151
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Deng Y, Wang ZV, Gordillo R, An Y, Zhang C, Liang Q, Yoshino J, Cautivo KM, De Brabander J, Elmquist JK, Horton JD, Hill JA, Klein S, Scherer PE. An adipo-biliary-uridine axis that regulates energy homeostasis. Science 2017; 355:355/6330/eaaf5375. [PMID: 28302796 DOI: 10.1126/science.aaf5375] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 01/17/2017] [Indexed: 12/12/2022]
Abstract
Uridine, a pyrimidine nucleoside present at high levels in the plasma of rodents and humans, is critical for RNA synthesis, glycogen deposition, and many other essential cellular processes. It also contributes to systemic metabolism, but the underlying mechanisms remain unclear. We found that plasma uridine levels are regulated by fasting and refeeding in mice, rats, and humans. Fasting increases plasma uridine levels, and this increase relies largely on adipocytes. In contrast, refeeding reduces plasma uridine levels through biliary clearance. Elevation of plasma uridine is required for the drop in body temperature that occurs during fasting. Further, feeding-induced clearance of plasma uridine improves glucose metabolism. We also present findings that implicate leptin signaling in uridine homeostasis and consequent metabolic control and thermoregulation. Our results indicate that plasma uridine governs energy homeostasis and thermoregulation in a mechanism involving adipocyte-dependent uridine biosynthesis and leptin signaling.
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Affiliation(s)
- Yingfeng Deng
- Touchstone Diabetes Center, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zhao V Wang
- Division of Cardiology, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ruth Gordillo
- Touchstone Diabetes Center, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yu An
- Touchstone Diabetes Center, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chen Zhang
- Touchstone Diabetes Center, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Qiren Liang
- Department of Biochemistry and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jun Yoshino
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO, USA
| | - Kelly M Cautivo
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jef De Brabander
- Department of Biochemistry and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joel K Elmquist
- Division of Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jay D Horton
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joseph A Hill
- Division of Cardiology, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel Klein
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO, USA
| | - Philipp E Scherer
- Touchstone Diabetes Center, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
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152
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Millius A, Ueda HR. Systems Biology-Derived Discoveries of Intrinsic Clocks. Front Neurol 2017; 8:25. [PMID: 28220104 PMCID: PMC5292584 DOI: 10.3389/fneur.2017.00025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/17/2017] [Indexed: 12/19/2022] Open
Abstract
A systems approach to studying biology uses a variety of mathematical, computational, and engineering tools to holistically understand and model properties of cells, tissues, and organisms. Building from early biochemical, genetic, and physiological studies, systems biology became established through the development of genome-wide methods, high-throughput procedures, modern computational processing power, and bioinformatics. Here, we highlight a variety of systems approaches to the study of biological rhythms that occur with a 24-h period-circadian rhythms. We review how systems methods have helped to elucidate complex behaviors of the circadian clock including temperature compensation, rhythmicity, and robustness. Finally, we explain the contribution of systems biology to the transcription-translation feedback loop and posttranslational oscillator models of circadian rhythms and describe new technologies and "-omics" approaches to understand circadian timekeeping and neurophysiology.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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153
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Gnocchi D, Bruscalupi G. Circadian Rhythms and Hormonal Homeostasis: Pathophysiological Implications. BIOLOGY 2017; 6:biology6010010. [PMID: 28165421 PMCID: PMC5372003 DOI: 10.3390/biology6010010] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 01/10/2017] [Accepted: 01/23/2017] [Indexed: 02/07/2023]
Abstract
Over recent years, a deeper comprehension of the molecular mechanisms that control biological clocks and circadian rhythms has been achieved. In fact, many studies have contributed to unravelling the importance of the molecular clock for the regulation of our physiology, including hormonal and metabolic homeostasis. Here we will review the structure, organisation and molecular machinery that make our circadian clock work, and its relevance for the proper functioning of physiological processes. We will also describe the interconnections between circadian rhythms and endocrine homeostasis, as well as the underlying consequences that circadian dysregulations might have in the development of several pathologic affections. Finally, we will discuss how a better knowledge of such relationships might prove helpful in designing new therapeutic approaches for endocrine and metabolic diseases.
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Affiliation(s)
- Davide Gnocchi
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm 14186, Sweden.
| | - Giovannella Bruscalupi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome 00185, Italy.
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154
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Abstract
Circadian rhythms govern multiple aspects of animal metabolism. Transcriptome-, proteome- and metabolome-wide measurements have revealed widespread circadian rhythms in metabolism governed by a cellular genetic oscillator, the circadian core clock. However, it remains unclear if and under which conditions transcriptional rhythms cause rhythms in particular metabolites and metabolic fluxes. Here, we analyzed the circadian orchestration of metabolic pathways by direct measurement of enzyme activities, analysis of transcriptome data, and developing a theoretical method called circadian response analysis. Contrary to a common assumption, we found that pronounced rhythms in metabolic pathways are often favored by separation rather than alignment in the times of peak activity of key enzymes. This property holds true for a set of metabolic pathway motifs (e.g., linear chains and branching points) and also under the conditions of fast kinetics typical for metabolic reactions. By circadian response analysis of pathway motifs, we determined exact timing separation constraints on rhythmic enzyme activities that allow for substantial rhythms in pathway flux and metabolite concentrations. Direct measurements of circadian enzyme activities in mouse skeletal muscle confirmed that such timing separation occurs in vivo.
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155
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Jaeger C, Xu C, Sun M, Krager S, Tischkau SA. Aryl hydrocarbon receptor-deficient mice are protected from high fat diet-induced changes in metabolic rhythms. Chronobiol Int 2017; 34:318-336. [PMID: 28102700 DOI: 10.1080/07420528.2016.1256298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
High fat diet (HFD) consumption alters the synchronized circadian timing system resulting in harmful loss, gain or shift of transcriptional oscillations. The aryl hydrocarbon receptor (AhR) shares structural homology to clock genes, containing both PAS domains and basic helix-loop helix structural motifs, allowing for interaction with components of the primary circadian feedback loop. Activation of AhR alters circadian rhythmicity, primarily through inhibition of Clock/Bmal1-mediated regulation of Per1. AhR-deficient mice are protected from diet-induced metabolic dysfunction, exhibiting enhanced insulin sensitivity and glucose tolerance. This study examined whether AhR haploinsufficiency can also protect against diet-induced alterations in rhythm. After feeding AhR+/+ and AhR+/- mice an HFD (60% fat) for 15 weeks, samples were collected every 4 hours over a 24-hour period. HFD altered the rhythm of serum glucose and the metabolic transcriptome, including hepatic nuclear receptors Rev-erbα and PPARγ in wild-type c57bl6/j mice. AhR reduction provided protection against diet-induced transcriptional oscillation changes; serum glucose and metabolic gene rhythms were protected from the disruption caused by HFD feeding. These data highlight the critical role of AhR signaling in the regulation of metabolism and provide a potential therapeutic target for diseases characterized by rhythmic desynchrony.
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Affiliation(s)
- Cassie Jaeger
- a Department of Pharmacology , Southern Illinois University School of Medicine , Springfield , IL , USA
| | - Canxin Xu
- a Department of Pharmacology , Southern Illinois University School of Medicine , Springfield , IL , USA
| | - Mingwei Sun
- a Department of Pharmacology , Southern Illinois University School of Medicine , Springfield , IL , USA
| | - Stacey Krager
- a Department of Pharmacology , Southern Illinois University School of Medicine , Springfield , IL , USA
| | - Shelley A Tischkau
- a Department of Pharmacology , Southern Illinois University School of Medicine , Springfield , IL , USA
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156
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Robles MS, Humphrey SJ, Mann M. Phosphorylation Is a Central Mechanism for Circadian Control of Metabolism and Physiology. Cell Metab 2017; 25:118-127. [PMID: 27818261 DOI: 10.1016/j.cmet.2016.10.004] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/12/2016] [Accepted: 10/05/2016] [Indexed: 12/21/2022]
Abstract
Circadian clocks are self-sustainable endogenous oscillators, present in virtually every cell, driving daily cycles of metabolism and physiology. The molecular mechanism of the circadian clock is based on interconnected transcriptional and translational feedback loops. While many studies have addressed circadian rhythms of the transcriptome and, to a lesser extent, the proteome, none have investigated the phosphoproteome. We apply mass spectrometry-based phosphoproteomics to obtain the first global in vivo quantification of circadian phosphorylation in mammals. Of more than 20,000 phosphosites, 25% significantly oscillate in the mouse liver, including novel sites on core clock proteins. The extent and amplitude of phosphorylation cycles far exceeds those observed in RNA and protein abundance. Our data indicate a dominant regulatory role for phosphorylation-dependent circadian tuning of signaling pathways. This allows the organism to integrate different signals and rapidly and economically respond to daily changes in nutrient availability and physiological states.
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Affiliation(s)
- Maria S Robles
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Sean J Humphrey
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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157
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Padmanabhan K, Billaud M. Desynchronization of Circadian Clocks in Cancer: A Metabolic and Epigenetic Connection. Front Endocrinol (Lausanne) 2017; 8:136. [PMID: 28674522 PMCID: PMC5474466 DOI: 10.3389/fendo.2017.00136] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/02/2017] [Indexed: 12/29/2022] Open
Abstract
Circadian clocks are innate oscillators that drive daily rhythms in metabolism, physiology, and behavior. 24-h rhythms in gene expression, driven by core clock transcription factors, reflect the epigenetic state of the cell, which in turn is dictated by the metabolic environment. Cancer cells alter their metabolic state and gene expression and therefore are likely to tweak circadian clock function in their favor. Over the past decade, we have witnessed an extraordinary increase in systems-level studies that suggest intricate mechanistic links between the cellular metabolome and the circadian epigenome. In parallel, reprogramming of cellular clock function in cancers is increasingly evident and the role of clock genes in the development of hematological tumors, as well as their pathophysiological effects on tissues distal to the tumor, has been described. Furthermore, the interplay between components of the circadian clock, metabolic enzymes, and oncogenes is starting to be better understood, such as the close association between overexpression of the Myc oncogene and perturbation of circadian and metabolic rhythms, thus opening new avenues to treat cancers. This review article explores current knowledge on the circadian metabolome and the molecular pathways they control, with a focus on their involvement in the development of hematopoietic malignancies.
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Affiliation(s)
- Kiran Padmanabhan
- “Molecular and Epigenetic Regulation of Biological Clocks”, Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- INSERM, Paris, France
- *Correspondence: Kiran Padmanabhan,
| | - Marc Billaud
- “Clinical and Experimental Model of Lymphomagenesis”, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France
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158
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Xiao B, Chen TM, Zhong Y. Possible molecular mechanism underlying cadmium-induced circadian rhythms disruption in zebrafish. Biochem Biophys Res Commun 2016; 481:201-205. [DOI: 10.1016/j.bbrc.2016.10.081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/22/2016] [Indexed: 12/16/2022]
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159
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Potter GDM, Skene DJ, Arendt J, Cade JE, Grant PJ, Hardie LJ. Circadian Rhythm and Sleep Disruption: Causes, Metabolic Consequences, and Countermeasures. Endocr Rev 2016; 37:584-608. [PMID: 27763782 PMCID: PMC5142605 DOI: 10.1210/er.2016-1083] [Citation(s) in RCA: 302] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Circadian (∼24-hour) timing systems pervade all kingdoms of life and temporally optimize behavior and physiology in humans. Relatively recent changes to our environments, such as the introduction of artificial lighting, can disorganize the circadian system, from the level of the molecular clocks that regulate the timing of cellular activities to the level of synchronization between our daily cycles of behavior and the solar day. Sleep/wake cycles are intertwined with the circadian system, and global trends indicate that these, too, are increasingly subject to disruption. A large proportion of the world's population is at increased risk of environmentally driven circadian rhythm and sleep disruption, and a minority of individuals are also genetically predisposed to circadian misalignment and sleep disorders. The consequences of disruption to the circadian system and sleep are profound and include myriad metabolic ramifications, some of which may be compounded by adverse effects on dietary choices. If not addressed, the deleterious effects of such disruption will continue to cause widespread health problems; therefore, implementation of the numerous behavioral and pharmaceutical interventions that can help restore circadian system alignment and enhance sleep will be important.
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Affiliation(s)
- Gregory D M Potter
- Division of Epidemiology and Biostatistics (G.D.M.P., L.J.H.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom; Chronobiology Section (D.J.S., J.A.), Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom; Nutritional Epidemiology Group (J.E.C.), School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, United Kingdom; and Division of Cardiovascular & Diabetes Research (P.J.G.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Debra J Skene
- Division of Epidemiology and Biostatistics (G.D.M.P., L.J.H.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom; Chronobiology Section (D.J.S., J.A.), Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom; Nutritional Epidemiology Group (J.E.C.), School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, United Kingdom; and Division of Cardiovascular & Diabetes Research (P.J.G.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Josephine Arendt
- Division of Epidemiology and Biostatistics (G.D.M.P., L.J.H.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom; Chronobiology Section (D.J.S., J.A.), Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom; Nutritional Epidemiology Group (J.E.C.), School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, United Kingdom; and Division of Cardiovascular & Diabetes Research (P.J.G.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Janet E Cade
- Division of Epidemiology and Biostatistics (G.D.M.P., L.J.H.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom; Chronobiology Section (D.J.S., J.A.), Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom; Nutritional Epidemiology Group (J.E.C.), School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, United Kingdom; and Division of Cardiovascular & Diabetes Research (P.J.G.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Peter J Grant
- Division of Epidemiology and Biostatistics (G.D.M.P., L.J.H.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom; Chronobiology Section (D.J.S., J.A.), Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom; Nutritional Epidemiology Group (J.E.C.), School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, United Kingdom; and Division of Cardiovascular & Diabetes Research (P.J.G.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Laura J Hardie
- Division of Epidemiology and Biostatistics (G.D.M.P., L.J.H.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom; Chronobiology Section (D.J.S., J.A.), Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom; Nutritional Epidemiology Group (J.E.C.), School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, United Kingdom; and Division of Cardiovascular & Diabetes Research (P.J.G.), LIGHT Laboratories, University of Leeds, Leeds LS2 9JT, United Kingdom
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160
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Thaiss CA, Levy M, Korem T, Dohnalová L, Shapiro H, Jaitin DA, David E, Winter DR, Gury-BenAri M, Tatirovsky E, Tuganbaev T, Federici S, Zmora N, Zeevi D, Dori-Bachash M, Pevsner-Fischer M, Kartvelishvily E, Brandis A, Harmelin A, Shibolet O, Halpern Z, Honda K, Amit I, Segal E, Elinav E. Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations. Cell 2016; 167:1495-1510.e12. [DOI: 10.1016/j.cell.2016.11.003] [Citation(s) in RCA: 478] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 09/27/2016] [Accepted: 11/01/2016] [Indexed: 12/13/2022]
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161
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Tran M, Yang Z, Liangpunsakul S, Wang L. Metabolomics Analysis Revealed Distinct Cyclic Changes of Metabolites Altered by Chronic Ethanol-Plus-Binge and Shp Deficiency. Alcohol Clin Exp Res 2016; 40:2548-2556. [PMID: 27790731 DOI: 10.1111/acer.13257] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/26/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Chronic ethanol (EtOH) consumption causes alcoholic liver disease (ALD), and disruption of the circadian system facilitates the development of ALD. Small heterodimer partner (SHP) is a nuclear receptor and critical regulator of hepatic lipid metabolism. This study aimed at depicting circadian metabolomes altered by chronic EtOH-plus-binge and Shp deficiency using high-throughput metabolomics. METHODS Wild-type (WT) C57BL/6 and Shp-/- mice were fed the control diet (CD) or Lieber-DeCarli EtOH liquid diet (ED) for 10 days followed by a single bout of maltose (CD + M) or EtOH (ED + E) binge on the 11th day. Serum and liver were collected over a 24-hour light/dark (LD) cycle at Zeitgeber time ZT12, ZT18, ZT0, and ZT6, and metabolomics was performed using gas chromatography-mass spectrometry. RESULTS A total of 110 metabolites were identified in liver and of those 80 were also present in serum from pathways of carbohydrates, lipids, pentose phosphate, amino acids, nucleotides, and tricarboxylic acid cycle. In the liver, 91% of metabolites displayed rhythmicity with ED + E, whereas in the serum, only 87% were rhythmic. Bioinformatics analysis identified unique metabolome patterns altered in WT CD + M, WT ED + E, Shp-/- CD + M, and Shp-/- ED + E groups. Specifically, metabolites from the nucleotide and amino acid pathway (ribose, glucose-6-phosphate, glutamic acid, aspartic acid, and sedoheptulose-7-P) were elevated in Shp-/- CD + M mice during the dark cycle, whereas metabolites including N-methylalanine, 2-hydroxybutyric acid, and 2-hydroxyglutarate were elevated in WT ED + E mice during the light cycle. The rhythmicity and abundance of other individual metabolites were also significantly altered by both control and EtOH diets. CONCLUSIONS Metabolomics provides a useful means to identify unique metabolites altered by chronic EtOH-plus-binge.
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Affiliation(s)
- Melanie Tran
- Department of Physiology and Neurobiology, Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut
| | - Zhihong Yang
- Department of Physiology and Neurobiology, Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut.,Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut
| | - Suthat Liangpunsakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.,Roudebush Veterans Administration Medical Center, Indianapolis, Indiana
| | - Li Wang
- Department of Physiology and Neurobiology, Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut.,Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut.,Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut.,School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
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162
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Early JO, Curtis AM. Immunometabolism: Is it under the eye of the clock? Semin Immunol 2016; 28:478-490. [DOI: 10.1016/j.smim.2016.10.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 02/06/2023]
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163
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Wu N, Kim KH, Zhou Y, Lee JM, Kettner NM, Mamrosh JL, Choi S, Fu L, Moore DD. Small Heterodimer Partner (NR0B2) Coordinates Nutrient Signaling and the Circadian Clock in Mice. Mol Endocrinol 2016; 30:988-95. [PMID: 27427832 PMCID: PMC5004116 DOI: 10.1210/me.2015-1295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 07/13/2016] [Indexed: 12/13/2022] Open
Abstract
Circadian rhythm regulates multiple metabolic processes and in turn is readily entrained by feeding-fasting cycles. However, the molecular mechanisms by which the peripheral clock senses nutrition availability remain largely unknown. Bile acids are under circadian control and also increase postprandially, serving as regulators of the fed state in the liver. Here, we show that nuclear receptor Small Heterodimer Partner (SHP), a regulator of bile acid metabolism, impacts the endogenous peripheral clock by directly regulating Bmal1. Bmal1-dependent gene expression is altered in Shp knockout mice, and liver clock adaptation is delayed in Shp knockout mice upon restricted feeding. These results identify SHP as a potential mediator connecting nutrient signaling with the circadian clock.
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Affiliation(s)
- Nan Wu
- Department of Molecular and Cellular Biology (N.W., K.H.K., Y.Z., J.M.L., N.M.K., J.L.M., S.C., L.F., D.D.M.) and Program in Developmental Biology (S.C.), Baylor College of Medicine, Houston, Texas 77030; and Department of Biochemistry and Cell Biology (J.M.L.), School of Medicine, Kyungpook National University, Jung-gu, Daegu 41944, Republic of Korea
| | - Kang Ho Kim
- Department of Molecular and Cellular Biology (N.W., K.H.K., Y.Z., J.M.L., N.M.K., J.L.M., S.C., L.F., D.D.M.) and Program in Developmental Biology (S.C.), Baylor College of Medicine, Houston, Texas 77030; and Department of Biochemistry and Cell Biology (J.M.L.), School of Medicine, Kyungpook National University, Jung-gu, Daegu 41944, Republic of Korea
| | - Ying Zhou
- Department of Molecular and Cellular Biology (N.W., K.H.K., Y.Z., J.M.L., N.M.K., J.L.M., S.C., L.F., D.D.M.) and Program in Developmental Biology (S.C.), Baylor College of Medicine, Houston, Texas 77030; and Department of Biochemistry and Cell Biology (J.M.L.), School of Medicine, Kyungpook National University, Jung-gu, Daegu 41944, Republic of Korea
| | - Jae Man Lee
- Department of Molecular and Cellular Biology (N.W., K.H.K., Y.Z., J.M.L., N.M.K., J.L.M., S.C., L.F., D.D.M.) and Program in Developmental Biology (S.C.), Baylor College of Medicine, Houston, Texas 77030; and Department of Biochemistry and Cell Biology (J.M.L.), School of Medicine, Kyungpook National University, Jung-gu, Daegu 41944, Republic of Korea
| | - Nicole M Kettner
- Department of Molecular and Cellular Biology (N.W., K.H.K., Y.Z., J.M.L., N.M.K., J.L.M., S.C., L.F., D.D.M.) and Program in Developmental Biology (S.C.), Baylor College of Medicine, Houston, Texas 77030; and Department of Biochemistry and Cell Biology (J.M.L.), School of Medicine, Kyungpook National University, Jung-gu, Daegu 41944, Republic of Korea
| | - Jennifer L Mamrosh
- Department of Molecular and Cellular Biology (N.W., K.H.K., Y.Z., J.M.L., N.M.K., J.L.M., S.C., L.F., D.D.M.) and Program in Developmental Biology (S.C.), Baylor College of Medicine, Houston, Texas 77030; and Department of Biochemistry and Cell Biology (J.M.L.), School of Medicine, Kyungpook National University, Jung-gu, Daegu 41944, Republic of Korea
| | - Sungwoo Choi
- Department of Molecular and Cellular Biology (N.W., K.H.K., Y.Z., J.M.L., N.M.K., J.L.M., S.C., L.F., D.D.M.) and Program in Developmental Biology (S.C.), Baylor College of Medicine, Houston, Texas 77030; and Department of Biochemistry and Cell Biology (J.M.L.), School of Medicine, Kyungpook National University, Jung-gu, Daegu 41944, Republic of Korea
| | - Loning Fu
- Department of Molecular and Cellular Biology (N.W., K.H.K., Y.Z., J.M.L., N.M.K., J.L.M., S.C., L.F., D.D.M.) and Program in Developmental Biology (S.C.), Baylor College of Medicine, Houston, Texas 77030; and Department of Biochemistry and Cell Biology (J.M.L.), School of Medicine, Kyungpook National University, Jung-gu, Daegu 41944, Republic of Korea
| | - David D Moore
- Department of Molecular and Cellular Biology (N.W., K.H.K., Y.Z., J.M.L., N.M.K., J.L.M., S.C., L.F., D.D.M.) and Program in Developmental Biology (S.C.), Baylor College of Medicine, Houston, Texas 77030; and Department of Biochemistry and Cell Biology (J.M.L.), School of Medicine, Kyungpook National University, Jung-gu, Daegu 41944, Republic of Korea
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164
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Souza-Smith FM, Lang CH, Nagy LE, Bailey SM, Parsons LH, Murray GJ. Physiological processes underlying organ injury in alcohol abuse. Am J Physiol Endocrinol Metab 2016; 311:E605-19. [PMID: 27436613 PMCID: PMC5142006 DOI: 10.1152/ajpendo.00270.2016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 02/07/2023]
Abstract
This review summarizes the American Physiological Society (APS) Presidential Symposium 1 entitled "Physiological Processes Underlying Organ Injury in Alcohol Abuse" at the 2016 Experimental Biology meeting. The symposium was organized by Dr. Patricia Molina, past president of the APS, was held on April 3 at the Convention Center in San Diego, CA, and was funded by the National Institute on Alcohol Abuse and Alcoholism. The "Physiological Processes Underlying Organ Injury in Alcohol Abuse Symposium" assembled experts and leaders in the field and served as a platform to discuss and share knowledge on the latest developments and scientific advances on the mechanisms underlying organ injury in alcohol abuse. This symposium provided unique, interdisciplinary alcohol research, including several organs, liver, muscle, adipose, and brain, affected by excessive alcohol use.
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Affiliation(s)
- Flavia M Souza-Smith
- Department of Physiology, Louisiana State University Health Science Center, New Orleans, Louisiana;
| | - Charles H Lang
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Laura E Nagy
- Department of Pathobiology, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio
| | - Shannon M Bailey
- Department of Pathology, University of Alabama, Birmingham, Alabama
| | | | - Gary J Murray
- National Institute on Alcohol Abuse and Alcoholism, Bethesda, Maryland
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165
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Jaeger C, Tischkau SA. Role of Aryl Hydrocarbon Receptor in Circadian Clock Disruption and Metabolic Dysfunction. ENVIRONMENTAL HEALTH INSIGHTS 2016; 10:133-141. [PMID: 27559298 PMCID: PMC4990151 DOI: 10.4137/ehi.s38343] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 06/01/2023]
Abstract
The prevalence of metabolic syndrome, a clustering of three or more risk factors that include abdominal obesity, increased blood pressure, and high levels of glucose, triglycerides, and high-density lipoproteins, has reached dangerous and costly levels worldwide. Increases in morbidity and mortality result from a combination of factors that promote altered glucose metabolism, insulin resistance, and metabolic dysfunction. Although diet and exercise are commonly touted as important determinants in the development of metabolic dysfunction, other environmental factors, including circadian clock disruption and activation of the aryl hydrocarbon receptor (AhR) by dietary or other environmental sources, must also be considered. AhR binds a range of ligands, which prompts protein-protein interactions with other Per-Arnt-Sim (PAS)-domain-containing proteins and subsequent transcriptional activity. This review focuses on the reciprocal crosstalk between the activated AhR and the molecular circadian clock. AhR exhibits a rhythmic expression and time-dependent sensitivity to activation by AhR agonists. Conversely, AhR activation influences the amplitude and phase of expression of circadian clock genes, hormones, and the behavioral responses of the clock system to changes in environmental illumination. Both the clock and AhR status and activation play significant and underappreciated roles in metabolic homeostasis. This review highlights the state of knowledge regarding how AhR may act together with the circadian clock to influence energy metabolism. Understanding the variety of AhR-dependent mechanisms, including its interactions with the circadian timing system that promote metabolic dysfunction, reveals new targets of interest for maintenance of healthy metabolism.
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166
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Higashi T, Aoki K, Nagano AJ, Honjo MN, Fukuda H. Circadian Oscillation of the Lettuce Transcriptome under Constant Light and Light-Dark Conditions. FRONTIERS IN PLANT SCIENCE 2016; 7:1114. [PMID: 27512400 PMCID: PMC4961695 DOI: 10.3389/fpls.2016.01114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/13/2016] [Indexed: 05/23/2023]
Abstract
Although, the circadian clock is a universal biological system in plants and it orchestrates important role of plant production such as photosynthesis, floral induction and growth, there are few such studies on cultivated species. Lettuce is one major cultivated species for both open culture and plant factories and there is little information concerning its circadian clock system. In addition, most of the relevant genes have not been identified. In this study, we detected circadian oscillation in the lettuce transcriptome using time-course RNA sequencing (RNA-Seq) data. Constant light (LL) and light-dark (LD) conditions were used to detect circadian oscillation because the circadian clock has some basic properties: one is self-sustaining oscillation under constant light and another is entrainment to environmental cycles such as light and temperature. In the results, 215 contigs were detected as common oscillating contigs under both LL and LD conditions. The 215 common oscillating contigs included clock gene-like contigs CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)-like, TOC1 (TIMING OF CAB EXPRESSION 1)-like and LHY (LATE ELONGATED HYPOCOTYL)-like, and their expression patterns were similar to those of Arabidopsis. Functional enrichment analysis by GO (gene ontology) Slim and GO Fat showed that the GO terms of response to light stimulus, response to stress, photosynthesis and circadian rhythms were enriched in the 215 common oscillating contigs and these terms were actually regulated by circadian clocks in plants. The 215 common oscillating contigs can be used to evaluate whether the gene expression pattern related to photosynthesis and optical response performs normally in lettuce.
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Affiliation(s)
- Takanobu Higashi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture UniversitySakai, Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture UniversitySakai, Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku UniversityOtsu, Japan
- Core Research for Evolutional Science and Technology – Japan Science and Technology AgencyKawaguchi, Japan
- Center for Ecological Research, Kyoto UniversityOtsu, Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto UniversityOtsu, Japan
| | - Hirokazu Fukuda
- Graduate School of Engineering, Osaka Prefecture UniversitySakai, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology AgencyKawaguchi, Japan
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167
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Kennedy AD, Miller MJ, Beebe K, Wulff JE, Evans AM, Miller LAD, Sutton VR, Sun Q, Elsea SH. Metabolomic Profiling of Human Urine as a Screen for Multiple Inborn Errors of Metabolism. Genet Test Mol Biomarkers 2016; 20:485-95. [PMID: 27448163 DOI: 10.1089/gtmb.2015.0291] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS We wished to determine the efficacy of using urine as an analyte to screen for a broad range of metabolic products associated with multiple different types of inborn errors of metabolism (IEMs), using an automated mass spectrometry-based assay. Urine was compared with plasma samples from a similar cohort analyzed using the same assay. Specimens were analyzed using two different commonly utilized urine normalization methods based on creatinine and osmolality, respectively. METHODS Biochemical profiles for each sample (from both affected and unaffected subjects) were obtained using a mass spectrometry-based platform and population-based statistical analyses. RESULTS We identified over 1200 biochemicals from among 100 clinical urine samples and identified clear biochemical signatures for 16 of 18 IEM diseases tested. The two diseases that did not result in clear signatures, X-linked creatine transporter deficiency and ornithine transcarbamylase deficiency, were from individuals under treatment, which masked biomarker signatures. Overall the process variability and coefficient of variation for isolating and identifying biochemicals by running technical replicates of each urine sample was 10%. CONCLUSIONS A single urine sample analyzed with our integrated metabolomic platform can identify signatures of IEMs that are traditionally identified using many different assays and multiple sample types. Creatinine and osmolality-normalized data were robust to the detection of the disorders and samples tested here.
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Affiliation(s)
| | - Marcus J Miller
- 2 Medical Genetics Laboratory, Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, Texas
| | - Kirk Beebe
- 1 Metabolon, Inc. , Durham, North Carolina
| | | | | | | | - V Reid Sutton
- 2 Medical Genetics Laboratory, Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, Texas
| | - Qin Sun
- 2 Medical Genetics Laboratory, Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, Texas
| | - Sarah H Elsea
- 2 Medical Genetics Laboratory, Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, Texas
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168
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Fleet T, Stashi E, Zhu B, Rajapakshe K, Marcelo KL, Kettner NM, Gorman BK, Coarfa C, Fu L, O'Malley BW, York B. Genetic and Environmental Models of Circadian Disruption Link SRC-2 Function to Hepatic Pathology. J Biol Rhythms 2016; 31:443-60. [PMID: 27432117 DOI: 10.1177/0748730416657921] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Circadian rhythmicity is a fundamental process that synchronizes behavioral cues with metabolic homeostasis. Disruption of daily cycles due to jet lag or shift work results in severe physiological consequences including advanced aging, metabolic syndrome, and even cancer. Our understanding of the molecular clock, which is regulated by intricate positive feedforward and negative feedback loops, has expanded to include an important metabolic transcriptional coregulator, Steroid Receptor Coactivator-2 (SRC-2), that regulates both the central clock of the suprachiasmatic nucleus (SCN) and peripheral clocks including the liver. We hypothesized that an environmental uncoupling of the light-dark phases, termed chronic circadian disruption (CCD), would lead to pathology similar to the genetic circadian disruption observed with loss of SRC-2 We found that CCD and ablation of SRC-2 in mice led to a common comorbidity of metabolic syndrome also found in humans with circadian disruption, non-alcoholic fatty liver disease (NAFLD). The combination of SRC-2(-/-) and CCD results in a more robust phenotype that correlates with human non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) gene signatures. Either CCD or SRC-2 ablation produces an advanced aging phenotype leading to increased mortality consistent with other circadian mutant mouse models. Collectively, our studies demonstrate that SRC-2 provides an essential link between the behavioral activities influenced by light cues and the metabolic homeostasis maintained by the liver.
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Affiliation(s)
- Tiffany Fleet
- Interdepartmental Department in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas
| | - Erin Stashi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Bokai Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Kathrina L Marcelo
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Nicole M Kettner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Blythe K Gorman
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas Weill Medical College, Cornell University, New York, New York
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Loning Fu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
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169
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Murakami M, Tognini P, Liu Y, Eckel-Mahan KL, Baldi P, Sassone-Corsi P. Gut microbiota directs PPARγ-driven reprogramming of the liver circadian clock by nutritional challenge. EMBO Rep 2016; 17:1292-303. [PMID: 27418314 DOI: 10.15252/embr.201642463] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/22/2016] [Indexed: 12/20/2022] Open
Abstract
The liver circadian clock is reprogrammed by nutritional challenge through the rewiring of specific transcriptional pathways. As the gut microbiota is tightly connected to host metabolism, whose coordination is governed by the circadian clock, we explored whether gut microbes influence circadian homeostasis and how they distally control the peripheral clock in the liver. Using fecal transplant procedures we reveal that, in response to high-fat diet, the gut microbiota drives PPARγ-mediated activation of newly oscillatory transcriptional programs in the liver. Moreover, antibiotics treatment prevents PPARγ-driven transcription in the liver, underscoring the essential role of gut microbes in clock reprogramming and hepatic circadian homeostasis. Thus, a specific molecular signature characterizes the influence of the gut microbiome in the liver, leading to the transcriptional rewiring of hepatic metabolism.
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Affiliation(s)
- Mari Murakami
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, U904 INSERM, University of California Irvine, Irvine, CA, USA
| | - Paola Tognini
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, U904 INSERM, University of California Irvine, Irvine, CA, USA
| | - Yu Liu
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, Irvine, CA, USA
| | - Kristin L Eckel-Mahan
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, U904 INSERM, University of California Irvine, Irvine, CA, USA Center for Metabolic and Degenerative Diseases, Institute of Molecular Medicine, University of Texas Health Sciences Center, Houston, TX, USA
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, Irvine, CA, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, U904 INSERM, University of California Irvine, Irvine, CA, USA
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170
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Altman BJ. Cancer Clocks Out for Lunch: Disruption of Circadian Rhythm and Metabolic Oscillation in Cancer. Front Cell Dev Biol 2016; 4:62. [PMID: 27500134 PMCID: PMC4971383 DOI: 10.3389/fcell.2016.00062] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 06/08/2016] [Indexed: 01/08/2023] Open
Abstract
Circadian rhythms are 24-h oscillations present in most eukaryotes and many prokaryotes that synchronize activity to the day-night cycle. They are an essential feature of organismal and cell physiology that coordinate many of the metabolic, biosynthetic, and signal transduction pathways studied in biology. The molecular mechanism of circadian rhythm is controlled both by signal transduction and gene transcription as well as by metabolic feedback. The role of circadian rhythm in cancer cell development and survival is still not well understood, but as will be discussed in this Review, accumulated research suggests that circadian rhythm may be altered or disrupted in many human cancers downstream of common oncogenic alterations. Thus, a complete understanding of the genetic and metabolic alterations in cancer must take potential circadian rhythm perturbations into account, as this disruption itself will influence how gene expression and metabolism are altered in the cancer cell compared to its non-transformed neighbor. It will be important to better understand these circadian changes in both normal and cancer cell physiology to potentially design treatment modalities to exploit this insight.
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Affiliation(s)
- Brian J Altman
- Abramson Family Cancer Research InstitutePhiladelphia, PA, USA; Abramson Cancer CenterPhiladelphia, PA, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of MedicinePhiladelphia, PA, USA
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171
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Beale AD, Whitmore D, Moran D. Life in a dark biosphere: a review of circadian physiology in "arrhythmic" environments. J Comp Physiol B 2016; 186:947-968. [PMID: 27263116 PMCID: PMC5090016 DOI: 10.1007/s00360-016-1000-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 05/05/2016] [Accepted: 05/17/2016] [Indexed: 11/25/2022]
Abstract
Most of the life with which humans interact is exposed to highly rhythmic and extremely predictable changes in illumination that occur with the daily events of sunrise and sunset. However, while the influence of the sun feels omnipotent to surface dwellers such as ourselves, life on earth is dominated, in terms of biomass, by organisms isolated from the direct effects of the sun. A limited understanding of what life is like away from the sun can be inferred from our knowledge of physiology and ecology in the light biosphere, but a full understanding can only be gained by studying animals from the dark biosphere, both in the laboratory and in their natural habitats. One of the least understood aspects of life in the dark biosphere is the rhythmicity of physiology and what it means to live in an environment of low or no rhythmicity. Here we describe methods that may be used to understand rhythmic physiology in the dark and summarise some of the studies of rhythmic physiology in "arrhythmic" environments, such as the poles, deep sea and caves. We review what can be understood about the adaptive value of rhythmic physiology on the Earth's surface from studies of animals from arrhythmic environments and what role a circadian clock may play in the dark.
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Affiliation(s)
- Andrew David Beale
- Department of Cell and Developmental Biology, Centre for Cell and Molecular Dynamics, University College London, 21 University Street, London, WC1E 6BT, UK.
| | - David Whitmore
- Department of Cell and Developmental Biology, Centre for Cell and Molecular Dynamics, University College London, 21 University Street, London, WC1E 6BT, UK
| | - Damian Moran
- Plant and Food Research, Seafood Technologies Group, Nelson, New Zealand.
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172
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Brown SA. Circadian Metabolism: From Mechanisms to Metabolomics and Medicine. Trends Endocrinol Metab 2016; 27:415-426. [PMID: 27113082 DOI: 10.1016/j.tem.2016.03.015] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/22/2016] [Accepted: 03/25/2016] [Indexed: 12/28/2022]
Abstract
The circadian clock directs nearly all aspects of diurnal physiology, including metabolism. Current research identifies several major axes by which it exerts these effects, including systemic signals as well as direct control of cellular processes by local clocks. This redundant network can transmit metabolic and timing information bidirectionally for optimal synchrony of metabolic processes. Recent advances in cellular profiling and metabolomics technologies have yielded unprecedented insights into the mechanisms behind this control. They have also helped to illuminate individual variation in these mechanisms that could prove important in personalized therapy for metabolic disease. Finally, these technologies have provided platforms with which to screen for the first potential drugs affecting clock-modulated metabolic function.
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Affiliation(s)
- Steven A Brown
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, 190 Winterthurerstrasse, 8057 Zürich, Switzerland.
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173
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Abstract
The circadian system temporally coordinates daily rhythms in feeding behaviour and energy metabolism. The objective of the present paper is to review the mechanisms that underlie circadian regulation of lipid metabolic pathways. Circadian rhythms in behaviour and physiology are generated by master clock neurons in the suprachiasmatic nucleus (SCN). The SCN and its efferent targets in the hypothalamus integrate light and feeding signals to entrain behavioural rhythms as well as clock cells located in peripheral tissues, including the liver, adipose tissue and muscle. Circadian rhythms in gene expression are regulated at the cellular level by a molecular clock comprising a core set of clock genes/proteins. In peripheral tissues, hundreds of genes involved in lipid biosynthesis and fatty acid oxidation are rhythmically activated and repressed by clock proteins, hence providing a direct mechanism for circadian regulation of lipids. Disruption of clock gene function results in abnormal metabolic phenotypes and impaired lipid absorption, demonstrating that the circadian system is essential for normal energy metabolism. The composition and timing of meals influence diurnal regulation of metabolic pathways, with food intake during the usual rest phase associated with dysregulation of lipid metabolism. Recent studies using metabolomics and lipidomics platforms have shown that hundreds of lipid species are circadian-regulated in human plasma, including but not limited to fatty acids, TAG, glycerophospholipids, sterol lipids and sphingolipids. In future work, these lipid profiling approaches can be used to understand better the interaction between diet, mealtimes and circadian rhythms on lipid metabolism and risk for obesity and metabolic diseases.
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174
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Abstract
The human circadian system anticipates and adapts to daily environmental changes to optimise behaviour according to time of day and temporally partitions incompatible physiological processes. At the helm of this system is a master clock in the suprachiasmatic nuclei (SCN) of the anterior hypothalamus. The SCN are primarily synchronised to the 24-h day by the light/dark cycle; however, feeding/fasting cycles are the primary time cues for clocks in peripheral tissues. Aligning feeding/fasting cycles with clock-regulated metabolic changes optimises metabolism, and studies of other animals suggest that feeding at inappropriate times disrupts circadian system organisation, and thereby contributes to adverse metabolic consequences and chronic disease development. 'High-fat diets' (HFD) produce particularly deleterious effects on circadian system organisation in rodents by blunting feeding/fasting cycles. Time-of-day-restricted feeding, where food availability is restricted to a period of several hours, offsets many adverse consequences of HFD in these animals; however, further evidence is required to assess whether the same is true in humans. Several nutritional compounds have robust effects on the circadian system. Caffeine, for example, can speed synchronisation to new time zones after jetlag. An appreciation of the circadian system has many implications for nutritional science and may ultimately help reduce the burden of chronic diseases.
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175
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Zhu Z, Hua B, Xu L, Yuan G, Li E, Li X, Sun N, Yan Z, Lu C, Qian R. CLOCK promotes 3T3-L1 cell proliferation via Wnt signaling. IUBMB Life 2016; 68:557-68. [DOI: 10.1002/iub.1512] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Zhu Zhu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Fudan University; Shanghai China
| | - Bingxuan Hua
- Department of Orthopedics; Zhongshan Hospital, Fudan University; Shanghai China
| | - Lirong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Fudan University; Shanghai China
| | - Gongsheng Yuan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Fudan University; Shanghai China
| | - Ermin Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Fudan University; Shanghai China
| | - Xiaobo Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Fudan University; Shanghai China
| | - Ning Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Fudan University; Shanghai China
| | - Zuoqin Yan
- Department of Orthopedics; Zhongshan Hospital, Fudan University; Shanghai China
| | - Chao Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Fudan University; Shanghai China
| | - Ruizhe Qian
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Fudan University; Shanghai China
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176
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He B, Nohara K, Park N, Park YS, Guillory B, Zhao Z, Garcia JM, Koike N, Lee CC, Takahashi JS, Yoo SH, Chen Z. The Small Molecule Nobiletin Targets the Molecular Oscillator to Enhance Circadian Rhythms and Protect against Metabolic Syndrome. Cell Metab 2016; 23:610-21. [PMID: 27076076 PMCID: PMC4832569 DOI: 10.1016/j.cmet.2016.03.007] [Citation(s) in RCA: 353] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/01/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023]
Abstract
Dysregulation of circadian rhythms is associated with metabolic dysfunction, yet it is unclear whether enhancing clock function can ameliorate metabolic disorders. In an unbiased chemical screen using fibroblasts expressing PER2::Luc, we identified Nobiletin (NOB), a natural polymethoxylated flavone, as a clock amplitude-enhancing small molecule. When administered to diet-induced obese (DIO) mice, NOB strongly counteracted metabolic syndrome and augmented energy expenditure and locomotor activity in a Clock gene-dependent manner. In db/db mutant mice, the clock is also required for the mitigating effects of NOB on metabolic disorders. In DIO mouse liver, NOB enhanced clock protein levels and elicited pronounced gene expression remodeling. We identified retinoid acid receptor-related orphan receptors as direct targets of NOB, revealing a pharmacological intervention that enhances circadian rhythms to combat metabolic disease via the circadian gene network.
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Affiliation(s)
- Baokun He
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Kazunari Nohara
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Noheon Park
- Department of Neuroscience, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yong-Sung Park
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Bobby Guillory
- Division of Endocrinology, Diabetes and Metabolism, MCL, Center for Translational Research in Inflammatory Diseases, Michael E. DeBakey Veterans Affairs Medical Center, and Department of Medicine, and Molecular and Cell Biology, Dan L. Duncan Cancer Center, Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhaoyang Zhao
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Jose M Garcia
- Division of Endocrinology, Diabetes and Metabolism, MCL, Center for Translational Research in Inflammatory Diseases, Michael E. DeBakey Veterans Affairs Medical Center, and Department of Medicine, and Molecular and Cell Biology, Dan L. Duncan Cancer Center, Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nobuya Koike
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Cheng Chi Lee
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Joseph S Takahashi
- Department of Neuroscience, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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177
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Nam D, Yechoor VK, Ma K. Molecular clock integration of brown adipose tissue formation and function. Adipocyte 2016; 5:243-50. [PMID: 27385482 PMCID: PMC4916866 DOI: 10.1080/21623945.2015.1082015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/31/2015] [Accepted: 08/06/2015] [Indexed: 12/14/2022] Open
Abstract
The circadian clock is an essential time-keeping mechanism that entrains internal physiology to environmental cues. Despite the well-established link between the molecular clock and metabolic homeostasis, an intimate interplay between the clock machinery and the metabolically active brown adipose tissue (BAT) is only emerging. Recently, we came to appreciate that the formation and metabolic functions of BAT, a key organ for body temperature maintenance, are under an orchestrated circadian clock regulation. Two complementary studies from our group uncover that the cell-intrinsic clock machinery exerts concerted control of brown adipogenesis with consequent impacts on adaptive thermogenesis, which adds a previously unappreciated temporal dimension to the regulatory mechanisms governing BAT development and function. The essential clock transcriptional activator, Bmal1, suppresses adipocyte lineage commitment and differentiation, whereas the clock repressor, Rev-erbα, promotes these processes. This newly discovered temporal mechanism in fine-tuning BAT thermogenic capacity may enable energy utilization and body temperature regulation in accordance with external timing signals during development and functional recruitment. Given the important role of BAT in whole-body metabolic homeostasis, pharmacological interventions targeting the BAT-modulatory activities of the clock circuit may offer new avenues for the prevention and treatment of metabolic disorders, particularly those associated with circadian dysregulation.
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Affiliation(s)
- Deokhwa Nam
- Center for Diabetes Research, Department of Medicine, The Methodist Hospital Research Institute, Houston, TX, USA
| | - Vijay K. Yechoor
- Diabetes and Endocrinology Research Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Ke Ma
- Center for Diabetes Research, Department of Medicine, The Methodist Hospital Research Institute, Houston, TX, USA
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178
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Johnston JD, Ordovás JM, Scheer FA, Turek FW. Circadian Rhythms, Metabolism, and Chrononutrition in Rodents and Humans. Adv Nutr 2016; 7:399-406. [PMID: 26980824 PMCID: PMC4785478 DOI: 10.3945/an.115.010777] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chrononutrition is an emerging discipline that builds on the intimate relation between endogenous circadian (24-h) rhythms and metabolism. Circadian regulation of metabolic function can be observed from the level of intracellular biochemistry to whole-organism physiology and even postprandial responses. Recent work has elucidated the metabolic roles of circadian clocks in key metabolic tissues, including liver, pancreas, white adipose, and skeletal muscle. For example, tissue-specific clock disruption in a single peripheral organ can cause obesity or disruption of whole-organism glucose homeostasis. This review explains mechanistic insights gained from transgenic animal studies and how these data are being translated into the study of human genetics and physiology. The principles of chrononutrition have already been demonstrated to improve human weight loss and are likely to benefit the health of individuals with metabolic disease, as well as of the general population.
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Affiliation(s)
| | - José M Ordovás
- Tufts University, Boston, MA;,Madrid Institutes of Advanced Studies-Food, Madrid, Spain
| | - Frank A Scheer
- Brigham and Women's Hospital, Boston, MA;,Harvard Medical School, Boston, MA; and
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179
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Feillet C, Guérin S, Lonchampt M, Dacquet C, Gustafsson JÅ, Delaunay F, Teboul M. Sexual Dimorphism in Circadian Physiology Is Altered in LXRα Deficient Mice. PLoS One 2016; 11:e0150665. [PMID: 26938655 PMCID: PMC4777295 DOI: 10.1371/journal.pone.0150665] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/16/2016] [Indexed: 11/28/2022] Open
Abstract
The mammalian circadian timing system coordinates key molecular, cellular and physiological processes along the 24-h cycle. Accumulating evidence suggests that many clock-controlled processes display a sexual dimorphism. In mammals this is well exemplified by the difference between the male and female circadian patterns of glucocorticoid hormone secretion and clock gene expression. Here we show that the non-circadian nuclear receptor and metabolic sensor Liver X Receptor alpha (LXRα) which is known to regulate glucocorticoid production in mice modulates the sex specific circadian pattern of plasma corticosterone. Lxrα-/- males display a blunted corticosterone profile while females show higher amplitude as compared to wild type animals. Wild type males are significantly slower than females to resynchronize their locomotor activity rhythm after an 8 h phase advance but this difference is abrogated in Lxrα-/- males which display a female-like phenotype. We also show that circadian expression patterns of liver 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) and Phosphoenolpyruvate carboxykinase (Pepck) differ between sexes and are differentially altered in Lxrα-/- animals. These changes are associated with a damped profile of plasma glucose oscillation in males but not in females. Sex specific alteration of the insulin and leptin circadian profiles were observed in Lxα-/- females and could be explained by the change in corticosterone profile. Together this data indicates that LXRα is a determinant of sexually dimorphic circadian patterns of key physiological parameters. The discovery of this unanticipated role for LXRα in circadian physiology underscores the importance of addressing sex differences in chronobiology studies and future LXRα targeted therapies.
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Affiliation(s)
- Céline Feillet
- University Nice Sophia Antipolis, Institute of Biology Valrose, 06108, Nice, France
- CNRS UMR 7277, 06108, Nice, France
- INSERM UMR 1091, 06108, Nice, France
| | - Sophie Guérin
- University Nice Sophia Antipolis, Institute of Biology Valrose, 06108, Nice, France
- CNRS UMR 7277, 06108, Nice, France
- INSERM UMR 1091, 06108, Nice, France
| | - Michel Lonchampt
- Metabolic Diseases Research, Institut de Recherches Servier, 92284, Suresnes, France
| | - Catherine Dacquet
- Metabolic Diseases Research, Institut de Recherches Servier, 92284, Suresnes, France
| | - Jan-Åke Gustafsson
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77204–5056, United States of America
| | - Franck Delaunay
- University Nice Sophia Antipolis, Institute of Biology Valrose, 06108, Nice, France
- CNRS UMR 7277, 06108, Nice, France
- INSERM UMR 1091, 06108, Nice, France
| | - Michèle Teboul
- University Nice Sophia Antipolis, Institute of Biology Valrose, 06108, Nice, France
- CNRS UMR 7277, 06108, Nice, France
- INSERM UMR 1091, 06108, Nice, France
- * E-mail:
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180
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Germain D. Sirtuins and the Estrogen Receptor as Regulators of the Mammalian Mitochondrial UPR in Cancer and Aging. Adv Cancer Res 2016; 130:211-56. [PMID: 27037754 DOI: 10.1016/bs.acr.2016.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
By being both the source of ATP and the mediator of apoptosis, the mitochondria are key regulators of cellular life and death. Not surprisingly alterations in the biology of the mitochondria have implications in a wide array of diseases including cancer and age-related diseases such as neurodegeneration. To protect the mitochondria against damage the mitochondrial unfolded protein response (UPR(mt)) orchestrates several pathways, including the protein quality controls, the antioxidant machinery, oxidative phosphorylation, mitophagy, and mitochondrial biogenesis. While several reports have implicated an array of transcription factors in the UPR(mt), most of the focus has been on studies of Caenorhabditis elegans, which led to the identification of ATFS-1, for which the mammalian homolog remains unknown. Meanwhile, there are studies which link the UPR(mt) to sirtuins and transcription factors of the Foxo family in both C. elegans and mammalian cells but those have been largely overlooked. This review aims at emphasizing the potential importance of these studies by building on the large body of literature supporting the key role of the sirtuins in the maintenance of the integrity of the mitochondria in both cancer and aging. Further, the estrogen receptor alpha (ERα) and beta (ERβ) are known to confer protection against mitochondrial stress, and at least ERα has been linked to the UPR(mt). Considering the difference in gender longevity, this chapter also includes a discussion of the link between the ERα and ERβ and the mitochondria in cancer and aging.
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Affiliation(s)
- D Germain
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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181
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Reinke H, Asher G. Circadian Clock Control of Liver Metabolic Functions. Gastroenterology 2016; 150:574-80. [PMID: 26657326 DOI: 10.1053/j.gastro.2015.11.043] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 02/08/2023]
Abstract
The circadian clock is an endogenous biological timekeeping system that synchronizes physiology and behavior to day/night cycles. A wide variety of processes throughout the entire gastrointestinal tract and notably the liver appear to be under circadian control. These include various metabolic functions such as nutrient uptake, processing, and detoxification, which align organ function to cycle with nutrient supply and demand. Remarkably, genetic or environmental disruption of the circadian clock can cause metabolic diseases or exacerbate pathological states. In addition, modern lifestyles force more and more people worldwide into asynchrony between the external time and their circadian clock, resulting in a constant state of social jetlag. Recent evidence indicates that interactions between altered energy metabolism and disruptions in the circadian clock create a downward spiral that can lead to diabetes and other metabolic diseases. In this review, we provide an overview of rhythmic processes in the liver and highlight the functions of circadian clock genes under physiological and pathological conditions; we focus on their roles in regulation of hepatic glucose as well as lipid and bile acid metabolism and detoxification and their potential effects on the development of fatty liver and nonalcoholic steatohepatitis.
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Affiliation(s)
- Hans Reinke
- Medical Faculty, Institute of Clinical Chemistry and Laboratory Diagnostics, University of Düsseldorf, Düsseldorf, Germany; IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany.
| | - Gad Asher
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
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182
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Nutrigenetics and Nutrimiromics of the Circadian System: The Time for Human Health. Int J Mol Sci 2016; 17:299. [PMID: 26927084 PMCID: PMC4813163 DOI: 10.3390/ijms17030299] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/08/2016] [Accepted: 02/16/2016] [Indexed: 12/15/2022] Open
Abstract
Even though the rhythmic oscillations of life have long been known, the precise molecular mechanisms of the biological clock are only recently being explored. Circadian rhythms are found in virtually all organisms and affect our lives. Thus, it is not surprising that the correct running of this clock is essential for cellular functions and health. The circadian system is composed of an intricate network of genes interwined in an intrincated transcriptional/translational feedback loop. The precise oscillation of this clock is controlled by the circadian genes that, in turn, regulate the circadian oscillations of many cellular pathways. Consequently, variations in these genes have been associated with human diseases and metabolic disorders. From a nutrigenetics point of view, some of these variations modify the individual response to the diet and interact with nutrients to modulate such response. This circadian feedback loop is also epigenetically modulated. Among the epigenetic mechanisms that control circadian rhythms, microRNAs are the least studied ones. In this paper, we review the variants of circadian-related genes associated to human disease and nutritional response and discuss the current knowledge about circadian microRNAs. Accumulated evidence on the genetics and epigenetics of the circadian system points to important implications of chronotherapy in the clinical practice, not only in terms of pharmacotherapy, but also for dietary interventions. However, interventional studies (especially nutritional trials) that include chronotherapy are scarce. Given the importance of chronobiology in human health such studies are warranted in the near future.
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183
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Abstract
Our understanding of the molecular underpinnings of the mammalian circadian oscillator and its tight connection to physiology has progressed tremendously during the past decades. The liver is considered the prototypic experimental model tissue for circadian research in peripheral organs. Studies on liver clocks have been highly productive and yielded information about widely different aspects of circadian biology. The liver, as one of the largest organs in the body, has often been used for the identification of core clock and auxiliary clock components, for example, by biochemical purifications. Because the liver is also a major metabolic hub, studies addressing the interplay between circadian clocks and metabolism have been insightful. In addition, the use of liver-specific loss-of-function models for clock components highlighted not only specific physiological roles of the hepatic clock but also its interplay with systemic cues and oscillators in other organs. Recently, technological advances in omics approaches have been successfully applied on the liver, providing a comprehensive depiction of pervasive circadian control of gene expression and protein and metabolite accumulation. In this review, we chose to illuminate specific examples that demonstrate how different experimental approaches--namely, biochemical, metabolic, genetic, and omics methodologies--have advanced our knowledge regarding circadian liver biology and chronobiology in general.
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Affiliation(s)
- Ziv Zwighaft
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Hans Reinke
- University of Düsseldorf, Medical Faculty, Institute of Clinical Chemistry and Laboratory Diagnostics, Düsseldorf, Germany IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Gad Asher
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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184
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Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals. Sci Rep 2016; 6:20127. [PMID: 26879573 PMCID: PMC4754633 DOI: 10.1038/srep20127] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/21/2015] [Indexed: 12/12/2022] Open
Abstract
The liver is a key organ of metabolic homeostasis with functions that oscillate in response to food intake. Although liver and gut microbiome crosstalk has been reported, microbiome-mediated effects on peripheral circadian clocks and their output genes are less well known. Here, we report that germ-free (GF) mice display altered daily oscillation of clock gene expression with a concomitant change in the expression of clock output regulators. Mice exposed to microbes typically exhibit characterized activities of nuclear receptors, some of which (PPARα, LXRβ) regulate specific liver gene expression networks, but these activities are profoundly changed in GF mice. These alterations in microbiome-sensitive gene expression patterns are associated with daily alterations in lipid, glucose, and xenobiotic metabolism, protein turnover, and redox balance, as revealed by hepatic metabolome analyses. Moreover, at the systemic level, daily changes in the abundance of biomarkers such as HDL cholesterol, free fatty acids, FGF21, bilirubin, and lactate depend on the microbiome. Altogether, our results indicate that the microbiome is required for integration of liver clock oscillations that tune output activators and their effectors, thereby regulating metabolic gene expression for optimal liver function.
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185
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Ray S, Reddy AB. Cross-talk between circadian clocks, sleep-wake cycles, and metabolic networks: Dispelling the darkness. Bioessays 2016; 38:394-405. [PMID: 26866932 PMCID: PMC4817226 DOI: 10.1002/bies.201500056] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Integration of knowledge concerning circadian rhythms, metabolic networks, and sleep‐wake cycles is imperative for unraveling the mysteries of biological cycles and their underlying mechanisms. During the last decade, enormous progress in circadian biology research has provided a plethora of new insights into the molecular architecture of circadian clocks. However, the recent identification of autonomous redox oscillations in cells has expanded our view of the clockwork beyond conventional transcription/translation feedback loop models, which have been dominant since the first circadian period mutants were identified in fruit fly. Consequently, non‐transcriptional timekeeping mechanisms have been proposed, and the antioxidant peroxiredoxin proteins have been identified as conserved markers for 24‐hour rhythms. Here, we review recent advances in our understanding of interdependencies amongst circadian rhythms, sleep homeostasis, redox cycles, and other cellular metabolic networks. We speculate that systems‐level investigations implementing integrated multi‐omics approaches could provide novel mechanistic insights into the connectivity between daily cycles and metabolic systems.
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Affiliation(s)
- Sandipan Ray
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, National Institutes of Health Biomedical Research Centre, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Akhilesh B Reddy
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, National Institutes of Health Biomedical Research Centre, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
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186
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Affiliation(s)
- Tracy A. Bedrosian
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Laura K. Fonken
- Department of Psychology and Neuroscience, University of Colorado, Boulder, Colorado 80309
| | - Randy J. Nelson
- Department of Neuroscience and Behavioral Neuroendocrinology Group, The Ohio State University, Columbus, Ohio 43210;
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187
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Circadian control of oscillations in mitochondrial rate-limiting enzymes and nutrient utilization by PERIOD proteins. Proc Natl Acad Sci U S A 2016; 113:E1673-82. [PMID: 26862173 DOI: 10.1073/pnas.1519650113] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mitochondria are major suppliers of cellular energy through nutrients oxidation. Little is known about the mechanisms that enable mitochondria to cope with changes in nutrient supply and energy demand that naturally occur throughout the day. To address this question, we applied MS-based quantitative proteomics on isolated mitochondria from mice killed throughout the day and identified extensive oscillations in the mitochondrial proteome. Remarkably, the majority of cycling mitochondrial proteins peaked during the early light phase. We found that rate-limiting mitochondrial enzymes that process lipids and carbohydrates accumulate in a diurnal manner and are dependent on the clock proteins PER1/2. In this conjuncture, we uncovered daily oscillations in mitochondrial respiration that peak during different times of the day in response to different nutrients. Notably, the diurnal regulation of mitochondrial respiration was blunted in mice lacking PER1/2 or on a high-fat diet. We propose that PERIOD proteins optimize mitochondrial metabolism to daily changes in energy supply/demand and thereby, serve as a rheostat for mitochondrial nutrient utilization.
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188
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Lück S, Westermark PO. Circadian mRNA expression: insights from modeling and transcriptomics. Cell Mol Life Sci 2016; 73:497-521. [PMID: 26496725 PMCID: PMC11108398 DOI: 10.1007/s00018-015-2072-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
Abstract
Circadian clocks synchronize organisms to the 24 h rhythms of the environment. These clocks persist under constant conditions, have their origin at the cellular level, and produce an output of rhythmic mRNA expression affecting thousands of transcripts in many mammalian cell types. Here, we review the charting of circadian output rhythms in mRNA expression, focusing on mammals. We emphasize the challenges in statistics, interpretation, and quantitative descriptions that such investigations have faced and continue to face, and outline remaining outstanding questions.
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Affiliation(s)
- Sarah Lück
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany
| | - Pål O Westermark
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany.
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189
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Interdependence of nutrient metabolism and the circadian clock system: Importance for metabolic health. Mol Metab 2016; 5:133-152. [PMID: 26977390 PMCID: PMC4770266 DOI: 10.1016/j.molmet.2015.12.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 12/15/2015] [Accepted: 12/29/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND While additional research is needed, a number of large epidemiological studies show an association between circadian disruption and metabolic disorders. Specifically, obesity, insulin resistance, cardiovascular disease, and other signs of metabolic syndrome all have been linked to circadian disruption in humans. Studies in other species support this association and generally reveal that feeding that is not in phase with the external light/dark cycle, as often occurs with night or rotating shift workers, is disadvantageous in terms of energy balance. As food is a strong driver of circadian rhythms in the periphery, understanding how nutrient metabolism drives clocks across the body is important for dissecting out why circadian misalignment may produce such metabolic effects. A number of circadian clock proteins as well as their accessory proteins (such as nuclear receptors) are highly sensitive to nutrient metabolism. Macronutrients and micronutrients can function as zeitgebers for the clock in a tissue-specific way and can thus impair synchrony between clocks across the body, or potentially restore synchrony in the case of circadian misalignment. Circadian nuclear receptors are particularly sensitive to nutrient metabolism and can alter tissue-specific rhythms in response to changes in the diet. Finally, SNPs in human clock genes appear to be correlated with diet-specific responses and along with chronotype eventually may provide valuable information from a clinical perspective on how to use diet and nutrition to treat metabolic disorders. SCOPE OF REVIEW This article presents a background of the circadian clock components and their interrelated metabolic and transcriptional feedback loops, followed by a review of some recent studies in humans and rodents that address the effects of nutrient metabolism on the circadian clock and vice versa. We focus on studies in which results suggest that nutrients provide an opportunity to restore or, alternatively, can destroy synchrony between peripheral clocks and the central pacemaker in the brain as well as between peripheral clocks themselves. In addition, we review several studies looking at clock gene SNPs in humans and the metabolic phenotypes or tendencies associated with particular clock gene mutations. MAJOR CONCLUSIONS Targeted use of specific nutrients based on chronotype has the potential for immense clinical utility in the future. Macronutrients and micronutrients have the ability to function as zeitgebers for the clock by activating or modulating specific clock proteins or accessory proteins (such as nuclear receptors). Circadian clock control by nutrients can be tissue-specific. With a better understanding of the mechanisms that support nutrient-induced circadian control in specific tissues, human chronotype and SNP information might eventually be used to tailor nutritional regimens for metabolic disease treatment and thus be an important part of personalized medicine's future.
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190
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Bromage TG, Idaghdour Y, Lacruz RS, Crenshaw TD, Ovsiy O, Rotter B, Hoffmeier K, Schrenk F. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth. PLoS One 2016; 11:e0145919. [PMID: 26735517 PMCID: PMC4703299 DOI: 10.1371/journal.pone.0145919] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/10/2015] [Indexed: 12/29/2022] Open
Abstract
The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien) chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA) drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the biological bases that regulate mammalian growth, body size, and life history.
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Affiliation(s)
- Timothy G. Bromage
- Department of Biomaterials & Biomimetics, New York University College of Dentistry, New York, New York, United States of America
- Department of Basic Science & Craniofacial Biology, New York University College of Dentistry, New York, New York, United States of America
- Department of Palaeoanthropology, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Youssef Idaghdour
- Department of Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Rodrigo S. Lacruz
- Department of Basic Science & Craniofacial Biology, New York University College of Dentistry, New York, New York, United States of America
| | - Thomas D. Crenshaw
- Department of Animal Science, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Olexandra Ovsiy
- Department of Biomaterials & Biomimetics, New York University College of Dentistry, New York, New York, United States of America
| | | | | | - Friedemann Schrenk
- Department of Palaeoanthropology, Senckenberg Research Institute, Frankfurt am Main, Germany
- Institute for Ecology, Evolution & Diversity, Goethe University, Frankfurt am Main, Germany
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191
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Sassone-Corsi P. The Epigenetic and Metabolic Language of the Circadian Clock. RESEARCH AND PERSPECTIVES IN ENDOCRINE INTERACTIONS 2016. [DOI: 10.1007/978-3-319-27069-2_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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192
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Neurometabolic roles of ApoE and Ldl-R in mouse brain. J Bioenerg Biomembr 2015; 48:13-21. [PMID: 26686234 DOI: 10.1007/s10863-015-9636-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Polymorphisms in ApoE are highly correlated with the progression of neurodegenerative disease, in particular Alzheimer's disease. Little is known, however, about the role of ApoE or cholesterol metabolism on brain neurochemistry in general. To better understand the role of lipoprotein and cholesterol metabolism in the brain, we profiled 6 and 12-week old Apoe KO and Ldlr KO mouse models via unbiased metabolomics to determine which metabolites were affected at an early age to identify those that may play a role in triggering pathology later in life. Steady-state metabolomics revealed only subtle differences among Apoe KO, Ldlr KO and WT mouse brains. Ldlr KO mice exhibited alterations in metabolites involved in neurotransmitter, amino acid and cholesterol metabolism. In contrast, Apoe KO mice only showed subtle changes in amino acid and neurotransmitter metabolism. These subtle changes in a broad range of metabolites indicate that ApoE and Ldl-R alone may not play a significant role in these mouse models at an early age, but instead require the cumulative effect from different pathways that lead to dysfunction at a much later stage of life.
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193
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Abbondante S, Eckel-Mahan KL, Ceglia NJ, Baldi P, Sassone-Corsi P. Comparative Circadian Metabolomics Reveal Differential Effects of Nutritional Challenge in the Serum and Liver. J Biol Chem 2015; 291:2812-28. [PMID: 26644470 DOI: 10.1074/jbc.m115.681130] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 01/07/2023] Open
Abstract
Diagnosis and therapeutic interventions in pathological conditions rely upon clinical monitoring of key metabolites in the serum. Recent studies show that a wide range of metabolic pathways are controlled by circadian rhythms whose oscillation is affected by nutritional challenges, underscoring the importance of assessing a temporal window for clinical testing and thereby questioning the accuracy of the reading of critical pathological markers in circulation. We have been interested in studying the communication between peripheral tissues under metabolic homeostasis perturbation. Here we present a comparative circadian metabolomic analysis on serum and liver in mice under high fat diet. Our data reveal that the nutritional challenge induces a loss of serum metabolite rhythmicity compared with liver, indicating a circadian misalignment between the tissues analyzed. Importantly, our results show that the levels of serum metabolites do not reflect the circadian liver metabolic signature or the effect of nutritional challenge. This notion reveals the possibility that misleading reads of metabolites in circulation may result in misdiagnosis and improper treatments. Our findings also demonstrate a tissue-specific and time-dependent disruption of metabolic homeostasis in response to altered nutrition.
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Affiliation(s)
- Serena Abbondante
- From the Center for Epigenetics and Metabolism, U904 INSERM, and the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and
| | - Kristin L Eckel-Mahan
- From the Center for Epigenetics and Metabolism, U904 INSERM, and the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and
| | - Nicholas J Ceglia
- the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and the Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, California 92697-3435
| | - Pierre Baldi
- the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and the Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, California 92697-3435
| | - Paolo Sassone-Corsi
- From the Center for Epigenetics and Metabolism, U904 INSERM, and the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and
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194
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Arble DM, Bass J, Behn CD, Butler MP, Challet E, Czeisler C, Depner CM, Elmquist J, Franken P, Grandner MA, Hanlon EC, Keene AC, Joyner MJ, Karatsoreos I, Kern PA, Klein S, Morris CJ, Pack AI, Panda S, Ptacek LJ, Punjabi NM, Sassone-Corsi P, Scheer FA, Saxena R, Seaquest ER, Thimgan MS, Van Cauter E, Wright KP. Impact of Sleep and Circadian Disruption on Energy Balance and Diabetes: A Summary of Workshop Discussions. Sleep 2015; 38:1849-60. [PMID: 26564131 DOI: 10.5665/sleep.5226] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 12/21/2022] Open
Abstract
A workshop was held at the National Institute for Diabetes and Digestive and Kidney Diseases with a focus on the impact of sleep and circadian disruption on energy balance and diabetes. The workshop identified a number of key principles for research in this area and a number of specific opportunities. Studies in this area would be facilitated by active collaboration between investigators in sleep/circadian research and investigators in metabolism/diabetes. There is a need to translate the elegant findings from basic research into improving the metabolic health of the American public. There is also a need for investigators studying the impact of sleep/circadian disruption in humans to move beyond measurements of insulin and glucose and conduct more in-depth phenotyping. There is also a need for the assessments of sleep and circadian rhythms as well as assessments for sleep-disordered breathing to be incorporated into all ongoing cohort studies related to diabetes risk. Studies in humans need to complement the elegant short-term laboratory-based human studies of simulated short sleep and shift work etc. with studies in subjects in the general population with these disorders. It is conceivable that chronic adaptations occur, and if so, the mechanisms by which they occur needs to be identified and understood. Particular areas of opportunity that are ready for translation are studies to address whether CPAP treatment of patients with pre-diabetes and obstructive sleep apnea (OSA) prevents or delays the onset of diabetes and whether temporal restricted feeding has the same impact on obesity rates in humans as it does in mice.
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Affiliation(s)
- Deanna M Arble
- Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Joseph Bass
- Department of Medicine, Endocrinology Division, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Cecilia Diniz Behn
- Department of Applied Mathematics & Statistics, Colorado School of Mines, Golden, CO
| | - Matthew P Butler
- Oregon Institute of Occupational Health Sciences, Oregon Health and Science University, Portland, OR
| | - Etienne Challet
- Institute for Cellular and Integrative Neuroscience, CNRS, University of Strasbourg, France
| | - Charles Czeisler
- Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, MA
| | | | - Joel Elmquist
- Departments of Internal Medicine, Pharmacology and Psychiatry, The University of Texas Southwestern Medical Center, Dallas, TX
| | - Paul Franken
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | | | - Erin C Hanlon
- Department of Medicine, The University of Chicago, Chicago, IL
| | - Alex C Keene
- Department of Biology, University of Nevada, Reno, NV
| | | | - Ilia Karatsoreos
- Department of Integrative Physiology and Neuroscience, College of Veterinary Medicine, Washington State University, Pullman, WA
| | - Philip A Kern
- Department of Medicine, Division of Endocrinology and Center for Clinical and Translational Sciences, University of Kentucky, Lexington, KY
| | - Samuel Klein
- Center for Human Nutrition, Washington University School of Medicine in St. Louis, St. Louis, MO
| | | | - Allan I Pack
- Division of Sleep Medicine/Department of Medicine and Center for Sleep and Circadian Neurobiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Satchidananda Panda
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA
| | - Louis J Ptacek
- Department of Neurology, Howard Hughes Medical Institute, University of California, San Francisco, CA
| | - Naresh M Punjabi
- Department of Medicine, The Johns Hopkins University, Baltimore, MD
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA
| | - Frank A Scheer
- Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, MA
| | - Richa Saxena
- Department of Anesthesia, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Elizabeth R Seaquest
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Matthew S Thimgan
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO
| | - Eve Van Cauter
- Sleep, Metabolism and Health Center, The University of Chicago, Chicago, IL
| | - Kenneth P Wright
- Department of Integrative Physiology, University of Colorado, Boulder, CO.,Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
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195
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Paredes JF, López-Olmeda JF, Martínez FJ, Sánchez-Vázquez FJ. Daily rhythms of lipid metabolic gene expression in zebra fish liver: Response to light/dark and feeding cycles. Chronobiol Int 2015; 32:1438-48. [PMID: 26595085 DOI: 10.3109/07420528.2015.1104327] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Despite numerous studies about fish nutrition and lipid metabolism, very little is known about the daily rhythm expression of lipogenesis and lipolysis genes. This research aimed to investigate the existence of daily rhythm expressions of the genes involved in lipid metabolism and their synchronization to different light/dark (LD) and feeding cycles in zebra fish liver. For this purpose, three groups of zebra fish were submitted to a 12:12 h LD cycle. A single daily meal was provided to each group at various times: in the middle of the light phase (ML); in the middle of the dark phase (MD); at random times. After 20 days of acclimation to these experimental conditions, liver samples were collected every 4 h in one 24-h cycle. The results revealed that most genes displayed a significant daily rhythm with an acrophase of expression in the dark phase. The acrophase of lipolytic genes (lipoprotein lipase - lpl, peroxisome proliferator-activated receptor - pparα and hydroxyacil CoA dehydrogenase - hadh) was displayed between ZT 02:17 h and ZT 18:31 h. That of lipogenic genes (leptin-a - lepa, peroxisome proliferator-activated receptor - pparγ, liver X receptor - lxr, insulin-like growth factor - igf1, sterol regulatory element-binding protein - srebp and fatty acid synthase - fas) was displayed between ZT 15:25 h and 20:06 h (dark phase). Feeding time barely influenced daily expression rhythms, except for lxr in the MD group, whose acrophase shifted by about 14 h compared with the ML group (ZT 04:31 h versus ZT 18:29 h, respectively). These results evidence a strong synchronization to the LD cycle, but not to feeding time, and most genes showed a nocturnal acrophase. These findings highlight the importance of considering light and feeding time to optimize lipid metabolism and feeding protocols in fish farming.
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Affiliation(s)
- J F Paredes
- a Department of Physiology , Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia , Murcia , Spain
| | - J F López-Olmeda
- a Department of Physiology , Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia , Murcia , Spain
| | - F J Martínez
- a Department of Physiology , Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia , Murcia , Spain
| | - F J Sánchez-Vázquez
- a Department of Physiology , Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia , Murcia , Spain
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196
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Bhargava A, Herzel H, Ananthasubramaniam B. Mining for novel candidate clock genes in the circadian regulatory network. BMC SYSTEMS BIOLOGY 2015; 9:78. [PMID: 26576534 PMCID: PMC4650315 DOI: 10.1186/s12918-015-0227-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND Most physiological processes in mammals are temporally regulated by means of a master circadian clock in the brain and peripheral oscillators in most other tissues. A transcriptional-translation feedback network of clock genes produces near 24 h oscillations in clock gene and protein expression. Here, we aim to identify novel additions to the clock network using a meta-analysis of public chromatin immunoprecipitation sequencing (ChIP-seq), proteomics and protein-protein interaction data starting from a published list of 1000 genes with robust transcriptional rhythms and circadian phenotypes of knockdowns. RESULTS We identified 20 candidate genes including nine known clock genes that received significantly high scores and were also robust to the relative weights assigned to different data types. Our scoring was consistent with the original ranking of the 1000 genes, but also provided novel complementary insights. Candidate genes were enriched for genes expressed in a circadian manner in multiple tissues with regulation driven mainly by transcription factors BMAL1 and REV-ERB α,β. Moreover, peak transcription of candidate genes was remarkably consistent across tissues. While peaks of the 1000 genes were distributed uniformly throughout the day, candidate gene peaks were strongly concentrated around dusk. Finally, we showed that binding of specific transcription factors to a gene promoter was predictive of peak transcription at a certain time of day and discuss combinatorial phase regulation. CONCLUSIONS Combining complementary publicly-available data targeting different levels of regulation within the circadian network, we filtered the original list and found 11 novel robust candidate clock genes. Using the criteria of circadian proteomic expression, circadian expression in multiple tissues and independent gene knockdown data, we propose six genes (Por, Mtss1, Dgat2, Pim3, Ppp1r3b, Upp2) involved in metabolism and cancer for further experimental investigation. The availability of public high-throughput databases makes such meta-analysis a promising approach to test consistency between sources and tap their entire potential.
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Affiliation(s)
- Anuprabha Bhargava
- Institute for Theoretical Biology, Charité Universitätsmedizin, Phillipstr. 13, Haus 4, Berlin, 10115, Germany.
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Invalidenstr. 43, Berlin, 10115, Germany.
| | - Bharath Ananthasubramaniam
- Institute for Theoretical Biology, Charité Universitätsmedizin, Phillipstr. 13, Haus 4, Berlin, 10115, Germany.
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197
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Ma D, Liu T, Chang L, Rui C, Xiao Y, Li S, Hogenesch JB, Chen YE, Lin JD. The Liver Clock Controls Cholesterol Homeostasis through Trib1 Protein-mediated Regulation of PCSK9/Low Density Lipoprotein Receptor (LDLR) Axis. J Biol Chem 2015; 290:31003-12. [PMID: 26547624 DOI: 10.1074/jbc.m115.685982] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Indexed: 12/27/2022] Open
Abstract
Disruption of the body clock has been recognized as a risk factor for cardiovascular disease. How the circadian pacemaker interacts with the genetic factors associated with plasma lipid traits remains poorly understood. Recent genome-wide association studies have identified an expanding list of genetic variants that influence plasma cholesterol and triglyceride levels. Here we analyzed circadian regulation of lipid-associated candidate genes in the liver and identified two distinct groups exhibiting rhythmic and non-rhythmic patterns of expression during light-dark cycles. Liver-specific inactivation of Bmal1 led to elevated plasma LDL/VLDL cholesterol levels as a consequence of the disruption of the PCSK9/LDL receptor regulatory axis. Ablation of the liver clock perturbed diurnal regulation of lipid-associated genes in the liver and markedly reduced the expression of the non-rhythmically expressed gene Trib1. Adenovirus-mediated rescue of Trib1 expression lowered plasma PCSK9 levels, increased LDL receptor protein expression, and restored plasma cholesterol homeostasis in mice lacking a functional liver clock. These results illustrate an unexpected mechanism through which the biological clock regulates cholesterol homeostasis through its regulation of non-rhythmic genes in the liver.
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Affiliation(s)
- Di Ma
- From the Life Sciences Institute and Department of Cell and Developmental Biology and
| | - Tongyu Liu
- From the Life Sciences Institute and Department of Cell and Developmental Biology and
| | - Lin Chang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Crystal Rui
- From the Life Sciences Institute and Department of Cell and Developmental Biology and
| | - Yuanyuan Xiao
- From the Life Sciences Institute and Department of Cell and Developmental Biology and
| | - Siming Li
- From the Life Sciences Institute and Department of Cell and Developmental Biology and
| | - John B Hogenesch
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Y Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Jiandie D Lin
- From the Life Sciences Institute and Department of Cell and Developmental Biology and
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198
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Opening the Debate: How to Fulfill the Need for Physicians' Training in Circadian-Related Topics in a Full Medical School Curriculum. J Circadian Rhythms 2015; 13:7. [PMID: 27103933 PMCID: PMC4835682 DOI: 10.5334/jcr.ah] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Circadian rhythms are daily changes in our physiology and behavior that are manifested as patterns of brain wave activity, periodic hormone production, recurring cell regeneration, and other oscillatory biological activities. Their importance to human health is becoming apparent; they are deranged by shift work and jet-lag and in disparate conditions such as insomnia, sleep syndromes, coronary heart attacks, and depression, and are endogenous factors that contribute to cancer development and progression. DISCUSSION As evidence of the circadian connection to human health has grown, so has the number of Americans experiencing disruption of circadian rhythms due to the demands of an industrialized society. Today, there is a growing work force that experiences night shift work and time-zone shifts shaping the demands on physicians to best meet the needs of patients exposed to chronic circadian disruptions. The diverse range of illness associated with altered rhythms suggests that physicians in various fields will see its impact in their patients. However, medical education, with an already full curriculum, struggles to address this issue. SUMMARY Here, we emphasize the need for incorporating the topic of circadian rhythms in the medical curriculum and propose strategies to accomplish this goal.
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199
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Udoh US, Valcin JA, Gamble KL, Bailey SM. The Molecular Circadian Clock and Alcohol-Induced Liver Injury. Biomolecules 2015; 5:2504-37. [PMID: 26473939 PMCID: PMC4693245 DOI: 10.3390/biom5042504] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 12/11/2022] Open
Abstract
Emerging evidence from both experimental animal studies and clinical human investigations demonstrates strong connections among circadian processes, alcohol use, and alcohol-induced tissue injury. Components of the circadian clock have been shown to influence the pathophysiological effects of alcohol. Conversely, alcohol may alter the expression of circadian clock genes and the rhythmic behavioral and metabolic processes they regulate. Therefore, we propose that alcohol-mediated disruption in circadian rhythms likely underpins many adverse health effects of alcohol that cut across multiple organ systems. In this review, we provide an overview of the circadian clock mechanism and showcase results from new studies in the alcohol field implicating the circadian clock as a key target of alcohol action and toxicity in the liver. We discuss various molecular events through which alcohol may work to negatively impact circadian clock-mediated processes in the liver, and contribute to tissue pathology. Illuminating the mechanistic connections between the circadian clock and alcohol will be critical to the development of new preventative and pharmacological treatments for alcohol use disorders and alcohol-mediated organ diseases.
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Affiliation(s)
- Uduak S Udoh
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
| | - Jennifer A Valcin
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
| | - Karen L Gamble
- Department of Psychiatry, Division of Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
| | - Shannon M Bailey
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
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200
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Flynn EM, Huang OW, Poy F, Oppikofer M, Bellon SF, Tang Y, Cochran AG. A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Structure 2015; 23:1801-1814. [PMID: 26365797 DOI: 10.1016/j.str.2015.08.004] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 01/09/2023]
Abstract
Bromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. None of the human bromodomains tested binds succinyl marks. We characterized structurally and biochemically the binding to different acyl groups, identifying bromodomain residues and structural attributes that contribute to specificity. These studies demonstrate a surprising degree of plasticity in some human bromodomains but no single factor controlling specificity across the family. The identification of candidate butyryl- and crotonyllysine readers supports the idea that these marks could have specific physiological functions.
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Affiliation(s)
- E Megan Flynn
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Oscar W Huang
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Florence Poy
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steve F Bellon
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Yong Tang
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA.
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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