metabolite concentrations. These state transitions are the effect of simultaneously manipulating fluxes through several reactions. While metabolic control analysis has provided a powerful framework for elucidating the principles governing this orchestrated action to understand metabolic control, its applications are restricted by the limited availability of kinetic information. Here, we introduce structural metabolic control as a framework to examine individual reactions' potential to control metabolic functions, such as biomass production, based on structural modeling. The capability to carry out a metabolic function is determined using flux balance analysis (FBA). We examine structural metabolic control on the example of the central carbon metabolism of Escherichia coli by the recently introduced framework of functional centrality (FC). This framework is based on the Shapley value from cooperative game theory and FBA, and we demonstrate its superior ability to assign “share of control” to individual reactions with respect to metabolic functions and environmental conditions. A comparative analysis of various scenarios illustrates the usefulness of FC and its relations to other structural approaches pertaining to metabolic control. We propose a Monte Carlo algorithm to estimate FCs for large networks, based on the enumeration of elementary flux modes. We further give detailed biological interpretation of FCs for production of lactate and ATP under various respiratory conditions. Insight into the functioning of metabolic control to meet changing demands is a first step in rational engineering of biological systems towards a desired behavior. Metabolic control analysis provides the means to examine the impact of change of reaction fluxes on a specific target flux based on kinetic modeling, but suffers from limitations of the kinetic approach. Here, we introduce and analyze structural metabolic control as a framework to overcome these limitations. We utilize functional centrality, a framework based on the Shapley value from cooperative game theory and flux balance analysis, to determine the contribution of individual reactions to the functions accomplished by a metabolic network. These contributions, in turn, depend on the control exerted on the remaining network. Functional centrality provides the mathematical means to gain further understanding of metabolic control. The potential applications range from facilitating strategies of rational strain design to drug target identification.
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19
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Nakajima K, Ito E, Ohtsubo K, Shirato K, Takamiya R, Kitazume S, Angata T, Taniguchi N. Mass isotopomer analysis of metabolically labeled nucleotide sugars and N- and O-glycans for tracing nucleotide sugar metabolisms. Mol Cell Proteomics 2013; 12:2468-80. [PMID: 23720760 PMCID: PMC3769324 DOI: 10.1074/mcp.m112.027151] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 05/20/2013] [Indexed: 12/14/2022] Open
Abstract
Nucleotide sugars are the donor substrates of various glycosyltransferases, and an important building block in N- and O-glycan biosynthesis. Their intercellular concentrations are regulated by cellular metabolic states including diseases such as cancer and diabetes. To investigate the fate of UDP-GlcNAc, we developed a tracing method for UDP-GlcNAc synthesis and use, and GlcNAc utilization using (13)C6-glucose and (13)C2-glucosamine, respectively, followed by the analysis of mass isotopomers using LC-MS. Metabolic labeling of cultured cells with (13)C6-glucose and the analysis of isotopomers of UDP-HexNAc (UDP-GlcNAc plus UDP-GalNAc) and CMP-NeuAc revealed the relative contributions of metabolic pathways leading to UDP-GlcNAc synthesis and use. In pancreatic insulinoma cells, the labeling efficiency of a (13)C6-glucose motif in CMP-NeuAc was lower compared with that in hepatoma cells. Using (13)C2-glucosamine, the diversity of the labeling efficiency was observed in each sugar residue of N- and O-glycans on the basis of isotopomer analysis. In the insulinoma cells, the low labeling efficiencies were found for sialic acids as well as tri- and tetra-sialo N-glycans, whereas asialo N-glycans were found to be abundant. Essentially no significant difference in secreted hyaluronic acids was found among hepatoma and insulinoma cell lines. This indicates that metabolic flows are responsible for the low sialylation in the insulinoma cells. Our strategy should be useful for systematically tracing each stage of cellular GlcNAc metabolism.
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Affiliation(s)
- Kazuki Nakajima
- From the ‡Disease Glycomics Team, Systems Glycobiology Research Group, Global Research Cluster, RIKEN Max Plank Joint Research Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Emi Ito
- From the ‡Disease Glycomics Team, Systems Glycobiology Research Group, Global Research Cluster, RIKEN Max Plank Joint Research Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kazuaki Ohtsubo
- From the ‡Disease Glycomics Team, Systems Glycobiology Research Group, Global Research Cluster, RIKEN Max Plank Joint Research Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ken Shirato
- §Laboratory of Physiological Sciences, Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima Tokorozawa, Saitama 359-1192, Japan
| | - Rina Takamiya
- From the ‡Disease Glycomics Team, Systems Glycobiology Research Group, Global Research Cluster, RIKEN Max Plank Joint Research Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shinobu Kitazume
- From the ‡Disease Glycomics Team, Systems Glycobiology Research Group, Global Research Cluster, RIKEN Max Plank Joint Research Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takashi Angata
- From the ‡Disease Glycomics Team, Systems Glycobiology Research Group, Global Research Cluster, RIKEN Max Plank Joint Research Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoyuki Taniguchi
- From the ‡Disease Glycomics Team, Systems Glycobiology Research Group, Global Research Cluster, RIKEN Max Plank Joint Research Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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20
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Puszyk WM, Le Trinh T, Chapple S, Liu C. Linking metabolism and epigenetic regulation in development of hepatocellular carcinoma. J Transl Med 2013; 93:983-90. [PMID: 23917878 PMCID: PMC4028619 DOI: 10.1038/labinvest.2013.94] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/07/2013] [Indexed: 12/29/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common form of cancer globally and is rarely curable once detected. The 5-year survival rate of patients diagnosed with late-stage HCC may be as low as 27%. HCC is a cancer largely driven by epigenetic changes that arise from exposure to exogenous environmental factors rather than coding sequence mutations. The liver is susceptible to effects from Hepatitis C and Hepatitis B viruses, exposure to aflatoxin and continuous excessive consumption of alcohol. The liver is a highly metabolic organ balancing many vital biochemical processes; exposure to any of the above environmental factors is associated with loss of liver function and is a major risk factor for the development of HCC. Emerging studies aim to examine the underlying metabolic processes that are abrogated in cancer and lead to the altered flux and availability of key metabolites important for epigenetic processes. Metabolites have been shown to act as substrates for many canonical epigenetic regulators. These enzymes are responsible for regulating histone modification, DNA methylation and micro RNA expression. By studying the impact of altered liver metabolism, we may better understand the long-term epigenetic processes, which lead to the development and progression of HCC.
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Affiliation(s)
- William Matthew Puszyk
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, USA
| | - Thu Le Trinh
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, USA
| | - Sarah Chapple
- Cardiovascular Division, BHF Centre of Research Excellence, School of Medicine, King’s College London, London, SE1 9NH, UK
| | - Chen Liu
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, USA,Shands Cancer Center, University of Florida, Gainesville, Florida 32610, USA,Correspondence: Chen Liu, M.D., Ph.D., Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, 1600 SW Archer Road, M651, PO 100275, Gainesville, FL 32610. Tel: 352-273-5413; Fax: 352-392-6249
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21
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Godoy P, Hewitt NJ, Albrecht U, Andersen ME, Ansari N, Bhattacharya S, Bode JG, Bolleyn J, Borner C, Böttger J, Braeuning A, Budinsky RA, Burkhardt B, Cameron NR, Camussi G, Cho CS, Choi YJ, Craig Rowlands J, Dahmen U, Damm G, Dirsch O, Donato MT, Dong J, Dooley S, Drasdo D, Eakins R, Ferreira KS, Fonsato V, Fraczek J, Gebhardt R, Gibson A, Glanemann M, Goldring CEP, Gómez-Lechón MJ, Groothuis GMM, Gustavsson L, Guyot C, Hallifax D, Hammad S, Hayward A, Häussinger D, Hellerbrand C, Hewitt P, Hoehme S, Holzhütter HG, Houston JB, Hrach J, Ito K, Jaeschke H, Keitel V, Kelm JM, Kevin Park B, Kordes C, Kullak-Ublick GA, LeCluyse EL, Lu P, Luebke-Wheeler J, Lutz A, Maltman DJ, Matz-Soja M, McMullen P, Merfort I, Messner S, Meyer C, Mwinyi J, Naisbitt DJ, Nussler AK, Olinga P, Pampaloni F, Pi J, Pluta L, Przyborski SA, Ramachandran A, Rogiers V, Rowe C, Schelcher C, Schmich K, Schwarz M, Singh B, Stelzer EHK, Stieger B, Stöber R, Sugiyama Y, Tetta C, Thasler WE, Vanhaecke T, Vinken M, Weiss TS, Widera A, Woods CG, Xu JJ, Yarborough KM, Hengstler JG. Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME. Arch Toxicol 2013; 87:1315-530. [PMID: 23974980 PMCID: PMC3753504 DOI: 10.1007/s00204-013-1078-5] [Citation(s) in RCA: 1051] [Impact Index Per Article: 95.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 05/06/2013] [Indexed: 12/15/2022]
Abstract
This review encompasses the most important advances in liver functions and hepatotoxicity and analyzes which mechanisms can be studied in vitro. In a complex architecture of nested, zonated lobules, the liver consists of approximately 80 % hepatocytes and 20 % non-parenchymal cells, the latter being involved in a secondary phase that may dramatically aggravate the initial damage. Hepatotoxicity, as well as hepatic metabolism, is controlled by a set of nuclear receptors (including PXR, CAR, HNF-4α, FXR, LXR, SHP, VDR and PPAR) and signaling pathways. When isolating liver cells, some pathways are activated, e.g., the RAS/MEK/ERK pathway, whereas others are silenced (e.g. HNF-4α), resulting in up- and downregulation of hundreds of genes. An understanding of these changes is crucial for a correct interpretation of in vitro data. The possibilities and limitations of the most useful liver in vitro systems are summarized, including three-dimensional culture techniques, co-cultures with non-parenchymal cells, hepatospheres, precision cut liver slices and the isolated perfused liver. Also discussed is how closely hepatoma, stem cell and iPS cell-derived hepatocyte-like-cells resemble real hepatocytes. Finally, a summary is given of the state of the art of liver in vitro and mathematical modeling systems that are currently used in the pharmaceutical industry with an emphasis on drug metabolism, prediction of clearance, drug interaction, transporter studies and hepatotoxicity. One key message is that despite our enthusiasm for in vitro systems, we must never lose sight of the in vivo situation. Although hepatocytes have been isolated for decades, the hunt for relevant alternative systems has only just begun.
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Affiliation(s)
- Patricio Godoy
- Leibniz Research Centre for Working Environment and Human Factors (IFADO), 44139 Dortmund, Germany
| | | | - Ute Albrecht
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Melvin E. Andersen
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Nariman Ansari
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Sudin Bhattacharya
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Johannes Georg Bode
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Jennifer Bolleyn
- Department of Toxicology, Centre for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Christoph Borner
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Jan Böttger
- Institute of Biochemistry, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Albert Braeuning
- Department of Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Wilhelmstr. 56, 72074 Tübingen, Germany
| | - Robert A. Budinsky
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, Midland, MI USA
| | - Britta Burkhardt
- BG Trauma Center, Siegfried Weller Institut, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Neil R. Cameron
- Department of Chemistry, Durham University, Durham, DH1 3LE UK
| | - Giovanni Camussi
- Department of Medical Sciences, University of Torino, 10126 Turin, Italy
| | - Chong-Su Cho
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921 Korea
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921 Korea
| | - J. Craig Rowlands
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, Midland, MI USA
| | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General Visceral, and Vascular Surgery, Friedrich-Schiller-University Jena, 07745 Jena, Germany
| | - Georg Damm
- Department of General-, Visceral- and Transplantation Surgery, Charité University Medicine Berlin, 13353 Berlin, Germany
| | - Olaf Dirsch
- Institute of Pathology, Friedrich-Schiller-University Jena, 07745 Jena, Germany
| | - María Teresa Donato
- Unidad de Hepatología Experimental, IIS Hospital La Fe Avda Campanar 21, 46009 Valencia, Spain
- CIBERehd, Fondo de Investigaciones Sanitarias, Barcelona, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, Valencia, Spain
| | - Jian Dong
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Steven Dooley
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Dirk Drasdo
- Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, 04107 Leipzig, Germany
- INRIA (French National Institute for Research in Computer Science and Control), Domaine de Voluceau-Rocquencourt, B.P. 105, 78153 Le Chesnay Cedex, France
- UPMC University of Paris 06, CNRS UMR 7598, Laboratoire Jacques-Louis Lions, 4, pl. Jussieu, 75252 Paris cedex 05, France
| | - Rowena Eakins
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Karine Sá Ferreira
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
- GRK 1104 From Cells to Organs, Molecular Mechanisms of Organogenesis, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Valentina Fonsato
- Department of Medical Sciences, University of Torino, 10126 Turin, Italy
| | - Joanna Fraczek
- Department of Toxicology, Centre for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Rolf Gebhardt
- Institute of Biochemistry, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Andrew Gibson
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Matthias Glanemann
- Department of General-, Visceral- and Transplantation Surgery, Charité University Medicine Berlin, 13353 Berlin, Germany
| | - Chris E. P. Goldring
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - María José Gómez-Lechón
- Unidad de Hepatología Experimental, IIS Hospital La Fe Avda Campanar 21, 46009 Valencia, Spain
- CIBERehd, Fondo de Investigaciones Sanitarias, Barcelona, Spain
| | - Geny M. M. Groothuis
- Department of Pharmacy, Pharmacokinetics Toxicology and Targeting, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Lena Gustavsson
- Department of Laboratory Medicine (Malmö), Center for Molecular Pathology, Lund University, Jan Waldenströms gata 59, 205 02 Malmö, Sweden
| | - Christelle Guyot
- Department of Clinical Pharmacology and Toxicology, University Hospital, 8091 Zurich, Switzerland
| | - David Hallifax
- Centre for Applied Pharmacokinetic Research (CAPKR), School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT UK
| | - Seddik Hammad
- Department of Forensic Medicine and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Adam Hayward
- Biological and Biomedical Sciences, Durham University, Durham, DH13LE UK
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Claus Hellerbrand
- Department of Medicine I, University Hospital Regensburg, 93053 Regensburg, Germany
| | | | - Stefan Hoehme
- Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, 04107 Leipzig, Germany
| | - Hermann-Georg Holzhütter
- Institut für Biochemie Abteilung Mathematische Systembiochemie, Universitätsmedizin Berlin (Charité), Charitéplatz 1, 10117 Berlin, Germany
| | - J. Brian Houston
- Centre for Applied Pharmacokinetic Research (CAPKR), School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT UK
| | | | - Kiyomi Ito
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo, 202-8585 Japan
| | - Hartmut Jaeschke
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | | | - B. Kevin Park
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Claus Kordes
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Gerd A. Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital, 8091 Zurich, Switzerland
| | - Edward L. LeCluyse
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Peng Lu
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | | | - Anna Lutz
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | - Daniel J. Maltman
- Reinnervate Limited, NETPark Incubator, Thomas Wright Way, Sedgefield, TS21 3FD UK
| | - Madlen Matz-Soja
- Institute of Biochemistry, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Patrick McMullen
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Irmgard Merfort
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | | | - Christoph Meyer
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jessica Mwinyi
- Department of Clinical Pharmacology and Toxicology, University Hospital, 8091 Zurich, Switzerland
| | - Dean J. Naisbitt
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Andreas K. Nussler
- BG Trauma Center, Siegfried Weller Institut, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Peter Olinga
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Francesco Pampaloni
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Jingbo Pi
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Linda Pluta
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Stefan A. Przyborski
- Reinnervate Limited, NETPark Incubator, Thomas Wright Way, Sedgefield, TS21 3FD UK
- Biological and Biomedical Sciences, Durham University, Durham, DH13LE UK
| | - Anup Ramachandran
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Vera Rogiers
- Department of Toxicology, Centre for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Cliff Rowe
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Celine Schelcher
- Department of Surgery, Liver Regeneration, Core Facility, Human in Vitro Models of the Liver, Ludwig Maximilians University of Munich, Munich, Germany
| | - Kathrin Schmich
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | - Michael Schwarz
- Department of Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Wilhelmstr. 56, 72074 Tübingen, Germany
| | - Bijay Singh
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921 Korea
| | - Ernst H. K. Stelzer
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Bruno Stieger
- Department of Clinical Pharmacology and Toxicology, University Hospital, 8091 Zurich, Switzerland
| | - Regina Stöber
- Leibniz Research Centre for Working Environment and Human Factors (IFADO), 44139 Dortmund, Germany
| | - Yuichi Sugiyama
- Sugiyama Laboratory, RIKEN Innovation Center, RIKEN, Yokohama Biopharmaceutical R&D Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Ciro Tetta
- Fresenius Medical Care, Bad Homburg, Germany
| | - Wolfgang E. Thasler
- Department of Surgery, Ludwig-Maximilians-University of Munich Hospital Grosshadern, Munich, Germany
| | - Tamara Vanhaecke
- Department of Toxicology, Centre for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mathieu Vinken
- Department of Toxicology, Centre for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Thomas S. Weiss
- Department of Pediatrics and Juvenile Medicine, University of Regensburg Hospital, Regensburg, Germany
| | - Agata Widera
- Leibniz Research Centre for Working Environment and Human Factors (IFADO), 44139 Dortmund, Germany
| | - Courtney G. Woods
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | | | | | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IFADO), 44139 Dortmund, Germany
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22
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Ghosh SP, Singh R, Chakraborty K, Kulkarni S, Uppal A, Luo Y, Kaur P, Pathak R, Kumar KS, Hauer-Jensen M, Cheema AK. Metabolomic changes in gastrointestinal tissues after whole body radiation in a murine model. MOLECULAR BIOSYSTEMS 2013; 9:723-31. [PMID: 23403731 PMCID: PMC3601576 DOI: 10.1039/c3mb25454b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Exposure to ionizing radiation (IR) elicits a set of complex biological responses involving gene expression and protein turnover that ultimately manifest as dysregulation of metabolic processes representing the cellular phenotype. Although radiation biomarkers have been reported in urine and serum, they are not informative about IR mediated tissue or organ specific injury. In the present study we report IR induced metabolic changes in gastrointestinal (GI) tissue of CD2F1 mice using ultra-performance liquid chromatography (UPLC) coupled with electrospray time-of-flight mass spectrometry. Post-radiation GI injury is a critical determinant of survival after exposure to IR. Our results show a distinct dose and time dependent response to GI tissue injury.
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Affiliation(s)
- Sanchita P Ghosh
- Armed Forces Radiobiology Research Institute, USUHS, Bethesda, MD 20889-5603, USA
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23
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Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K, Klamt S, Rocha M, Saez-Rodriguez J. Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. MOLECULAR BIOSYSTEMS 2013; 9:1576-83. [DOI: 10.1039/c3mb25489e] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Niklas J, Diaz Ochoa JG, Bucher J, Mauch K. Quantitative Evaluation and Prediction of Drug Effects and Toxicological Risk Using Mechanistic Multiscale Models. Mol Inform 2012; 32:14-23. [DOI: 10.1002/minf.201200043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/21/2012] [Indexed: 01/06/2023]
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25
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Niklas J, Bonin A, Mangin S, Bucher J, Kopacz S, Matz-Soja M, Thiel C, Gebhardt R, Hofmann U, Mauch K. Central energy metabolism remains robust in acute steatotic hepatocytes challenged by a high free fatty acid load. BMB Rep 2012; 45:396-401. [DOI: 10.5483/bmbrep.2012.45.7.070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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26
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Samanez CH, Caron S, Briand O, Dehondt H, Duplan I, Kuipers F, Hennuyer N, Clavey V, Staels B. The human hepatocyte cell lines IHH and HepaRG: models to study glucose, lipid and lipoprotein metabolism. Arch Physiol Biochem 2012; 118:102-11. [PMID: 22594799 DOI: 10.3109/13813455.2012.683442] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Metabolic diseases reach epidemic proportions. A better knowledge of the associated alterations in the metabolic pathways in the liver is necessary. These studies need in vitro human cell models. Several human hepatoma models are used, but the response of many metabolic pathways to physiological stimuli is often lost. Here, we characterize two human hepatocyte cell lines, IHH and HepaRG, by analysing the expression and regulation of genes involved in glucose and lipid metabolism. Our results show that the glycolysis pathway is activated by glucose and insulin in both lines. Gluconeogenesis gene expression is induced by forskolin in IHH cells and inhibited by insulin in both cell lines. The lipogenic pathway is regulated by insulin in IHH cells. Finally, both cell lines secrete apolipoprotein B-containing lipoproteins, an effect promoted by increasing glucose concentrations. These two human cell lines are thus interesting models to study the regulation of glucose and lipid metabolism.
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27
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Klein S, Heinzle E. Isotope labeling experiments in metabolomics and fluxomics. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:261-72. [DOI: 10.1002/wsbm.1167] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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28
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Xu K, Morgan KT, Todd Gehris A, Elston TC, Gomez SM. A whole-body model for glycogen regulation reveals a critical role for substrate cycling in maintaining blood glucose homeostasis. PLoS Comput Biol 2011; 7:e1002272. [PMID: 22163177 PMCID: PMC3233304 DOI: 10.1371/journal.pcbi.1002272] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 09/27/2011] [Indexed: 01/08/2023] Open
Abstract
Timely, and sometimes rapid, metabolic adaptation to changes in food supply is critical for survival as an organism moves from the fasted to the fed state, and vice versa. These transitions necessitate major metabolic changes to maintain energy homeostasis as the source of blood glucose moves away from ingested carbohydrates, through hepatic glycogen stores, towards gluconeogenesis. The integration of hepatic glycogen regulation with extra-hepatic energetics is a key aspect of these adaptive mechanisms. Here we use computational modeling to explore hepatic glycogen regulation under fed and fasting conditions in the context of a whole-body model. The model was validated against previous experimental results concerning glycogen phosphorylase a (active) and glycogen synthase a dynamics. The model qualitatively reproduced physiological changes that occur during transition from the fed to the fasted state. Analysis of the model reveals a critical role for the inhibition of glycogen synthase phosphatase by glycogen phosphorylase a. This negative regulation leads to high levels of glycogen synthase activity during fasting conditions, which in turn increases substrate (futile) cycling, priming the system for a rapid response once an external source of glucose is restored. This work demonstrates that a mechanistic understanding of the design principles used by metabolic control circuits to maintain homeostasis can benefit from the incorporation of mathematical descriptions of these networks into “whole-body” contextual models that mimic in vivo conditions. Homeostasis of blood glucose concentrations during circadian shifts in survival-related activities, sleep and food availability is crucial for the survival of mammals. This process depends upon glucose intake, short-term storage as glycogen, and gluconeogenesis. The integration of hepatic glycogen anabolic and catabolic dynamics with whole body energetics is critical for survival. In this paper we use computational modeling to investigate the potential survival advantage of substrate (futile) cycling of glycogen and glycogen precursors. Our simulations, combined with published experimental results of other researchers, indicate that as the body enters a state of fasting, the activity of enzymes involved in the synthesis of glycogen increases leading to increased substrate cycling. This increase in substrate cycling allows the system to respond more rapidly once new external sources of glucose become available. The whole-body computational model developed for this work allows the metabolic control circuitry to be studied under simulated in vivo conditions, providing functional insights that are not evident when individual modules of glycogen regulatory circuitry are examined in isolation.
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Affiliation(s)
- Ke Xu
- Department of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Kevin T. Morgan
- Old Dogs in Training, Carrboro, North Carolina, United States of America
| | - Abby Todd Gehris
- Department of Mathematics, Broome Community College, Binghamton, New York, United States of America
| | - Timothy C. Elston
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- * E-mail: (TCE); (SMG)
| | - Shawn M. Gomez
- Department of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (TCE); (SMG)
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29
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Oncogenic stress induced by acute hyper-activation of Bcr-Abl leads to cell death upon induction of excessive aerobic glycolysis. PLoS One 2011; 6:e25139. [PMID: 21949869 PMCID: PMC3176818 DOI: 10.1371/journal.pone.0025139] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 08/29/2011] [Indexed: 01/15/2023] Open
Abstract
In response to deregulated oncogene activation, mammalian cells activate disposal programs such as programmed cell death. To investigate the mechanisms behind this oncogenic stress response we used Bcr-Abl over-expressing cells cultivated in presence of imatinib. Imatinib deprivation led to rapid induction of Bcr-Abl activity and over-stimulation of PI3K/Akt-, Ras/MAPK-, and JAK/STAT pathways. This resulted in a delayed necrosis-like cell death starting not before 48 hours after imatinib withdrawal. Cell death was preceded by enhanced glycolysis, glutaminolysis, and amino acid metabolism leading to elevated ATP and protein levels. This enhanced metabolism could be linked to induction of cell death as inhibition of glycolysis or glutaminolysis was sufficient to sustain cell viability. Therefore, these data provide first evidence that metabolic changes induced by Bcr-Abl hyper-activation are important mediators of oncogenic stress-induced cell death. During the first 30 hours after imatinib deprivation, Bcr-Abl hyper-activation did not affect proliferation but resulted in cellular swelling, vacuolization, and induction of eIF2α phosphorylation, CHOP expression, as well as alternative splicing of XPB, indicating endoplasmic reticulum stress response. Cell death was dependent on p38 and RIP1 signaling, whereas classical death effectors of ER stress, namely CHOP-BIM were antagonized by concomitant up-regulation of Bcl-xL. Screening of 1,120 compounds for their potential effects on oncogenic stress-induced cell death uncovered that corticosteroids antagonize cell death upon Bcr-Abl hyper-activation by normalizing cellular metabolism. This protective effect is further demonstrated by the finding that corticosteroids rendered lymphocytes permissive to the transforming activity of Bcr-Abl. As corticosteroids are used together with imatinib for treatment of Bcr-Abl positive acute lymphoblastic leukemia these data could have important implications for the design of combination therapy protocols. In conclusion, excessive induction of Warburg type metabolic alterations can cause cell death. Our data indicate that these metabolic changes are major mediators of oncogenic stress induced by Bcr-Abl.
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Gerosa L, Sauer U. Regulation and control of metabolic fluxes in microbes. Curr Opin Biotechnol 2011; 22:566-75. [PMID: 21600757 DOI: 10.1016/j.copbio.2011.04.016] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 04/20/2011] [Indexed: 01/09/2023]
Abstract
After about ten years of research renaissance in metabolism, the present challenge is to understand how metabolic fluxes are controlled by a complex interplay of overlapping regulatory mechanisms. Reconstruction of various regulatory network topologies is steaming, illustrating that we underestimated the broad importance of post-translational modifications such as enzyme phosphorylation or acetylation for microbial metabolism. With the growing topological knowledge, the functional relevance of these regulatory events becomes an even more pressing need. A major knowledge gap resides in the regulatory network of protein-metabolite interactions, simply because we lacked pertinent methods for systematic analyses - but a start has now been made. Perhaps most dramatic was the conceptual shift in our perception of metabolism from an engine of cellular operation to a generator of input and feedback signals for regulatory circuits that govern many important decisions on cell proliferation, differentiation, death, and naturally metabolism.
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Affiliation(s)
- Luca Gerosa
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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Costa R, Rocha I, Ferreira E, Machado D. Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling. IET Syst Biol 2011; 5:157-63. [DOI: 10.1049/iet-syb.2009.0058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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