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Sulaimani N, Houghton MJ, Bonham MP, Williamson G. Effects of (Poly)phenols on Circadian Clock Gene-Mediated Metabolic Homeostasis in Cultured Mammalian Cells: A Scoping Review. Adv Nutr 2024; 15:100232. [PMID: 38648895 PMCID: PMC11107464 DOI: 10.1016/j.advnut.2024.100232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/02/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024] Open
Abstract
Circadian clocks regulate metabolic homeostasis. Disruption to our circadian clocks, by lifestyle behaviors such as timing of eating and sleeping, has been linked to increased rates of metabolic disorders. There is now considerable evidence that selected dietary (poly)phenols, including flavonoids, phenolic acids and tannins, may modulate metabolic and circadian processes. This review evaluates the effects of (poly)phenols on circadian clock genes and linked metabolic homeostasis in vitro, and potential mechanisms of action, by critically evaluating the literature on mammalian cells. A systematic search was conducted to ensure full coverage of the literature and identified 43 relevant studies addressing the effects of (poly)phenols on cellular circadian processes. Nobiletin and tangeretin, found in citrus, (-)-epigallocatechin-3-gallate from green tea, urolithin A, a gut microbial metabolite from ellagitannins in fruit, curcumin, bavachalcone, cinnamic acid, and resveratrol at low micromolar concentrations all affect circadian molecular processes in multiple types of synchronized cells. Nobiletin emerges as a putative retinoic acid-related orphan receptor (RORα/γ) agonist, leading to induction of the circadian regulator brain and muscle ARNT-like 1 (BMAL1), and increased period circadian regulator 2 (PER2) amplitude and period. These effects are clear despite substantial variations in the protocols employed, and this review suggests a methodological framework to help future study design in this emerging area of research.
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Affiliation(s)
- Noha Sulaimani
- Department of Nutrition, Dietetics and Food, Monash University, Notting Hill, Australia; Victorian Heart Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Australia; Department of Food and Nutrition, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Michael J Houghton
- Department of Nutrition, Dietetics and Food, Monash University, Notting Hill, Australia; Victorian Heart Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Australia
| | - Maxine P Bonham
- Department of Nutrition, Dietetics and Food, Monash University, Notting Hill, Australia
| | - Gary Williamson
- Department of Nutrition, Dietetics and Food, Monash University, Notting Hill, Australia; Victorian Heart Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Australia.
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2
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Patlin BH, Mok H, Arra M, Haspel JA. Circadian rhythms in solid organ transplantation. J Heart Lung Transplant 2024; 43:849-857. [PMID: 38310995 PMCID: PMC11070314 DOI: 10.1016/j.healun.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/17/2024] [Accepted: 01/29/2024] [Indexed: 02/06/2024] Open
Abstract
Circadian rhythms are daily cycles in physiology that can affect medical interventions. This review considers how these rhythms may relate to solid organ transplantation. It begins by summarizing the mechanism for circadian rhythm generation known as the molecular clock, and basic research connecting the clock to biological activities germane to organ acceptance. Next follows a review of clinical evidence relating time of day to adverse transplantation outcomes. The concluding section discusses knowledge gaps and practical areas where applying circadian biology might improve transplantation success.
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Affiliation(s)
- Brielle H Patlin
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Huram Mok
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Monaj Arra
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jeffrey A Haspel
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri.
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3
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Park Y, Kang HG, Kang SJ, Ku HO, Zarbl H, Fang MZ, Park JH. Combined use of multiparametric high-content-screening and in vitro circadian reporter assays in neurotoxicity evaluation. Arch Toxicol 2024; 98:1485-1498. [PMID: 38483585 PMCID: PMC10965668 DOI: 10.1007/s00204-024-03686-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/23/2024] [Indexed: 03/27/2024]
Abstract
Accumulating evidence indicates that chronic circadian rhythm disruption is associated with the development of neurodegenerative diseases induced by exposure to neurotoxic chemicals. Herein, we examined the relationship between cellular circadian rhythm disruption and cytotoxicity in neural cells. Moreover, we evaluated the potential application of an in vitro cellular circadian rhythm assay in determining circadian rhythm disruption as a sensitive and early marker of neurotoxicant-induced adverse effects. To explore these objectives, we established an in vitro cellular circadian rhythm assay using human glioblastoma (U87 MG) cells stably transfected with a circadian reporter vector (PER2-dLuc) and determined the lowest-observed-adverse-effect levels (LOAELs) of several common neurotoxicants. Additionally, we determined the LOAEL of each compound on multiple cytotoxicity endpoints (nuclear size [NC], mitochondrial membrane potential [MMP], calcium ions, or lipid peroxidation) using a multiparametric high-content screening (HCS) assay using transfected U87 MG cells treated with the same neurotoxicants for 24 and 72 h. Based on our findings, the LOAEL for cellular circadian rhythm disruption for most chemicals was slightly higher than that for most cytotoxicity indicators detected using HCS, and the LOAEL for MMP in the first 24 h was the closest to that for cellular circadian rhythm disruption. Dietary antioxidants (methylselenocysteine and N-acetyl-l-cysteine) prevented or restored neurotoxicant-induced cellular circadian rhythm disruption. Our results suggest that cellular circadian rhythm disruption is as sensitive as cytotoxicity indicators and occurs early as much as cytotoxic events during disease development. Moreover, the in vitro cellular circadian rhythm assay warrants further evaluation as an early screening tool for neurotoxicants.
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Affiliation(s)
- Youngil Park
- Laboratory Animal Medicine, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Korea
- Veterinary Drugs and Biologics Division, Animal and Plant Quarantine Agency, Gimcheon-Si, 39660, Korea
| | - Hwan-Goo Kang
- Veterinary Drugs and Biologics Division, Animal and Plant Quarantine Agency, Gimcheon-Si, 39660, Korea
- Department of Animal Health and Welfare, Semyung University, 65, Semyung Ro, Jecheon, Chungcheongbuk‑do, Korea
| | - Seok-Jin Kang
- Veterinary Drugs and Biologics Division, Animal and Plant Quarantine Agency, Gimcheon-Si, 39660, Korea
| | - Hyun-Ok Ku
- Veterinary Drugs and Biologics Division, Animal and Plant Quarantine Agency, Gimcheon-Si, 39660, Korea
| | - Helmut Zarbl
- Department of Environmental and Occupational Health, School of Public Health, NIEHS Center for Environmental Exposure and Disease, Environmental and Occupational Health Sciences Institute, Rutgers, The State University of New Jersey, Piscataway, NJ08854, USA
| | - Ming-Zhu Fang
- Department of Environmental and Occupational Health, School of Public Health, NIEHS Center for Environmental Exposure and Disease, Environmental and Occupational Health Sciences Institute, Rutgers, The State University of New Jersey, Piscataway, NJ08854, USA
| | - Jae-Hak Park
- Laboratory Animal Medicine, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Korea.
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4
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Alcántara-Alonso V, Dallmann R, Lehnert H, de Gortari P, Grammatopoulos DK. CRH-R2 signalling modulates feeding and circadian gene expression in hypothalamic mHypoA-2/30 neurons. Front Endocrinol (Lausanne) 2023; 14:1266081. [PMID: 37900150 PMCID: PMC10600019 DOI: 10.3389/fendo.2023.1266081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/13/2023] [Indexed: 10/31/2023] Open
Abstract
The hypothalamic type 2 corticotropin releasing hormone receptor (CRH-R2) plays critical roles in homeostatic regulation, particularly in fine tuning stress recovery. During acute stress, the CRH-R2 ligands CRH and urocortins promote adaptive responses and feeding inhibition. However, in rodent models of chronic stress, over-exposure of hypothalamic CRH-R2 to its cognate agonists is associated with urocortin 2 (Ucn2) resistance; attenuated cAMP-response element binding protein (CREB) phosphorylation and increased food intake. The molecular mechanisms involved in these altered CRH-R2 signalling responses are not well described. In the present study, we used the adult mouse hypothalamus-derived cell line mHypoA-2/30 to investigate CRH-R2 signalling characteristics focusing on gene expression of molecules involved in feeding and circadian regulation given the role of clock genes in metabolic control. We identified functional CRH-R2 receptors expressed in mHypoA-2/30 cells that differentially regulate CREB and AMP-activated protein kinase (AMPK) phosphorylation and downstream expression of the appetite-regulatory genes proopiomelanocortin (Pomc) and neuropeptide Y (Npy) in accordance with an anorexigenic effect. We studied for the first time the effects of Ucn2 on clock genes in native and in a circadian bioluminescence reporter expressing mHypoA-2/30 cells, detecting enhancing effects of Ucn2 on mRNA levels and rhythm amplitude of the circadian regulator Aryl hydrocarbon receptor nuclear translocator-like protein 1 (Bmal1), which could facilitate anorexic responses in the activity circadian phase. These data uncover novel aspects of CRH-R2 hypothalamic signalling that might be important in regulation of circadian feeding during stress responses.
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Affiliation(s)
- Viridiana Alcántara-Alonso
- Translational Medicine, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- Laboratorio de Neurofisiología Molecular, Instituto Nacional de Psiquiatría Ramón de la Fuente Muñiz, Ciudad de México, Mexico
| | - Robert Dallmann
- Translational Medicine, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Hendrik Lehnert
- Rectorate, Paris Lodron Universität Salzburg, Salzburg, Austria
| | - Patricia de Gortari
- Laboratorio de Neurofisiología Molecular, Instituto Nacional de Psiquiatría Ramón de la Fuente Muñiz, Ciudad de México, Mexico
| | - Dimitris K. Grammatopoulos
- Translational Medicine, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- Institute of Precision Diagnostics and Translational Medicine, Pathology, University Hospital Coventry and Warwickshire (UHCW), National Health Service (NHS) Trust, Coventry, United Kingdom
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5
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Jachim SK, Zhong J, Ordog T, Lee JH, Bhagwate AV, Nagaraj NK, Westendorf JJ, Passos JF, Matveyenko AV, LeBrasseur NK. BMAL1 modulates senescence programming via AP-1. Aging (Albany NY) 2023; 15:9984-10009. [PMID: 37819791 PMCID: PMC10599731 DOI: 10.18632/aging.205112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Cellular senescence and circadian dysregulation are biological hallmarks of aging. Whether they are coordinately regulated has not been thoroughly studied. We hypothesize that BMAL1, a pioneer transcription factor and master regulator of the molecular circadian clock, plays a role in the senescence program. Here, we demonstrate BMAL1 is significantly upregulated in senescent cells and has altered rhythmicity compared to non-senescent cells. Through BMAL1-ChIP-seq, we show that BMAL1 is uniquely localized to genomic motifs associated with AP-1 in senescent cells. Integration of BMAL1-ChIP-seq data with RNA-seq data revealed that BMAL1 presence at AP-1 motifs is associated with active transcription. Finally, we showed that BMAL1 contributes to AP-1 transcriptional control of key features of the senescence program, including altered regulation of cell survival pathways, and confers resistance to drug-induced apoptosis. Overall, these results highlight a previously unappreciated role of the core circadian clock component BMAL1 on the molecular phenotype of senescent cells.
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Affiliation(s)
- Sarah K. Jachim
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Zhong
- Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
- Center for Cell Signaling in Gastroenterology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Center for Cell Signaling in Gastroenterology, Mayo Clinic, Rochester, MN 55905, USA
| | - Aditya V. Bhagwate
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - João F. Passos
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Aleksey V. Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
- Department of Medicine, Division of Endocrinology, Metabolism, Diabetes, and Nutrition, Mayo Clinic, Rochester, MN 55905, USA
| | - Nathan K. LeBrasseur
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN 55905, USA
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6
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Watanabe E, Muranaka T, Nakamura S, Isoda M, Horikawa Y, Aiso T, Ito S, Oyama T. A non-cell-autonomous circadian rhythm of bioluminescence reporter activities in individual duckweed cells. PLANT PHYSIOLOGY 2023; 193:677-688. [PMID: 37042358 DOI: 10.1093/plphys/kiad218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
The circadian clock is responsible for the temporal regulation of various physiological processes in plants. Individual cells contain a circadian oscillator consisting of a clock gene circuit that coordinates physiological rhythms within the plant body in an orderly manner. The coordination of time information has been studied from the perspective of cell-cell local coupling and long-distance communication between tissues based on the view that the behavior of circadian oscillators represents physiological rhythms. Here, we report the cellular circadian rhythm of bioluminescence reporters that are not governed by the clock gene circuit in expressing cells. We detected cellular bioluminescence rhythms with different free-running periods in the same cells using a dual-color bioluminescence monitoring system in duckweed (Lemna minor) transfected with Arabidopsis CIRCADIAN CLOCK ASSOCIATED 1::luciferace+ (AtCCA1::LUC+) and Cauliflower mosaic virus 35S::modified click-beetle red-color luciferase (CaMV35S::PtRLUC) reporters. Co-transfection experiments with the two reporters and a clock gene-overexpressing effector revealed that the AtCCA1::LUC+ rhythm, but not the CaMV35S::PtRLUC rhythm, was altered in cells with a dysfunctional clock gene circuit. This indicated that the AtCCA1::LUC+ rhythm is a direct output of the cellular circadian oscillator, whereas the CaMV35S::PtRLUC rhythm is not. After plasmolysis, the CaMV35S::PtRLUC rhythm disappeared, whereas the AtCCA1::LUC+ rhythm persisted. This suggests that the CaMV35S::PtRLUC bioluminescence has a symplast/apoplast-mediated circadian rhythm generated at the organismal level. The CaMV35S::PtRLUC-type bioluminescence rhythm was also observed when other bioluminescence reporters were expressed. These results reveal that the plant circadian system consists of both cell-autonomous and noncell-autonomous rhythms that are unaffected by cellular oscillators.
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Affiliation(s)
- Emiri Watanabe
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Tomoaki Muranaka
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Shunji Nakamura
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Minako Isoda
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yu Horikawa
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tsuyoshi Aiso
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shogo Ito
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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7
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Masuda K, Kon N, Iizuka K, Fukada Y, Sakurai T, Hirano A. Singularity response reveals entrainment properties in mammalian circadian clock. Nat Commun 2023; 14:2819. [PMID: 37198169 DOI: 10.1038/s41467-023-38392-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Entrainment is characterized by phase response curves (PRCs), which provide a summary of responses to perturbations at each circadian phase. The synchronization of mammalian circadian clocks is accomplished through the receipt of a variety of inputs from both internal and external time cues. A comprehensive comparison of PRCs for various stimuli in each tissue is required. Herein, we demonstrate that PRCs in mammalian cells can be characterized using a recently developed estimation method based on singularity response (SR), which represents the response of desynchronized cellular clocks. We confirmed that PRCs can be reconstructed using single SR measurements and quantified response properties for various stimuli in several cell lines. SR analysis reveals that the phase and amplitude after resetting are distinguishable among stimuli. SRs in tissue slice cultures reveal tissue-specific entrainment properties. These results demonstrate that SRs can be employed to unveil entrainment mechanisms with diverse stimuli in multiscale mammalian clocks.
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Affiliation(s)
- Kosaku Masuda
- Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Naohiro Kon
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Laboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0032, Japan
- Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE), 8‑1‑1 Seikadai, Seika‑cho, Soraku‑gun, Kyoto, 619‑0284, Japan
| | - Kosuke Iizuka
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Laboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Yoshitaka Fukada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0032, Japan
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takeshi Sakurai
- Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan.
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Arisa Hirano
- Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan.
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan.
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8
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Manella G, Bolshette N, Golik M, Asher G. Input integration by the circadian clock exhibits nonadditivity and fold-change detection. Proc Natl Acad Sci U S A 2022; 119:e2209933119. [PMID: 36279450 PMCID: PMC9636907 DOI: 10.1073/pnas.2209933119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/21/2022] [Indexed: 11/18/2022] Open
Abstract
Circadian clocks are synchronized by external timing cues to align with one another and the environment. Various signaling pathways have been shown to independently reset the phase of the clock. However, in the body, circadian clocks are exposed to a multitude of potential timing cues with complex temporal dynamics, raising the question of how clocks integrate information in response to multiple signals. To investigate different modes of signal integration by the circadian clock, we used Circa-SCOPE, a method we recently developed for high-throughput phase resetting analysis. We found that simultaneous exposure to different combinations of known pharmacological resetting agents elicits a diverse range of responses. Often, the response was nonadditive and could not be readily predicted by the response to the individual signals. For instance, we observed that dexamethasone is dominant over other tested inputs. In the case of signals administered sequentially, the background levels of a signal attenuated subsequent resetting by the same signal, but not by signals acting through a different pathway. This led us to examine whether the circadian clock is sensitive to relative rather than absolute levels of the signal. Importantly, our analysis revealed the involvement of a signal-specific fold-change detection mechanism in the clock response. This mechanism likely stems from properties of the signaling pathway that are upstream to the clock. Overall, our findings elucidate modes of input integration by the circadian clock, with potential relevance to clock resetting under both physiological and pathological conditions.
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Affiliation(s)
- Gal Manella
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Nityanand Bolshette
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Marina Golik
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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9
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Kelly KP, Borsetti H, Wenzler ME, Ustione A, Kim K, Christov PP, Ramirez B, Bauer JA, Piston DW, Johnson CH, Sulikowski GA. Screen for Small-Molecule Modulators of Circadian Rhythms Reveals Phenazine as a Redox-State Modifying Clockwork Tuner. ACS Chem Biol 2022; 17:1658-1664. [PMID: 35679588 PMCID: PMC9398883 DOI: 10.1021/acschembio.2c00240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A high-throughput cell-based screen identified redox-active small molecules that produce a period lengthening of the circadian rhythm. The strongest period lengthening phenotype was induced by a phenazine carboxamide (VU661). Comparison to two isomeric benzquinoline carboxamides (VU673 and VU164) shows the activity is associated with the redox modulating phenazine functionality. Furthermore, ex vivo cell analysis using optical redox ratio measurements shows the period lengthening phenotype to be associated with a shift to the NAD/FAD oxidation state of nicotinamide and flavine coenzymes.
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Affiliation(s)
- Kevin P Kelly
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Hugo Borsetti
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Marta E Wenzler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Alessandro Ustione
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Kwangho Kim
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Plamen P Christov
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Bianca Ramirez
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Joshua A Bauer
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - David W Piston
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Gary A Sulikowski
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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10
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Narayanan V, Rodrigues AL, Dordick JS. Influence of Circadian Rhythm on Drug Metabolism in 3D Hepatic Spheroids. Biotechnol Bioeng 2022; 119:2842-2856. [PMID: 35822281 DOI: 10.1002/bit.28180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022]
Abstract
Circadian rhythms are characterized as oscillations that fluctuate based on a 24h cycle and are responsible for regulation of physiological functions. While the internal clock synchronizes gene expression using external cues like light, a similar synchronization can be induced in vitro by incubating the cells with an increased percentage of serum followed by its rapid removal. Previous studies have suggested that synchronization of HepG2 cell line induced the rhythmic expression of drug metabolizing enzymes (DME) most specifically the cytochrome P450 enzymes. However, there is a lack of evidence demonstrating the influence of 3D microenvironment on the rhythmicity of these genes. To understand this interplay, gene expression of the circadian machinery and CYP450s were compared using the model human hepatocarcinoma cell line, HepG2. Upon serum shock synchronization, gene and protein expression of core clock regulators was assessed and rhythmic expression of these genes was demonstrated. Further insight into the interrelations between various gene pairs was obtained using statistical analysis. Using RNA sequencing, an in-depth understanding of the widespread effects of circadian regulation on genes involved in metabolic processes in the liver was obtained. This study aids in the better understanding of chronopharmacokinetic events in humans using physiologically relevant 3D culture systems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Vibha Narayanan
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Andre L Rodrigues
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Departments of Biological Sciences and Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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11
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Mihelakis M, Ndikung J, Oelgeschläger M, Ertych N. The 4th dimension of in vitro systems - Time to level up. ENVIRONMENT INTERNATIONAL 2022; 164:107256. [PMID: 35472563 DOI: 10.1016/j.envint.2022.107256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
Various in vitro model systems have been established over the last decades to understand physiological processes, the causalities of diseases and the response of humans to environmental and industrial chemicals or therapeutic drugs. Common to all is a limited biological significance due to the impairment of functionality, for instance by the lack of physiological 3D tissue architecture or the loss of fundamental regulatory mechanisms including the circadian rhythm. The circadian rhythm is an adaption of living organisms to rhythmic environmental changes of the day-night cycle and coordinates behavior as well as various crucial physiological processes in a 24-hour pattern. Here, we discuss the impact of integrating circadian regulation in experimental approaches and toxicological assessments to improve the biological relevance of the obtained results. In particular, it is known for some time that an ongoing disruption of the circadian rhythmicity is associated with an increased risk for cardiovascular disease, metabolic dysfunction or cancer. In the context of health recovery, the importance of circadian control mechanism is recognized by chronopharmacological concepts to increase the efficiency of pharmacological treatment strategies. Despite the undeniable circadian dependency and the biological relevance of manifold cellular and molecular processes, the impact of circadian regulation is hardly considered in a wide range of biomedical and toxicological research areas. Reactivating the circadian regulation holds the promise to enhance the biological relevance and reliability of in vitro approaches. In the context of human health protection the implementation of a circadian regulation will subsequently generate advanced physiologically relevant in vitro approaches and allows an improved toxicological assessment of health risks. In addition, the establishment of circadian disruption as a novel toxicological endpoint will provide a better understanding of toxicological mode of actions of environmental and industrial chemicals or drugs and enlarge the knowledge of disease development.
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Affiliation(s)
- Melina Mihelakis
- German Federal Institute for Risk Assessment, German Centre for the Protection of Laboratory Animals (Bf3R), Diedersdorfer Weg 1, 12277 Berlin, Germany
| | - Johanna Ndikung
- German Federal Institute for Risk Assessment, German Centre for the Protection of Laboratory Animals (Bf3R), Diedersdorfer Weg 1, 12277 Berlin, Germany
| | - Michael Oelgeschläger
- German Federal Institute for Risk Assessment, German Centre for the Protection of Laboratory Animals (Bf3R), Diedersdorfer Weg 1, 12277 Berlin, Germany
| | - Norman Ertych
- German Federal Institute for Risk Assessment, German Centre for the Protection of Laboratory Animals (Bf3R), Diedersdorfer Weg 1, 12277 Berlin, Germany.
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12
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Core clock regulators in dexamethasone-treated HEK 293T cells at 4 h intervals. BMC Res Notes 2022; 15:23. [PMID: 35090555 PMCID: PMC8796574 DOI: 10.1186/s13104-021-05871-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/30/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The study of the circadian clock and its mechanisms is easily facilitated through clock resetting in cell culture. Among the various established synchronizers of the circadian clock in cell culture (temperature, serum shock, glucocorticoids), the artificial glucocorticoid Dexamethasone (DEX) is the most widely used. DEX treatment as a protocol to reset the circadian clock in culture gives simple readout with minimal laboratory requirements. Even though there are many studies regarding clock resetting in culture using DEX, reference points or expression patterns of core clock genes and their protein products are scarce and sometimes contradict other works with similar methodology. We synchronise a cell line of human origin with DEX to be used for studies on circadian rhythms. RESULTS We treat HEK 293T cells with DEX and describe the patterns of mRNA and proteins of core clock regulators, while making a clear point on how CLOCK is less than an ideal molecule to help monitor rhythms in this cell line.
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13
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Schroder EA, Delisle BP. Time Restricted Feeding to the Light Cycle Dissociates Canonical Circadian Clocks and Physiological Rhythms in Heart Rate. Front Pharmacol 2022; 13:910195. [PMID: 35645828 PMCID: PMC9133719 DOI: 10.3389/fphar.2022.910195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Circadian rhythms are approximate 24-h biological cycles that optimize molecular and physiological functions to predictable daily environmental changes in order to maintain internal and organismal homeostasis. Environmental stimuli (light, feeding, activity) capable of altering the phase of molecular rhythms are important tools employed by circadian biologists to increase understanding of the synchronization of circadian rhythms to the environment and to each other within multicellular systems. The central circadian clock, located in the suprachiasmatic nucleus (SCN) of the hypothalamus is largely responsive to light and is thought to entrain the phase of peripheral clocks via neurohumoral signals. Mice are nocturnal and consume most of their food during the dark cycle. Early studies demonstrated that altered metabolic cues in the form of time restricted feeding, specifically, feeding mice during the light cycle, resulted in an uncoupling of molecular clocks in peripheral tissues with those from the SCN. These studies showed as much as a 12-h shift in gene expression in some peripheral tissues but not others. The shifts occurred without corresponding changes in the central clock in the brain. More recent studies have demonstrated that changes in cardiac physiology (heart rate, MAP) in response to time of food intake occur independent of the cardiac molecular clock. Understanding differences in the physiology/function and gene expression in other organs both independently and in relation to the heart in response to altered feeding will be important in dissecting the roles of the various clocks throughout the body, as well as, understanding their links to cardiovascular pathology.
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Affiliation(s)
- Elizabeth A. Schroder
- Department of Physiology, University of Kentucky, Lexington, KY, United States
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Kentucky, Lexington, KY, United States
- *Correspondence: Elizabeth A. Schroder, ; Brian P. Delisle,
| | - Brian P. Delisle
- Department of Physiology, University of Kentucky, Lexington, KY, United States
- *Correspondence: Elizabeth A. Schroder, ; Brian P. Delisle,
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14
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Park M, Cao Y, Hong CI. Methods for Assessing Circadian Rhythms and Cell Cycle in Intestinal Enteroids. Methods Mol Biol 2022; 2482:105-124. [PMID: 35610422 DOI: 10.1007/978-1-0716-2249-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Endogenous circadian clocks play a key role in regulating a vast array of biological processes from cell cycle to metabolism, and disruption of circadian rhythms exacerbates a range of human ailments including cardiovascular, metabolic, and gastrointestinal diseases. Determining the state of a patient's circadian rhythms and clock-controlled signaling pathways has important implications for precision and personalized medicine, from improving the diagnosis of circadian-related disorders to optimizing the timing of drug delivery. Patient-derived 3-dimensional enteroids or in vitro "mini gut" is an attractive model uncovering human- and patient-specific circadian target genes that may be critical for personalized medicine. Here, we introduce several procedures to assess circadian rhythms and cell cycle dynamics in enteroids through time course sample collection methods and assay techniques including immunofluorescence, live cell confocal microscopy, and bioluminescence. These methods can be applied to evaluate the state of circadian rhythms and circadian clock-gated cell division cycles using mouse and human intestinal enteroids.
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Affiliation(s)
- Miri Park
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yuhui Cao
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Christian I Hong
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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15
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Liu Z, Meng M, Zhang S, Qiu H, Liu Z, Huang M. Rhythmic Component Analysis Tool (RCAT): A Precise, Efficient and User-Friendly Tool for Circadian Clock Genes Analysis. Interdiscip Sci 2021; 14:269-278. [PMID: 34374039 DOI: 10.1007/s12539-021-00471-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/31/2021] [Accepted: 07/31/2021] [Indexed: 11/29/2022]
Abstract
High-throughput next-generation sequencing (NGS) technologies and real-time circadian dynamics reporting systems produce large amounts of experimental data on RNA and protein levels in the field of circadian rhythm and therefore require statistical knowledge and computational skills for quantitative analysis. Although there are many software applications that can process these data, they are often difficult to use and computationally inefficient. Hence, a convenient, user-friendly tool that can accurately acquire rhythmic components (period, amplitude, and phase) of circadian clock genes is necessary. Here, we develop a new analysis tool named rhythmic component analysis tool (RCAT), which has an easily understood interface featuring a one-button operation, that presents all results as tables and images and automatically saves them as CSV files. We use the relative amplitude error (RAE), widely-adopted criteria on the circadian research field to estimate the quality of results. To illustrate the analytical ability of the RCAT under different situations, we generate four groups of time-series data by CircaInSilico (a web server for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms) with different collection intervals and amplitude ranges and use RCAT to analyze them. To demonstrate the effectiveness of RCAT, we analyze two sets of case studies with time-series data: one set uses microarray and RNA-Seq data from the gene expression omnibus (GEO) repository to identify core clock genes (CCGs) with significant periodicity in the liver, and the other set uses real-time fluorescence reporting data collected by Lumicycle® (a commonly-used luminometer) to calculate the precise period, amplitude and phase. In these examples, most cycling samples are successfully detected by the RCAT within a short collection time, and accurate rhythmic components are also successfully computed. These results indicate that RCAT improves flexibility and convenience in periodic oscillation data analysis. RCAT, is freely available at: https://github.com/lzbbest/Rhythmic-Component-Analysis-Tool/releases . It, as a cross-platform software, can be run not only on Linux, but also on Win10, Win8 and Win7.
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Affiliation(s)
- Zhibo Liu
- Department of Bioinformatics, School of Biological and Basic Medical Sciences, Soochow University, 199 Ren-ai Road, Suzhou, 215123, China
| | - Meng Meng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Shufan Zhang
- Department of Bioinformatics, School of Biological and Basic Medical Sciences, Soochow University, 199 Ren-ai Road, Suzhou, 215123, China
| | - Hao Qiu
- Department of Biochemistry and Molecular Biology, School of Biological and Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Research Center, Soochow University, Suzhou, 215123, China
| | - Moli Huang
- Department of Bioinformatics, School of Biological and Basic Medical Sciences, Soochow University, 199 Ren-ai Road, Suzhou, 215123, China.
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16
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Clock-Modulating Activities of the Anti-Arrhythmic Drug Moricizine. Clocks Sleep 2021; 3:351-365. [PMID: 34206497 PMCID: PMC8293187 DOI: 10.3390/clockssleep3030022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/09/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Dysregulated circadian functions contribute to various diseases, including cardiovascular disease. Much progress has been made on chronotherapeutic applications of drugs against cardiovascular disease (CVD); however, the direct effects of various medications on the circadian system are not well characterized. We previously conducted high-throughput chemical screening for clock modulators and identified an off-patent anti-arrhythmic drug, moricizine, as a clock-period lengthening compound. In Per2:LucSV reporter fibroblast cells, we showed that under both dexamethasone and forskolin synchronization, moricizine was able to increase the circadian period length, with greater effects seen with the former. Titration studies revealed a dose-dependent effect of moricizine to lengthen the period. In contrast, flecainide, another Class I anti-arrhythmic, showed no effects on circadian reporter rhythms. Real-time qPCR analysis in fibroblast cells treated with moricizine revealed significant circadian time- and/or treatment-dependent expression changes in core clock genes, consistent with the above period-lengthening effects. Several clock-controlled cardiac channel genes also displayed altered expression patterns. Using tissue explant culture, we showed that moricizine was able to significantly prolong the period length of circadian reporter rhythms in atrial ex vivo cultures. Using wild-type C57BL/6J mice, moricizine treatment was found to promote sleep, alter circadian gene expression in the heart, and show a slight trend of increasing free-running periods. Together, these observations demonstrate novel clock-modulating activities of moricizine, particularly the period-lengthening effects on cellular oscillators, which may have clinical relevance against heart diseases.
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17
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Chen X, Yu F, Guo X, Su C, Li SS, Wu B. Clock gene Bmal1 controls diurnal rhythms in expression and activity of intestinal carboxylesterase 1. J Pharm Pharmacol 2021; 73:52-59. [PMID: 33791812 DOI: 10.1093/jpp/rgaa035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES We aimed to characterize diurnal rhythms in CES1 expression and activity in mouse intestine, and to investigate a potential role of the core clock gene Bmal1 in generating diurnal rhythms. METHODS The regulatory effects of intestinal Bmal1 on diurnal CES1 expression were assessed using intestine-specific Bmal1 knockout (Bmal1iKO) mice and colon cancer cells. The relative mRNA and protein levels were determined by qPCR and Western blotting, respectively. Metabolic activity of CES1 in vitro and in vivo were determined by microsomal assays and pharmacokinetic studies, respectively. Transcriptional gene regulation was investigated using luciferase reporter assay. KEY FINDINGS Total CES1 protein varied significantly according to time of the day in wild-type (Bmal1fl/fl) mice, peaking at ZT6. Of detectable Ces1 genes, Ces1d mRNA displayed a robust diurnal rhythm with a peak level at ZT6, whereas mRNAs of Ces1e, 1f and 1g showed no rhythms in wild-type mice. Loss of intestinal Bmal1 reduced the levels of total CES1 protein and Ces1d mRNA, and blunted their diurnal rhythms in mice. In vitro microsomal assays indicated that intestinal metabolism of mycophenolate mofetil (MMF, a known CES1 substrate) was more extensive at ZT6 than at ZT18. ZT6 dosing of MMF to wild-type mice generated a higher systemic exposure of mycophenolic acid (the active metabolite of MMF) as compared with ZT18 dosing. Intestinal ablation of Bmal1 down-regulated CES1 metabolism at ZT6, and abolished its time-dependency both in vitro and in vivo. Furthermore, Ces1d/CES1 rhythmicity and positive regulation of Ces1d/CES1 by BMAL1 were confirmed in CT26 and Caco-2 cells. Mechanistically, BMAL1 trans-activated Ces1d/CES1 probably via binding to the E-box elements in the gene promoters. CONCLUSIONS Bmal1 controls diurnal rhythms in expression and activity of intestinal CES1. Our findings have implications for understanding the crosstalk between circadian clock and xenobiotic metabolism in the intestine.
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Affiliation(s)
- Xun Chen
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, Guangzhou, Guangzhou, Guangdong Province, China
| | - Fangjun Yu
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, Guangzhou, Guangzhou, Guangdong Province, China
| | - Xiaolei Guo
- Binzhou Polytechnic, Binzhou, Shandong, China
| | - Chong Su
- Zhuhai United Laboratories, Zhuhai, Guangdong, China
| | - Shu-Shu Li
- Department of Orthodontics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Baojian Wu
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, Guangzhou, Guangzhou, Guangdong Province, China
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18
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Kim SM, Vadnie CA, Philip VM, Gagnon LH, Chowdari KV, Chesler EJ, McClung CA, Logan RW. High-throughput measurement of fibroblast rhythms reveals genetic heritability of circadian phenotypes in diversity outbred mice and their founder strains. Sci Rep 2021; 11:2573. [PMID: 33510298 PMCID: PMC7843998 DOI: 10.1038/s41598-021-82069-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/14/2021] [Indexed: 01/21/2023] Open
Abstract
Circadian variability is driven by genetics and Diversity Outbred (DO) mice is a powerful tool for examining the genetics of complex traits because their high genetic and phenotypic diversity compared to conventional mouse crosses. The DO population combines the genetic diversity of eight founder strains including five common inbred and three wild-derived strains. In DO mice and their founders, we established a high-throughput system to measure cellular rhythms using in vitro preparations of skin fibroblasts. Among the founders, we observed strong heritability for rhythm period, robustness, phase and amplitude. We also found significant sex and strain differences for these rhythms. Extreme differences in period for molecular and behavioral rhythms were found between the inbred A/J strain and the wild-derived CAST/EiJ strain, where A/J had the longest period and CAST/EiJ had the shortest. In addition, we measured cellular rhythms in 329 DO mice, which displayed far greater phenotypic variability than the founders—80% of founders compared to only 25% of DO mice had periods of ~ 24 h. Collectively, our findings demonstrate that genetic diversity contributes to phenotypic variability in circadian rhythms, and high-throughput characterization of fibroblast rhythms in DO mice is a tractable system for examining the genetics of circadian traits.
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Affiliation(s)
- Sam-Moon Kim
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA.,Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA
| | - Chelsea A Vadnie
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Vivek M Philip
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA
| | - Leona H Gagnon
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA
| | - Kodavali V Chowdari
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Elissa J Chesler
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA
| | - Colleen A McClung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA. .,Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA.
| | - Ryan W Logan
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA. .,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, 700 Albany Street, Boston, 02118, MA, USA.
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19
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Nikulin SV, Raigorodskaya MP, Sakharov DA. Transcriptome Analysis of Signaling Pathways in Caco-2 Cells Involved in the Formation of Intestinal Villi. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820090069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Small L, Altıntaş A, Laker RC, Ehrlich A, Pattamaprapanont P, Villarroel J, Pillon NJ, Zierath JR, Barrès R. Contraction influences Per2 gene expression in skeletal muscle through a calcium-dependent pathway. J Physiol 2020; 598:5739-5752. [PMID: 32939754 PMCID: PMC7756801 DOI: 10.1113/jp280428] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
KEY POINTS Exercising at different times of day elicits different effects on exercise performance and metabolic health. However, the specific signals driving the observed time-of-day specific effects of exercise have not been fully identified. Exercise influences the skeletal muscle circadian clock, although the relative contribution of muscle contraction and extracellular signals is unknown. Here, we show that contraction acutely increases the expression of the core circadian clock gene Period Circadian Regulator 2 (Per2) and phase-shifts Per2 rhythmicity in muscle cells. This contraction effect on core clock genes is mediated through a calcium-dependant mechanism; The results obtained in the present study suggest that a proportion of the ability of exercise to entrain the skeletal muscle clock is driven directly by muscle contraction. Contraction interventions may be used to mimic some time-of-day specific effects of exercise on metabolism and muscle performance. ABSTRACT Exercise entrains the central and peripheral circadian clocks, although the mechanism by which exercise modulates expression of skeletal muscle clock genes is unclear. The present study aimed to determine whether skeletal muscle contraction alone could directly influence circadian rhythmicity and uncover the underlying mechanism by which contraction modulates clock gene expression. We investigated the expression of core clock genes in human skeletal muscle after acute exercise, as well as following in vitro contraction in mouse soleus muscle and cultured C2C12 skeletal muscle myotubes. Additionally, we interrogated the molecular pathways by which skeletal muscle contraction could influence clock gene expression. Contraction acutely increased the expression of the core circadian clock gene Period Circadian Regulator 2 (Per2) and phase-shifted Per2 rhythmicity in C2C12 myotubes in vitro. Further investigation revealed that pharmacologically increasing cytosolic calcium concentrations by ionomycin treatment mimicked the effect of contraction on Per2 expression. Similarly, treatment with a calcium channel blocker, nifedipine, blocked the effect of electric pulse stimulation-induced contraction on Per2 expression. Increased calcium influx from contraction lead to binding of the phosphorylated form of cAMP response element-binding protein (CREB) to the Per2 promoter, suggesting a role of CREB in contraction-induced Per2 transcription. Thus, by dissociating the effect of muscle contraction alone from the whole effect of exercise, our investigations indicate that a proportion of the ability of exercise to entrain the skeletal muscle clock is driven directly by contraction.
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Affiliation(s)
- Lewin Small
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ali Altıntaş
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rhianna C Laker
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Amy Ehrlich
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pattarawan Pattamaprapanont
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julia Villarroel
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas J Pillon
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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21
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Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa. Sci Rep 2020; 10:15168. [PMID: 32938998 PMCID: PMC7495483 DOI: 10.1038/s41598-020-72213-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/25/2020] [Indexed: 11/09/2022] Open
Abstract
Stochastic networks for the clock were identified by ensemble methods using genetic algorithms that captured the amplitude and period variation in single cell oscillators of Neurospora crassa. The genetic algorithms were at least an order of magnitude faster than ensemble methods using parallel tempering and appeared to provide a globally optimum solution from a random start in the initial guess of model parameters (i.e., rate constants and initial counts of molecules in a cell). The resulting goodness of fit [Formula: see text] was roughly halved versus solutions produced by ensemble methods using parallel tempering, and the resulting [Formula: see text] per data point was only [Formula: see text] = 2,708.05/953 = 2.84. The fitted model ensemble was robust to variation in proxies for "cell size". The fitted neutral models without cellular communication between single cells isolated by microfluidics provided evidence for only one Stochastic Resonance at one common level of stochastic intracellular noise across days from 6 to 36 h of light/dark (L/D) or in a D/D experiment. When the light-driven phase synchronization was strong as measured by the Kuramoto (K), there was degradation in the single cell oscillations away from the stochastic resonance. The rate constants for the stochastic clock network are consistent with those determined on a macroscopic scale of 107 cells.
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22
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Lellupitiyage Don SS, Robertson KL, Lin HH, Labriola C, Harrington ME, Taylor SR, Farkas ME. Nobiletin affects circadian rhythms and oncogenic characteristics in a cell-dependent manner. PLoS One 2020; 15:e0236315. [PMID: 32706791 PMCID: PMC7380617 DOI: 10.1371/journal.pone.0236315] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/03/2020] [Indexed: 12/11/2022] Open
Abstract
The natural product nobiletin is a small molecule, widely studied with regard to its therapeutic effects, including in cancer cell lines and tumors. Recently, nobiletin has also been shown to affect circadian rhythms via their enhancement, resulting in protection against metabolic syndrome. We hypothesized that nobiletin's anti-oncogenic effects, such as prevention of cell migration and formation of anchorage independent colonies, are correspondingly accompanied by modulation of circadian rhythms. Concurrently, we wished to determine whether the circadian and anti-oncogenic effects of nobiletin differed across cancer cell lines. In this study, we assessed nobiletin's circadian and therapeutic characteristics to ascertain whether these effects depend on cell line, which here also varied in terms of baseline circadian rhythmicity. Three cell culture models where nobiletin's effects on cell proliferation and migration have been studied previously were evaluated: U2OS (bone osteosarcoma), which possesses robust circadian rhythms; MCF7 (breast adenocarcinoma), which has weak circadian rhythms; and MDA-MB-231 (breast adenocarcinoma), which is arrhythmic. We found that circadian, migration, and proliferative effects following nobiletin treatment were subtle in the U2OS and MCF7 cells. On the other hand, changes were clear in MDA-MB-231s, where nobiletin rescued rhythmicity and substantially reduced oncogenic features, specifically two-dimensional cell motility and anchorage-independent growth. Based on these results and those previously described, we posit that the effects of nobiletin are indeed cell-type dependent, and that a positive correlation may exist between nobiletin's circadian and therapeutic effects.
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Affiliation(s)
| | - Kelly L. Robertson
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, MA, United States of America
| | - Hui-Hsien Lin
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, United States of America
| | - Caroline Labriola
- Department of Psychology, Smith College, Northampton, MA, United States of America
| | - Mary E. Harrington
- Department of Psychology, Smith College, Northampton, MA, United States of America
| | - Stephanie R. Taylor
- Department of Computer Science, Colby College, Waterville, ME, United States of America
| | - Michelle E. Farkas
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, United States of America
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23
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Chemical modulation of circadian rhythms and assessment of cellular behavior via indirubin and derivatives. Methods Enzymol 2020; 639:115-140. [PMID: 32475398 DOI: 10.1016/bs.mie.2020.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Circadian rhythms are critical regulators of many physiological and behavioral functions. The use and abilities of small molecules to affect oscillations have recently received significant attention. These manipulations can be reversible and tunable, and have been used to study various biological mechanisms and molecular properties. Here, we outline procedures for assessment of cellular circadian changes following treatment with small molecules, using luminescent reporters. We describe reporter generation, luminometry experiments, and data analysis. Protocols for studies of accompanying effects on cells, including motility, viability, and anchorage-independent proliferation assays are also presented. As examples, we use indirubin-3'-oxime and two derivatives, 5-iodo-indirubin-3'-oxime and 5-sulfonic acid-indirubin-3'-oxime. In this case study, we analyze effects of these compounds on Bmal1 and Per2 (positive and negative core circadian elements) oscillations and provide step-by-step protocols for data analysis, including removal of trends from raw data, period estimations, and statistical analysis. The reader is provided with detailed protocols, and guidance regarding selection of and alternative approaches.
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Ahmed R, Ashimori A, Iwamoto S, Matsui T, Nakahata Y, Bessho Y. Replicative senescent human cells possess altered circadian clocks with a prolonged period and delayed peak-time. Aging (Albany NY) 2020; 11:950-973. [PMID: 30738414 PMCID: PMC6382424 DOI: 10.18632/aging.101794] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/24/2019] [Indexed: 01/16/2023]
Abstract
Over the last decade, a wide array of evidence has been accumulated that disruption of circadian clock is prone to cause age-related diseases and premature aging. On the other hand, aging has been identified as one of the risk factors linked to the alteration of circadian clock. These evidences suggest that the processes of aging and circadian clock feedback on each other at the animal level. However, at the cellular level, we recently revealed that the primary fibroblast cells derived from Bmal1-/- mouse embryo, in which circadian clock is completely disrupted, do not demonstrate the acceleration of cellular aging, i.e., cellular senescence. In addition, little is known about the impact of cellular senescence on circadian clock. In this study, we show for the first time that senescent cells possess a longer circadian period with delayed peak-time and that the variability in peak-time is wider in the senescent cells compared to their proliferative counterparts, indicating that senescent cells show alterations of circadian clock. We, furthermore, propose that investigation at cellular level is a powerful and useful approach to dissect molecular mechanisms of aging in the circadian clock.
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Affiliation(s)
- Rezwana Ahmed
- Laboratory of Gene Regulation Research, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Atsushige Ashimori
- Laboratory of Gene Regulation Research, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Satoshi Iwamoto
- Laboratory of Gene Regulation Research, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Takaaki Matsui
- Laboratory of Gene Regulation Research, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Yasukazu Nakahata
- Laboratory of Gene Regulation Research, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Yasumasa Bessho
- Laboratory of Gene Regulation Research, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
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Ishikawa M, Kawai K, Kaneko M, Tanaka K, Nakanishi S, Hori K. Extracellular electron transfer mediated by a cytocompatible redox polymer to study the crosstalk among the mammalian circadian clock, cellular metabolism, and cellular redox state. RSC Adv 2020; 10:1648-1657. [PMID: 35494713 PMCID: PMC9047959 DOI: 10.1039/c9ra10023g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/30/2019] [Indexed: 01/11/2023] Open
Abstract
The circadian clock is an endogenous biological timekeeping system that controls various physiological and cellular processes with a 24 h rhythm. The crosstalk among the circadian clock, cellular metabolism, and cellular redox state has attracted much attention. To elucidate this crosstalk, chemical compounds have been used to perturb cellular metabolism and the redox state. However, an electron mediator that facilitates extracellular electron transfer (EET) has not been used to study the mammalian circadian clock due to potential cytotoxic effects of the mediator. Here, we report evidence that a cytocompatible redox polymer pMFc (2-methacryloyloxyethyl phosphorylcholine-co-vinyl ferrocene) can be used as the mediator to study the mammalian circadian clock. EET mediated by oxidized pMFc (ox-pMFc) extracted intracellular electrons from human U2OS cells, resulting in a longer circadian period. Analyses of the metabolome and intracellular redox species imply that ox-pMFc receives an electron from glutathione, thereby inducing pentose phosphate pathway activation. These results suggest novel crosstalk among the circadian clock, metabolism, and redox state. We anticipate that EET mediated by a redox cytocompatible polymer will provide new insights into the mammalian circadian clock system, which may lead to the development of new treatments for circadian clock disorders. Cytocompatible redox polymer pMFc altered the cellular redox state and metabolism, resulting in a longer circadian period.![]()
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Affiliation(s)
- Masahito Ishikawa
- Department of Biomolecular Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Kazuki Kawai
- Department of Biomolecular Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Masahiro Kaneko
- Department of Materials Engineering
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
| | - Kenya Tanaka
- Graduate School of Engineering Science
- Osaka University
- Osaka 560-8531
- Japan
| | - Shuji Nakanishi
- Graduate School of Engineering Science
- Osaka University
- Osaka 560-8531
- Japan
- Research Center for Solar Energy Chemistry
| | - Katsutoshi Hori
- Department of Biomolecular Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
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Gaspar LS, Álvaro AR, Carmo‐Silva S, Mendes AF, Relógio A, Cavadas C. The importance of determining circadian parameters in pharmacological studies. Br J Pharmacol 2019; 176:2827-2847. [PMID: 31099023 PMCID: PMC6637036 DOI: 10.1111/bph.14712] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/26/2019] [Accepted: 04/01/2019] [Indexed: 12/25/2022] Open
Abstract
In mammals, most molecular and cellular processes show circadian changes, leading to daily variations in physiology and ultimately in behaviour. Such daily variations induce a temporal coordination of processes that is essential to ensure homeostasis and health. Thus, it is of no surprise that pharmacokinetics (PK) and pharmacodynamics (PD) of many drugs are also subject to circadian variations, profoundly affecting their efficacy and tolerability. Understanding how circadian rhythms influence drug PK, PD, and toxicity might significantly improve treatment efficacy and decrease related side effects. Therefore, it is essential to take circadian variations into account and to determine circadian parameters in pharmacological studies, especially when drugs have a short half-life or target rhythmic processes. This review provides an overview of the current knowledge on circadian rhythms and their relevance to the field of pharmacology. Methodologies to evaluate circadian rhythms in vitro, in rodent models and in humans, from experimental to computational approaches, are described and discussed. Lastly, we aim at alerting the scientific, medical, and regulatory communities to the relevance of the physiological time, as a key parameter to be considered when designing pharmacological studies. This will eventually lead to more successful preclinical and clinical trials and pave the way to a more personalized treatment to the benefit of the patients.
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Affiliation(s)
- Laetitia S. Gaspar
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Institute for Interdisciplinary Research (IIIUC)University of CoimbraCoimbraPortugal
| | - Ana Rita Álvaro
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
| | - Sara Carmo‐Silva
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
| | - Alexandrina Ferreira Mendes
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Faculty of PharmacyUniversity of CoimbraCoimbraPortugal
| | - Angela Relógio
- Institute for Theoretical BiologyCharité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt—Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Medical Department of Hematology, Oncology, and Tumor Immunology, Molecular Cancer Research CenterCharité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt—Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Cláudia Cavadas
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Faculty of PharmacyUniversity of CoimbraCoimbraPortugal
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Xie Y, Tang Q, Chen G, Xie M, Yu S, Zhao J, Chen L. New Insights Into the Circadian Rhythm and Its Related Diseases. Front Physiol 2019; 10:682. [PMID: 31293431 PMCID: PMC6603140 DOI: 10.3389/fphys.2019.00682] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/13/2019] [Indexed: 12/18/2022] Open
Abstract
Circadian rhythms (CR) are a series of endogenous autonomous oscillators generated by the molecular circadian clock which acting on coordinating internal time with the external environment in a 24-h daily cycle. The circadian clock system is a major regulatory factor for nearly all physiological activities and its disorder has severe consequences on human health. CR disruption is a common issue in modern society, and researches about people with jet lag or shift works have revealed that CR disruption can cause cognitive impairment, psychiatric illness, metabolic syndrome, dysplasia, and cancer. In this review, we summarized the synchronizers and the synchronization methods used in experimental research, and introduced CR monitoring and detection methods. Moreover, we evaluated conventional CR databases, and analyzed experiments that characterized the underlying causes of CR disorder. Finally, we further discussed the latest developments in understanding of CR disruption, and how it may be relevant to health and disease. Briefly, this review aimed to synthesize previous studies to aid in future studies of CR and CR-related diseases.
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Affiliation(s)
- Yanling Xie
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingming Tang
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guangjin Chen
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengru Xie
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaoling Yu
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiajia Zhao
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lili Chen
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Elkhenany H, AlOkda A, El-Badawy A, El-Badri N. Tissue regeneration: Impact of sleep on stem cell regenerative capacity. Life Sci 2018; 214:51-61. [PMID: 30393021 DOI: 10.1016/j.lfs.2018.10.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 10/23/2018] [Accepted: 10/25/2018] [Indexed: 12/31/2022]
Abstract
The circadian rhythm orchestrates many cellular functions, such as cell division, cell migration, metabolism and numerous intracellular biological processes. The physiological changes during sleep are believed to promote a suitable microenvironment for stem cells to proliferate, migrate and differentiate. These effects are mediated either directly by circadian clock genes or indirectly via hormones and cytokines. Hormones, such as melatonin and cortisol, are secreted in response to neural optic signals and act in harmony to regulate many biological functions during sleep. Herein, we correlate the effects of the main circadian genes on the expression of certain stem cell genes responsible for the regeneration of different tissues, including bone, cartilage, skin, and intestine. We also review the effects of different hormones and cytokines on stem cell activation or suppression and their relationship to the day/night cycle. The correlation of circadian rhythm with tissue regeneration could have implications in understanding the biology of sleep and tissue regeneration and in enhancing the efficacy and timing of surgical procedures.
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Affiliation(s)
- Hoda Elkhenany
- Centre of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 12588, Egypt; Department of Surgery, Faculty of Veterinary Medicine, Alexandria University, 22785, Egypt
| | - Abdelrahman AlOkda
- Centre of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 12588, Egypt
| | - Ahmed El-Badawy
- Centre of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 12588, Egypt
| | - Nagwa El-Badri
- Centre of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 12588, Egypt.
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Caranica C, Al-Omari A, Deng Z, Griffith J, Nilsen R, Mao L, Arnold J, Schüttler HB. Ensemble methods for stochastic networks with special reference to the biological clock of Neurospora crassa. PLoS One 2018; 13:e0196435. [PMID: 29768444 PMCID: PMC5955539 DOI: 10.1371/journal.pone.0196435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/12/2018] [Indexed: 11/18/2022] Open
Abstract
A major challenge in systems biology is to infer the parameters of regulatory networks that operate in a noisy environment, such as in a single cell. In a stochastic regime it is hard to distinguish noise from the real signal and to infer the noise contribution to the dynamical behavior. When the genetic network displays oscillatory dynamics, it is even harder to infer the parameters that produce the oscillations. To address this issue we introduce a new estimation method built on a combination of stochastic simulations, mass action kinetics and ensemble network simulations in which we match the average periodogram and phase of the model to that of the data. The method is relatively fast (compared to Metropolis-Hastings Monte Carlo Methods), easy to parallelize, applicable to large oscillatory networks and large (~2000 cells) single cell expression data sets, and it quantifies the noise impact on the observed dynamics. Standard errors of estimated rate coefficients are typically two orders of magnitude smaller than the mean from single cell experiments with on the order of ~1000 cells. We also provide a method to assess the goodness of fit of the stochastic network using the Hilbert phase of single cells. An analysis of phase departures from the null model with no communication between cells is consistent with a hypothesis of Stochastic Resonance describing single cell oscillators. Stochastic Resonance provides a physical mechanism whereby intracellular noise plays a positive role in establishing oscillatory behavior, but may require model parameters, such as rate coefficients, that differ substantially from those extracted at the macroscopic level from measurements on populations of millions of communicating, synchronized cells.
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Affiliation(s)
- C. Caranica
- Department of Statistics, University of Georgia, Athens, Georgia
| | - A. Al-Omari
- Department of Biomedical Systems and Informatics Engineering, Yarmouk University, Irbid, Jordan
| | - Z. Deng
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, Georgia
| | - J. Griffith
- Genetics Department, University of Georgia, Athens, Georgia
- College of Agricultural and Environmental Sciences, University of Georgia, Athens, Georgia
| | - R. Nilsen
- Genetics Department, University of Georgia, Athens, Georgia
| | - L. Mao
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, Georgia
| | - J. Arnold
- Genetics Department, University of Georgia, Athens, Georgia
- * E-mail:
| | - H.-B. Schüttler
- Department of Physics and Astronomy, University of Georgia, Athens, Georgia
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30
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Poliner E, Takeuchi T, Du ZY, Benning C, Farré EM. Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, Nannochloropsis oceanica CCMP1779. ACS Synth Biol 2018; 99:112-127. [PMID: 29518315 PMCID: PMC6616531 DOI: 10.1111/tpj.14314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 04/25/2023]
Abstract
Utilization of microalgae has been hampered by limited tools for creating loss-of-function mutants. Furthermore, modified strains for deployment into the field must be free of antibiotic resistance genes and face fewer regulatory hurdles if they are transgene free. The oleaginous microalga, Nannochloropsis oceanica CCMP1779, is an emerging model for microalgal lipid metabolism. We present a one-vector episomal CRISPR/Cas9 system for N. oceanica that enables the generation of marker-free mutant lines. The CEN/ARS6 region from Saccharomyces cerevisiae was included in the vector to facilitate its maintenance as circular extrachromosal DNA. The vector utilizes a bidirectional promoter to produce both Cas9 and a ribozyme flanked sgRNA. This system efficiently generates targeted mutations, and allows the loss of episomal DNA after the removal of selection pressure, resulting in marker-free nontransgenic engineered lines. To test this system, we disrupted the nitrate reductase gene ( NR) and subsequently removed the CRISPR episome to generate nontransgenic marker-free nitrate reductase knockout lines (NR-KO).
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Affiliation(s)
- Eric Poliner
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
| | - Tomomi Takeuchi
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
| | - Zhi-Yan Du
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
| | - Christoph Benning
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
- Plant Biology Department, Michigan State University, East Lansing, Michigan
| | - Eva M. Farré
- Plant Biology Department, Michigan State University, East Lansing, Michigan
- Corresponding Author: Eva M. Farré (), Phone: +1-517-353-5215
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Son GH, Cha HK, Chung S, Kim K. Multimodal Regulation of Circadian Glucocorticoid Rhythm by Central and Adrenal Clocks. J Endocr Soc 2018; 2:444-459. [PMID: 29713692 PMCID: PMC5915959 DOI: 10.1210/js.2018-00021] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/03/2018] [Indexed: 02/08/2023] Open
Abstract
Adrenal glucocorticoids (GCs) control a wide range of physiological processes, including metabolism, cardiovascular and pulmonary activities, immune and inflammatory responses, and various brain functions. During stress responses, GCs are secreted through activation of the hypothalamic-pituitary-adrenal axis, whereas circulating GC levels in unstressed states follow a robust circadian oscillation with a peak around the onset of the active period of a day. A recent advance in chronobiological research has revealed that multiple regulatory mechanisms, along with classical neuroendocrine regulation, underlie this GC circadian rhythm. The hierarchically organized circadian system, with a central pacemaker in the suprachiasmatic nucleus of the hypothalamus and local oscillators in peripheral tissues, including the adrenal gland, mediates periodicities in physiological processes in mammals. In this review, we primarily focus on our understanding of the circadian regulation of adrenal GC rhythm, with particular attention to the cooperative actions of the suprachiasmatic nucleus central and adrenal local clocks, and the clinical implications of this rhythm in human diseases.
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Affiliation(s)
- Gi Hoon Son
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Korea
| | - Hyo Kyeong Cha
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Korea
| | - Sooyoung Chung
- Department of Brain and Cognitive Sciences, Scranton College, Ewha Womans University, Seoul, Korea
| | - Kyungjin Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Korea.,Korea Brain Research Institute, Daegu, Korea
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Lin HH, Farkas ME. Altered Circadian Rhythms and Breast Cancer: From the Human to the Molecular Level. Front Endocrinol (Lausanne) 2018; 9:219. [PMID: 29780357 PMCID: PMC5945923 DOI: 10.3389/fendo.2018.00219] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 04/18/2018] [Indexed: 01/20/2023] Open
Abstract
Circadian clocks are fundamental, time-tracking systems that allow organisms to adapt to the appropriate time of day and drive many physiological and cellular processes. Altered circadian rhythms can result from night-shift work, chronic jet lag, exposure to bright lights at night, or other conditioning, and have been shown to lead to increased likelihood of cancer, metabolic and cardiovascular diseases, and immune dysregulation. In cases of cancer, worse patient prognoses and drug resistance during treatment have also been observed. Breast, colon, prostate, lung, and ovarian cancers and hepatocellular carcinoma have all been linked in one way or another with altered circadian rhythms. Critical elements at the molecular level of the circadian system have been associated with cancer, but there have been fairly few studies in this regard. In this mini-review, we specifically focus on the role of altered circadian rhythms in breast cancer, providing an overview of studies performed at the epidemiological level through assessments made in animal and cellular models of the disease. We also address the disparities present among studies that take into account the rhythmicity of core clock and other proteins, and those which do not, and offer insights to the use of small molecules for studying the connections between circadian rhythms and cancer. This article will provide the reader with a concise, but thorough account of the research landscape as it pertains to altered circadian rhythms and breast cancer.
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Salavaty A, Mohammadi N, Shahmoradi M, Naderi Soorki M. Bioinformatic Analysis of Circadian Expression of Oncogenes and Tumor Suppressor Genes. Bioinform Biol Insights 2017; 11:1177932217746991. [PMID: 29276378 PMCID: PMC5734456 DOI: 10.1177/1177932217746991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/11/2017] [Indexed: 01/09/2023] Open
Abstract
Background Circadian rhythms are physiological and behavioral cycles with a period of approximately 24 hours that control various functions including gene expression. Circadian disruption is associated with a variety of diseases, especially cancer. Although some of the oncogenes and tumor suppressor genes (TSGs) are known as clock-controlled genes (CCGs), the analysis and annotation of circadian expression of most human oncogenes and TSGs are still lacking. This study aims to investigate the circadian expression of a list of human oncogenes and TSGs. Methods A bioinformatic analysis was conducted on a gene library comprising 120 genes to investigate the circadian expression of human oncogenes and TSGs. To achieve this purpose, the genotranscriptomic data were retrieved from COSMIC and analyzed by R statistical software. Furthermore, the acquired data were analyzed at the transcriptomic and proteomic levels using several publicly available databases. Also, the significance of all analyses was confirmed statistically. Results Altogether, our results indicated that 7 human oncogenes/TSGs may be expressed and function in a circadian manner. These oncogenes/TSGs showed a circadian expression pattern at CircaDB database and associated with at least one of the circadian genes/CCGs based on both genotranscriptomic and correlation analyses. Conclusions Although 4 of 7 finally outputted genes have been previously reported to be clock controlled, heretofore there is no report about the circadian expression of 3 other genes. Considering the importance of oncogenes/TSGs in the initiation and progression of cancer, further studies are suggested for the identification of exact circadian expression patterns of these 3 human oncogenes/TSGs.
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Affiliation(s)
- Adrian Salavaty
- Division of Biotechnology, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Niloufar Mohammadi
- Department of Biology, Friedrich Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Mozhdeh Shahmoradi
- Division of Biotechnology, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Maryam Naderi Soorki
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Entrainment of Breast Cell Lines Results in Rhythmic Fluctuations of MicroRNAs. Int J Mol Sci 2017; 18:ijms18071499. [PMID: 28704935 PMCID: PMC5535989 DOI: 10.3390/ijms18071499] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/12/2017] [Accepted: 07/05/2017] [Indexed: 12/13/2022] Open
Abstract
Circadian rhythms are essential for temporal (~24 h) regulation of molecular processes in diverse species. Dysregulation of circadian gene expression has been implicated in the pathogenesis of various disorders, including hypertension, diabetes, depression, and cancer. Recently, microRNAs (miRNAs) have been identified as critical modulators of gene expression post-transcriptionally, and perhaps involved in circadian clock architecture or their output functions. The aim of the present study is to explore the temporal expression of miRNAs among entrained breast cell lines. For this purpose, we evaluated the temporal (28 h) expression of 2006 miRNAs in MCF-10A, MCF-7, and MDA-MB-231 cells using microarrays after serum shock entrainment. We noted hundreds of miRNAs that exhibit rhythmic fluctuations in each breast cell line, and some of them across two or three cell lines. Afterwards, we validated the rhythmic profiles exhibited by miR-141-5p, miR-1225-5p, miR-17-5p, miR-222-5p, miR-769-3p, and miR-548ay-3p in the above cell lines, as well as in ZR-7530 and HCC-1954 using RT-qPCR. Our results show that serum shock entrainment in breast cells lines induces rhythmic fluctuations of distinct sets of miRNAs, which have the potential to be related to endogenous circadian clock, but extensive investigation is required to elucidate that connection.
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35
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Zhang Z, Lai S, Wang Y, Li L, Yin H, Wang Y, Zhao X, Li D, Yang M, Zhu Q. Rhythmic expression of circadian clock genes in the preovulatory ovarian follicles of the laying hen. PLoS One 2017; 12:e0179019. [PMID: 28604799 PMCID: PMC5467841 DOI: 10.1371/journal.pone.0179019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 05/23/2017] [Indexed: 11/18/2022] Open
Abstract
The circadian clock is reported to play a role in the ovaries in a variety of vertebrate species, including the domestic hen. However, the ovary is an organ that changes daily, and the laying hen maintains a strict follicular hierarchy. The aim of this study was to examine the spatial-temporal expression of several known canonical clock genes in the granulosa and theca layers of six hierarchy follicles. We demonstrated that the granulosa cells (GCs) of the F1-F3 follicles harbored intrinsic oscillatory mechanisms in vivo. In addition, cultured granulosa cells (GCs) from F1 follicles exposed to luteinizing hormone (LH) synchronization displayed Per2 mRNA oscillations, whereas, the less mature GCs (F5 plus F6) displayed no circadian change in Per2 mRNA levels. Cultures containing follicle-stimulating hormone (FSH) combined with LH expressed levels of Per2 mRNA that were 2.5-fold higher than those in cultures with LH or FSH alone. These results show that there is spatial specificity in the localization of clock cells in hen preovulatory follicles. In addition, our results support the hypothesis that gonadotropins provide a cue for the development of the functional cellular clock in immature GCs.
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Affiliation(s)
- Zhichao Zhang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Shuang Lai
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Yagang Wang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Liang Li
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Huadong Yin
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Yan Wang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Xiaoling Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Mingyao Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Qing Zhu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
- * E-mail:
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Brunson JK, Griffith J, Bowles D, Case ME, Arnold J. lac-1 and lag-1 with ras-1 affect aging and the biological clock in Neurospora crassa. Ecol Evol 2016; 6:8341-8351. [PMID: 28031787 PMCID: PMC5167027 DOI: 10.1002/ece3.2554] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 09/17/2016] [Accepted: 09/22/2016] [Indexed: 12/22/2022] Open
Abstract
Using an automated cell counting technique developed previously (Case et al., Ecology and Evolution 2014; 4: 3494), we explore the lifespan effects of lac‐1, a ceramide synthase gene paralogous to lag‐1 in Neurospora crassa in conjunction with the band bd (ras‐1) gene. We find that the replicative lifespan of a lac‐1KObd double mutants is short, about one race tube cycle, and this double mutant lacks a strong ~21‐hr clock cycle as shown by race tube and fluorometer analysis of fluorescent strains including lac‐1KO. This short replicative lifespan phenotype is contrasted with a very long estimated chronological lifespan for lac‐1KObd double mutants from 247 to 462 days based on our regression analyses on log viability, and for the single mutant lac‐1KO, 161 days. Both of these estimated lifespans are much higher than that of previously studied WT and bd single mutant strains. In a lac‐1 rescue and induction experiment, the expression of lac‐1+ as driven by a quinic acid‐dependent promoter actually decreases the median chronological lifespan of cells down to only 7 days, much lower than the 34‐day median lifespan found in control bd conidia also grown on quinic acid media, which we interpret as an effect of balancing selection acting on ceramide levels based on previous findings from the literature. Prior work has shown phytoceramides can act as a signal for apoptosis in stressed N. crassa cells. To test this hypothesis of balancing selection on phytoceramide levels, we examine the viability of WT, lag‐1KObd, and lac‐1KObd strains following the dual stresses of heat and glycolysis inhibition, along with phytoceramide treatments of different dosages. We find that the phytoceramide dosage–response curve is altered in the lag‐1KObd mutant, but not in the lac‐1KObd mutant. We conclude that phytoceramide production is responsible for the previously reported longevity effects in the lag‐1KObd mutant, but a different ceramide may be responsible for the longevity effect observed in the lac‐1KObd mutant.
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Affiliation(s)
- John K Brunson
- Center for Marine Biotechnology and Biomedicine J. Craig Venter Institute-West Coast Campus University of California San Diego Scripps Institution of Oceanography La Jolla CA USA
| | - James Griffith
- College of Agricultural and Environmental Sciences University of Georgia Athens GA USA; Genetics Department University of Georgia Athens GA USA
| | | | - Mary E Case
- Genetics Department University of Georgia Athens GA USA
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Deng Z, Arsenault S, Caranica C, Griffith J, Zhu T, Al-Omari A, Schüttler HB, Arnold J, Mao L. Synchronizing stochastic circadian oscillators in single cells of Neurospora crassa. Sci Rep 2016; 6:35828. [PMID: 27786253 PMCID: PMC5082370 DOI: 10.1038/srep35828] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/05/2016] [Indexed: 11/09/2022] Open
Abstract
The synchronization of stochastic coupled oscillators is a central problem in physics and an emerging problem in biology, particularly in the context of circadian rhythms. Most measurements on the biological clock are made at the macroscopic level of millions of cells. Here measurements are made on the oscillators in single cells of the model fungal system, Neurospora crassa, with droplet microfluidics and the use of a fluorescent recorder hooked up to a promoter on a clock controlled gene-2 (ccg-2). The oscillators of individual cells are stochastic with a period near 21 hours (h), and using a stochastic clock network ensemble fitted by Markov Chain Monte Carlo implemented on general-purpose graphical processing units (or GPGPUs) we estimated that >94% of the variation in ccg-2 expression was stochastic (as opposed to experimental error). To overcome this stochasticity at the macroscopic level, cells must synchronize their oscillators. Using a classic measure of similarity in cell trajectories within droplets, the intraclass correlation (ICC), the synchronization surface ICC is measured on >25,000 cells as a function of the number of neighboring cells within a droplet and of time. The synchronization surface provides evidence that cells communicate, and synchronization varies with genotype.
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Affiliation(s)
- Zhaojie Deng
- College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Sam Arsenault
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Cristian Caranica
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - James Griffith
- Genetics Department, University of Georgia, Athens, GA 30602, USA.,College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA 30602, USA
| | - Taotao Zhu
- College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Ahmad Al-Omari
- Department of Biomedical Systems and Informatics Engineering, Yarmouk University, Irbid, 21163, Jordan
| | | | - Jonathan Arnold
- Genetics Department, University of Georgia, Athens, GA 30602, USA
| | - Leidong Mao
- College of Engineering, University of Georgia, Athens, GA 30602, USA
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Mohamadian S, Golalipour M, Yazdani Y, Farazmandfar T, Tabarraei A, Shahbazi M. Oscillation in expression of Adenylyl Cyclase isoforms: new insight to regulation of molecular clock. BIOL RHYTHM RES 2016. [DOI: 10.1080/09291016.2016.1234756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Muranaka T, Oyama T. Heterogeneity of cellular circadian clocks in intact plants and its correction under light-dark cycles. SCIENCE ADVANCES 2016; 2:e1600500. [PMID: 27453946 PMCID: PMC4956400 DOI: 10.1126/sciadv.1600500] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/21/2016] [Indexed: 05/18/2023]
Abstract
Recent advances in single-cell analysis have revealed the stochasticity and nongenetic heterogeneity inherent to cellular processes. However, our knowledge of the actual cellular behaviors in a living multicellular organism is still limited. By using a single-cell bioluminescence imaging technique on duckweed, Lemna gibba, we demonstrate that, under constant conditions, cells in the intact plant work as individual circadian clocks that oscillate with their own frequencies and respond independently to external stimuli. Quantitative analysis uncovered the heterogeneity and instability of cellular clocks and partial synchronization between neighboring cells. Furthermore, we found that cellular clocks in the plant body under light-dark cycles showed a centrifugal phase pattern in which the effect of cell-to-cell heterogeneity in period lengths was almost masked. The inherent heterogeneity in the properties of cellular clocks observed under constant conditions is corrected under light-dark cycles to coordinate the daily rhythms of the plant body. These findings provide a novel perspective of spatiotemporal architectures in the plant circadian system.
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Shi G, Xie P, Qu Z, Zhang Z, Dong Z, An Y, Xing L, Liu Z, Dong Y, Xu G, Yang L, Liu Y, Xu Y. Distinct Roles of HDAC3 in the Core Circadian Negative Feedback Loop Are Critical for Clock Function. Cell Rep 2016; 14:823-834. [PMID: 26776516 DOI: 10.1016/j.celrep.2015.12.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 10/11/2015] [Accepted: 12/15/2015] [Indexed: 01/30/2023] Open
Abstract
In the core mammalian circadian negative feedback loop, the BMAL1-CLOCK complex activates the transcription of the genes Period (Per) and Cryptochrome (Cry). To close the negative feedback loop, the PER-CRY complex interacts with the BMAL1-CLOCK complex to repress its activity. These two processes are separated temporally to ensure clock function. Here, we show that histone deacetylase 3 (HDAC3) is a critical component of the circadian negative feedback loop by regulating both the activation and repression processes in a deacetylase activity-independent manner. Genetic depletion of Hdac3 results in low-amplitude circadian rhythms and dampened E-box-driven transcription. In subjective morning, HDAC3 is required for the efficient transcriptional activation process by regulating BMAL1 stability. In subjective night, however, HDAC3 blocks FBXL3-mediated CRY1 degradation and strongly promotes BMAL1 and CRY1 association. Therefore, these two opposing but temporally separated roles of HDAC3 in the negative feedback loop provide a mechanism for robust circadian gene expression.
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Affiliation(s)
- Guangsen Shi
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Pancheng Xie
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhipeng Qu
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhihui Zhang
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhen Dong
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Yang An
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Lijuan Xing
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Yingying Dong
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Guoqiang Xu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Ling Yang
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Ying Xu
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China; Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China.
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41
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A Period2 Phosphoswitch Regulates and Temperature Compensates Circadian Period. Mol Cell 2016; 60:77-88. [PMID: 26431025 DOI: 10.1016/j.molcel.2015.08.022] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 06/01/2015] [Accepted: 08/25/2015] [Indexed: 01/05/2023]
Abstract
Period (PER) protein phosphorylation is a critical regulator of circadian period, yet an integrated understanding of the role and interaction between phosphorylation sites that can both increase and decrease PER2 stability remains elusive. Here, we propose a phosphoswitch model, where two competing phosphorylation sites determine whether PER2 has a fast or slow degradation rate. This mathematical model accurately reproduces the three-stage degradation kinetics of endogenous PER2. We predict and demonstrate that the phosphoswitch is intrinsically temperature sensitive, slowing down PER2 degradation as a result of faster reactions at higher temperatures. The phosphoswitch provides a biochemical mechanism for circadian temperature compensation of circadian period. This phosphoswitch additionally explains the phenotype of Familial Advanced Sleep Phase (FASP) and CK1ε(tau) genetic circadian rhythm disorders, metabolic control of PER2 stability, and how drugs that inhibit CK1 alter period. The phosphoswitch provides a general mechanism to integrate diverse stimuli to regulate circadian period.
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42
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Identifying Novel Transcriptional Regulators with Circadian Expression. Mol Cell Biol 2015; 36:545-58. [PMID: 26644408 DOI: 10.1128/mcb.00701-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/19/2015] [Indexed: 01/06/2023] Open
Abstract
Organisms adapt their physiology and behavior to the 24-h day-night cycle to which they are exposed. On a cellular level, this is regulated by intrinsic transcriptional-translational feedback loops that are important for maintaining the circadian rhythm. These loops are organized by members of the core clock network, which further regulate transcription of downstream genes, resulting in their circadian expression. Despite progress in understanding circadian gene expression, only a few players involved in circadian transcriptional regulation, including transcription factors, epigenetic regulators, and long noncoding RNAs, are known. Aiming to discover such genes, we performed a high-coverage transcriptome analysis of a circadian time course in murine fibroblast cells. In combination with a newly developed algorithm, we identified many transcription factors, epigenetic regulators, and long intergenic noncoding RNAs that are cyclically expressed. In addition, a number of these genes also showed circadian expression in mouse tissues. Furthermore, the knockdown of one such factor, Zfp28, influenced the core clock network. Mathematical modeling was able to predict putative regulator-effector interactions between the identified circadian genes and may help for investigations into the gene regulatory networks underlying circadian rhythms.
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Okubo N, Fujiwara H, Minami Y, Kunimoto T, Hosokawa T, Umemura Y, Inokawa H, Asada M, Oda R, Kubo T, Yagita K. Parathyroid hormone resets the cartilage circadian clock of the organ-cultured murine femur. Acta Orthop 2015; 86:627-31. [PMID: 25765847 PMCID: PMC4564788 DOI: 10.3109/17453674.2015.1029393] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND AND PURPOSE The circadian clock governs endogenous day-night variations. In bone, the metabolism and growth show diurnal rhythms. The circadian clock is based on a transcription-translation feedback loop composed of clock genes including Period2 (Per2), which encodes the protein period circadian protein homolog 2. Because plasma parathyroid hormone (PTH) levels show diurnal variation, we hypothesized that PTH could carry the time information to bone and cartilage. In this study, we analyzed the effect of PTH on the circadian clock of the femur. PATIENTS AND METHODS Per2::Luciferase (Per2::Luc) knock-in mice were used and their femurs were organ-cultured. The bioluminescence was measured using photomultiplier tube-based real-time bioluminescence monitoring equipment or real-time bioluminescence microscopic imaging devices. PTH or its vehicle was administered and the phase shifts were calculated. Immunohistochemistry was performed to detect PTH type 1 receptor (PTH1R) expression. RESULTS Real-time bioluminescence monitoring revealed that PTH reset the circadian rhythm of the Per2::Luc activity in the femurs in an administration time-dependent and dose-dependent manner. Microscopic bioluminescence imaging revealed that Per2::Luc activity in the growth plate and the articular cartilage showed that the circadian rhythms and their phase shifts were induced by PTH. PTH1R was expressed in the growth plate cartilage. INTERPRETATION In clinical practice, teriparatide (PTH (1-34)) treatment is widely used for osteoporosis. We found that PTH administration regulated the femoral circadian clock oscillation, particularly in the cartilage. Regulation of the local circadian clock by PTH may lead to a more effective treatment for not only osteoporosis but also endochondral ossification in bone growth and fracture repair.
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Affiliation(s)
- Naoki Okubo
- 1Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine,2Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine,3Department of Musculoskeletal Chronobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, Japan
| | - Hiroyoshi Fujiwara
- 2Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Yoichi Minami
- 1Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine,3Department of Musculoskeletal Chronobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, Japan
| | - Tatsuya Kunimoto
- 1Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine,2Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine,3Department of Musculoskeletal Chronobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, Japan
| | - Toshihiro Hosokawa
- 1Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine,2Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine,3Department of Musculoskeletal Chronobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, Japan
| | - Yasuhiro Umemura
- 1Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine
| | - Hitoshi Inokawa
- 1Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine
| | - Maki Asada
- 2Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Ryo Oda
- 2Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Toshikazu Kubo
- 2Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine,3Department of Musculoskeletal Chronobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, Japan
| | - Kazuhiro Yagita
- 1Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine
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Ranieri D, Cucina A, Bizzarri M, Alimandi M, Torrisi MR. Microgravity influences circadian clock oscillation in human keratinocytes. FEBS Open Bio 2015; 5:717-23. [PMID: 26448904 PMCID: PMC4571538 DOI: 10.1016/j.fob.2015.08.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/31/2015] [Accepted: 08/22/2015] [Indexed: 11/30/2022] Open
Abstract
Changes of gravitational forces affect oscillations of circadian clock genes. The effects of microgravity on the circadian clock persist during the recovery process from microgravity. Linking of mechanotransduction to circadian rhythms reveals changes in physiology.
Microgravity and sudden changes of gravitational forces exert numerous effects on tissues, organs and apparatus. Responses to these forces variably applied to cells indicate the existence of mechanotransduction pathways able to modulate transcription. Oscillation of circadian clocks similarly influences many cellular and metabolic processes. Here we hypothesized that signals derived from changes of gravitational forces applied to epidermal cells might influence their physiology in harmony with the oscillation of the molecular clock. In this study, we describe amplified oscillations of Bmal1 circadian clock gene in human keratinocytes exposed to short simulated microgravity and to rapid variation of gravitational forces. We found that exposure to microgravity enhances the amplitude of the Bmal1 feedback loop sustained by an apparently lower variability of Rev-erbα transcription, while recovery from microgravity is characterized by increased amplitude of Bmal1 expression and elongation of the oscillatory periods of Bmal1 and Rev-erbα. These data highlight the existence of integrated signaling network connecting mechanosensitive pathways to circadian gene regulation.
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Affiliation(s)
- Danilo Ranieri
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Medicina Clinica e Molecolare, Sapienza Università di Roma, Italy
| | - Alessandra Cucina
- Dipartimento di Chirurgia "P. Valdoni", Sapienza Università di Roma, Italy
| | - Mariano Bizzarri
- Dipartimento di Medicina Sperimentale, Sapienza Università di Roma, Italy
| | - Maurizio Alimandi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Medicina Clinica e Molecolare, Sapienza Università di Roma, Italy
| | - Maria Rosaria Torrisi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Medicina Clinica e Molecolare, Sapienza Università di Roma, Italy ; Azienda Ospedaliera S. Andrea, Rome, Italy
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45
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Dual-Color Monitoring Overcomes the Limitations of Single Bioluminescent Reporters in Fast-Growing Microbes and Reveals Phase-Dependent Protein Productivity during the Metabolic Rhythms of Saccharomyces cerevisiae. Appl Environ Microbiol 2015; 81:6484-95. [PMID: 26162874 DOI: 10.1128/aem.01631-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/06/2015] [Indexed: 01/19/2023] Open
Abstract
Luciferase is a useful, noninvasive reporter of gene regulation that can be continuously monitored over long periods of time; however, its use is problematic in fast-growing microbes like bacteria and yeast because rapidly changing cell numbers and metabolic states also influence bioluminescence, thereby confounding the reporter's signal. Here we show that these problems can be overcome in the budding yeast Saccharomyces cerevisiae by simultaneously monitoring bioluminescence from two different colors of beetle luciferase, where one color (green) reports activity of a gene of interest, while a second color (red) is stably expressed and used to continuously normalize green bioluminescence for fluctuations in signal intensity that are unrelated to gene regulation. We use this dual-luciferase strategy in conjunction with a light-inducible promoter system to test whether different phases of yeast respiratory oscillations are more suitable for heterologous protein production than others. By using pulses of light to activate production of a green luciferase while normalizing signal variation to a red luciferase, we show that the early reductive phase of the yeast metabolic cycle produces more luciferase than other phases.
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Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL. Cancer/Testis Antigen PASD1 Silences the Circadian Clock. Mol Cell 2015; 58:743-54. [PMID: 25936801 PMCID: PMC4458219 DOI: 10.1016/j.molcel.2015.03.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 02/13/2015] [Accepted: 03/25/2015] [Indexed: 01/06/2023]
Abstract
The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms.
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Affiliation(s)
- Alicia K Michael
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Stacy L Harvey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patrick J Sammons
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Amanda P Anderson
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Hema M Kopalle
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alison H Banham
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, San Diego, CA 92093, USA.
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Luna A, McFadden GB, Aladjem MI, Kohn KW. Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response. PLoS Comput Biol 2015; 11:e1004144. [PMID: 26020938 PMCID: PMC4462596 DOI: 10.1371/journal.pcbi.1004144] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 01/20/2015] [Indexed: 02/06/2023] Open
Abstract
The circadian clock is a set of regulatory steps that oscillate with a period of approximately 24 hours influencing many biological processes. These oscillations are robust to external stresses, and in the case of genotoxic stress (i.e. DNA damage), the circadian clock responds through phase shifting with primarily phase advancements. The effect of DNA damage on the circadian clock and the mechanism through which this effect operates remains to be thoroughly investigated. Here we build an in silico model to examine damage-induced circadian phase shifts by investigating a possible mechanism linking circadian rhythms to metabolism. The proposed model involves two DNA damage response proteins, SIRT1 and PARP1, that are each consumers of nicotinamide adenine dinucleotide (NAD), a metabolite involved in oxidation-reduction reactions and in ATP synthesis. This model builds on two key findings: 1) that SIRT1 (a protein deacetylase) is involved in both the positive (i.e. transcriptional activation) and negative (i.e. transcriptional repression) arms of the circadian regulation and 2) that PARP1 is a major consumer of NAD during the DNA damage response. In our simulations, we observe that increased PARP1 activity may be able to trigger SIRT1-induced circadian phase advancements by decreasing SIRT1 activity through competition for NAD supplies. We show how this competitive inhibition may operate through protein acetylation in conjunction with phosphorylation, consistent with reported observations. These findings suggest a possible mechanism through which multiple perturbations, each dominant during different points of the circadian cycle, may result in the phase advancement of the circadian clock seen during DNA damage. Many physiological processes are regulated by the circadian clock, and we are continuing to learn about the role of the circadian clock in disease. Research in recent years has begun to shed light on the feedback mechanisms that exist between circadian regulation and other processes, including metabolism and the response to DNA damage. A challenge has been to understand the dynamic nature of the protein interactions of these processes, which often involve protein modification as a means of communicating cellular states, such as damaged DNA. Here we have devised a model that simulates an alteration of the circadian clock that is observed during DNA damage response. A novel aspect of this model is the inclusion of SIRT1, a protein that regulates core circadian proteins through modification and helps to repress gene expression. SIRT1 is dependent on a metabolite regulated by the circadian clock and is depleted during DNA damage. In conjunction with a second form of protein modification, our results suggest that multiple forms of protein modification may contribute to the experimentally observed alterations to circadian function.
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Affiliation(s)
- Augustin Luna
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
- Department of Bioinformatics, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
| | - Geoffrey B. McFadden
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
| | - Mirit I. Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Kurt W. Kohn
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
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48
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Izumo M, Pejchal M, Schook AC, Lange RP, Walisser JA, Sato TR, Wang X, Bradfield CA, Takahashi JS. Differential effects of light and feeding on circadian organization of peripheral clocks in a forebrain Bmal1 mutant. eLife 2014; 3:e04617. [PMID: 25525750 PMCID: PMC4298698 DOI: 10.7554/elife.04617] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/18/2014] [Indexed: 12/14/2022] Open
Abstract
In order to assess the contribution of a central clock in the hypothalamic suprachiasmatic nucleus (SCN) to circadian behavior and the organization of peripheral clocks, we generated forebrain/SCN-specific Bmal1 knockout mice by using floxed Bmal1 and pan-neuronal Cre lines. The forebrain knockout mice showed >90% deletion of BMAL1 in the SCN and exhibited an immediate and complete loss of circadian behavior in constant conditions. Circadian rhythms in peripheral tissues persisted but became desynchronized and damped in constant darkness. The loss of synchrony was rescued by light/dark cycles and partially by restricted feeding (only in the liver and kidney but not in the other tissues) in a distinct manner. These results suggest that the forebrain/SCN is essential for internal temporal order of robust circadian programs in peripheral clocks, and that individual peripheral clocks are affected differently by light and feeding in the absence of a functional oscillator in the forebrain.
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Affiliation(s)
- Mariko Izumo
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Martina Pejchal
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Andrew C Schook
- Department of Neurobiology, Northwestern University, Evanston, United States
- Howard Hughes Medical Institute, Northwestern University, Evanston, United States
| | - Ryan P Lange
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Jacqueline A Walisser
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, United States
| | - Takashi R Sato
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
- JST, PRESTO, University of Tübingen, Tübingen, Germany
| | - Xiaozhong Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | | | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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Du Pré BC, Van Veen TAB, Young ME, Vos MA, Doevendans PA, Van Laake LW. Circadian rhythms in cell maturation. Physiology (Bethesda) 2014; 29:72-83. [PMID: 24382873 DOI: 10.1152/physiol.00036.2013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Circadian rhythms are of major importance in mammalian physiology and disease. In this review, we give an overview of the present knowledge on origination of circadian rhythms. We discuss the development of both master and peripheral clocks and compare the origination of circadian rhythms in utero and in vitro.
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Affiliation(s)
- Bastiaan C Du Pré
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
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50
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Okubo N, Minami Y, Fujiwara H, Umemura Y, Tsuchiya Y, Shirai T, Oda R, Inokawa H, Kubo T, Yagita K. Prolonged bioluminescence monitoring in mouse ex vivo bone culture revealed persistent circadian rhythms in articular cartilages and growth plates. PLoS One 2013; 8:e78306. [PMID: 24223788 PMCID: PMC3817244 DOI: 10.1371/journal.pone.0078306] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 09/11/2013] [Indexed: 12/19/2022] Open
Abstract
The bone is a metabolically active organ which undergoes repeated remodeling cycles of bone resorption and formation. In this study, we revealed a robust and extremely long-lasting circadian rhythm in ex vivo culture maintained for over six months from the femoral bone of a PERIOD2(Luciferase) mouse. Furthermore, we also identified robust circadian clocks in flat bones. High- or low-magnification real-time bioluminescence microscopic imaging revealed that the robust circadian rhythms emanated from the articular cartilage and the epiphyseal cartilage within the growth plate of juvenile animals. Stimulation by forskolin or dexamethasone treatment caused type 0 phase resetting, indicating canonical entraining properties of the bone clock. Together, our findings from long-term ex vivo culture revealed that "tissue-autonomous" circadian rhythm in the articular cartilage and the growth plate of femoral bone functions for several months even in an organ culture condition, and provided a useful in vitro assay system investigating the role of the biological clock in bone formation or development.
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Affiliation(s)
- Naoki Okubo
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Musculoskeletal Chronobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoichi Minami
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Musculoskeletal Chronobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroyoshi Fujiwara
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yasuhiro Umemura
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiki Tsuchiya
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshiharu Shirai
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Orthopaedic Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Ryo Oda
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hitoshi Inokawa
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshikazu Kubo
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Musculoskeletal Chronobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Musculoskeletal Chronobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Precursory Research for Embryonic Science and Technology (PREST), Japan Science and Technology Agency, Saitama, Japan
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