101
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Bartman CM, Prakash YS. Bringing the cellular clock into understanding lung disease: it's time, period! Am J Physiol Lung Cell Mol Physiol 2020; 319:L273-L276. [PMID: 32639868 DOI: 10.1152/ajplung.00320.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
| | - Y S Prakash
- Department of Anesthesiology, Mayo Clinic, Rochester, Minnesota.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
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102
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Rajendran S, Barbon S, Pucciarelli S. Spotlight on Circadian Genes and Colorectal Cancer Crosstalk. Endocr Metab Immune Disord Drug Targets 2020; 21:4-11. [PMID: 32579510 DOI: 10.2174/1871530320666200624192517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/19/2020] [Accepted: 04/22/2020] [Indexed: 11/22/2022]
Abstract
Mammalian physiology is regulated by circadian clock through oscillating feedback loops controlling cellular processes and behaviors. Recent findings have led to an interesting connection between circadian disruption and colorectal cancer progression and incidence through controlling the hallmarks of cancer, namely cell cycle, cell metabolism and cell death. Deeper understanding of the circadian mechanisms that define the colorectal cancer pathophysiology is the need of the hour to define a chronotherapy for improving colorectal cancer patient survival. This review identifies the key areas in which circadian genes interact with cellular pathways to modify the outcome with respect to colorectal cancer incidence and progression.
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Affiliation(s)
| | - Silvia Barbon
- Department of Neurosciences, University of Padova, Padua, Italy
| | - Salvatore Pucciarelli
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padua, Italy
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103
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Greco CM, Sassone-Corsi P. Personalized medicine and circadian rhythms: Opportunities for modern society. J Exp Med 2020; 217:e20200702. [PMID: 32433754 PMCID: PMC7971139 DOI: 10.1084/jem.20200702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Circadian rhythms govern physiology and metabolism, leading to controlled homeostasis. We discuss the impact of circadian rhythms on society and the challenges for the imminent future of personalized medicine.
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Affiliation(s)
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California Irvine, Irvine, CA
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104
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Kim DW, Zavala E, Kim JK. Wearable technology and systems modeling for personalized chronotherapy. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.coisb.2020.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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105
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Affiliation(s)
- Marc D Ruben
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, USA
| | - David F Smith
- Divisions of Pediatric Otolaryngology and Pulmonary and Sleep Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.,Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati School of Medicine, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
| | - Garret A FitzGerald
- Department of Systems Pharmacology and Translational Therapeutics, at the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. .,Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.,Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - John B Hogenesch
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, USA.
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106
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Latent periodic process inference from single-cell RNA-seq data. Nat Commun 2020; 11:1441. [PMID: 32188848 PMCID: PMC7080821 DOI: 10.1038/s41467-020-15295-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 03/03/2020] [Indexed: 11/15/2022] Open
Abstract
The development of a phenotype in a multicellular organism often involves multiple, simultaneously occurring biological processes. Advances in single-cell RNA-sequencing make it possible to infer latent developmental processes from the transcriptomic profiles of cells at various developmental stages. Accurate characterization is challenging however, particularly for periodic processes such as cell cycle. To address this, we develop Cyclum, an autoencoder approach identifying circular trajectories in the gene expression space. Cyclum substantially improves the accuracy and robustness of cell-cycle characterization beyond existing approaches. Applying Cyclum to removing cell-cycle effects substantially improves delineations of cell subpopulations, which is useful for establishing various cell atlases and studying tumor heterogeneity. Traditional methods for determining cell type composition lack scalability, while single-cell technologies remain costly and noisy compared to bulk RNA-seq. Here, the authors present a highly efficient tool to measure cellular heterogeneity in bulk expression through robust integration of single-cell information.
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107
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Morris AR, Stanton DL, Roman D, Liu AC. Systems Level Understanding of Circadian Integration with Cell Physiology. J Mol Biol 2020; 432:3547-3564. [PMID: 32061938 DOI: 10.1016/j.jmb.2020.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 02/07/2023]
Abstract
The mammalian circadian clock regulates a wide variety of physiological and behavioral processes. In turn, its disruption is associated with sleep deficiency, metabolic syndrome, neurological and psychiatric disorders, and cancer. At the turn of the century, the circadian clock was determined to be regulated by a transcriptional negative feedback mechanism composed of a dozen core clock genes. More recently, large-scale genomic studies have expanded the clock into a complex network composed of thousands of gene outputs and inputs. A major task of circadian research is to utilize systems biological approaches to uncover the governing principles underlying cellular oscillatory behavior and advance understanding of biological functions at the genomic level with spatiotemporal resolution. This review focuses on the genes and pathways that provide inputs to the circadian clock. Several emerging examples include AMP-activated protein kinase AMPK, nutrient/energy sensor mTOR, NAD+-dependent deacetylase SIRT1, hypoxia-inducible factor HIF1α, oxidative stress-inducible factor NRF2, and the proinflammatory factor NF-κB. Among others that continue to be revealed, these input pathways reflect the extensive interplay between the clock and cell physiology through the regulation of core clock genes and proteins. While the scope of this crosstalk is well-recognized, precise molecular links are scarce, and the underlying regulatory mechanisms are not well understood. Future research must leverage genetic and genomic tools and technologies, network analysis, and computational modeling to characterize additional modifiers and input pathways. This systems-based framework promises to advance understanding of the circadian timekeeping system and may enable the enhancement of circadian functions through related input pathways.
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Affiliation(s)
- Andrew R Morris
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Daniel L Stanton
- Department of Animal Sciences, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, United States of America
| | - Destino Roman
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Andrew C Liu
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States of America.
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108
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Abstract
Circadian rhythms are daily cycles in biological function that are ubiquitous in nature. Understood as a means for organisms to anticipate daily environmental changes, circadian rhythms are also important for orchestrating complex biological processes such as immunity. Nowhere is this more evident than in the respiratory system, where circadian rhythms in inflammatory lung disease have been appreciated since ancient times. In this focused review we examine how emerging research on circadian rhythms is being applied to the study of fundamental lung biology and respiratory disease. We begin with a general introduction to circadian rhythms and the molecular circadian clock that underpins them. We then focus on emerging data tying circadian clock function to immunologic activities within the respiratory system. We conclude by considering outstanding questions about biological timing in the lung and how a better command of chronobiology could inform our understanding of complex lung diseases.
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Affiliation(s)
- Charles Nosal
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
| | - Anna Ehlers
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
| | - Jeffrey A Haspel
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
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109
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Larriba Y, Rueda C, Fernández MA, Peddada SD. Order restricted inference in chronobiology. Stat Med 2020; 39:265-278. [PMID: 31769057 DOI: 10.1002/sim.8397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 06/11/2019] [Accepted: 09/21/2019] [Indexed: 01/25/2023]
Abstract
This paper is motivated by applications in oscillatory systems where researchers are typically interested in discovering components of those systems that display rhythmic temporal patterns. The contributions of this paper are twofold. First, a methodology is developed based on a circular signal plus error model that is defined using order restrictions. This mathematical formulation of rhythmicity is simple, easily interpretable and very flexible, with the latter property derived from the nonparametric formulation of the signal. Second, we address various commonly encountered problems in the analysis of oscillatory systems data. Specifically, we propose a methodology for (a) detecting rhythmic signals in an oscillatory system and (b) estimating the unknown sampling time that occurs when tissues are obtained from subjects whose time of death is unknown. The proposed methodology is computationally efficient, outperforms the existing methods, and is broadly applicable to address a wide range of questions related to oscillatory systems.
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Affiliation(s)
- Yolanda Larriba
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Valladolid, Spain
| | - Cristina Rueda
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Valladolid, Spain
| | - Miguel A Fernández
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Valladolid, Spain
| | - Shyamal D Peddada
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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110
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Crawford J, Greene CS. Incorporating biological structure into machine learning models in biomedicine. Curr Opin Biotechnol 2020; 63:126-134. [PMID: 31962244 PMCID: PMC7308204 DOI: 10.1016/j.copbio.2019.12.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/19/2022]
Abstract
In biomedical applications of machine learning, relevant information
often has a rich structure that is not easily encoded as real-valued predictors.
Examples of such data include DNA or RNA sequences, gene sets or pathways, gene
interaction or coexpression networks, ontologies, and phylogenetic trees. We
highlight recent examples of machine learning models that use structure to
constrain model architecture or incorporate structured data into model training.
For machine learning in biomedicine, where sample size is limited and model
interpretability is crucial, incorporating prior knowledge in the form of
structured data can be particularly useful. The area of research would benefit
from performant open source implementations and independent benchmarking
efforts.
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Affiliation(s)
- Jake Crawford
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA, United States.
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111
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Haspel JA, Anafi R, Brown MK, Cermakian N, Depner C, Desplats P, Gelman AE, Haack M, Jelic S, Kim BS, Laposky AD, Lee YC, Mongodin E, Prather AA, Prendergast BJ, Reardon C, Shaw AC, Sengupta S, Szentirmai É, Thakkar M, Walker WE, Solt LA. Perfect timing: circadian rhythms, sleep, and immunity - an NIH workshop summary. JCI Insight 2020; 5:131487. [PMID: 31941836 PMCID: PMC7030790 DOI: 10.1172/jci.insight.131487] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Recent discoveries demonstrate a critical role for circadian rhythms and sleep in immune system homeostasis. Both innate and adaptive immune responses - ranging from leukocyte mobilization, trafficking, and chemotaxis to cytokine release and T cell differentiation -are mediated in a time of day-dependent manner. The National Institutes of Health (NIH) recently sponsored an interdisciplinary workshop, "Sleep Insufficiency, Circadian Misalignment, and the Immune Response," to highlight new research linking sleep and circadian biology to immune function and to identify areas of high translational potential. This Review summarizes topics discussed and highlights immediate opportunities for delineating clinically relevant connections among biological rhythms, sleep, and immune regulation.
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Affiliation(s)
- Jeffrey A. Haspel
- Division of Pulmonary, Critical Care and Sleep Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Ron Anafi
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marishka K. Brown
- National Center on Sleep Disorders Research, Division of Lung Diseases, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Nicolas Cermakian
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
| | - Christopher Depner
- Sleep and Chronobiology Laboratory, Department of Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | - Paula Desplats
- Department of Neurosciences and
- Department of Pathology, UCSD, La Jolla, California, USA
| | - Andrew E. Gelman
- Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Monika Haack
- Human Sleep and Inflammatory Systems Laboratory, Department of Neurology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Sanja Jelic
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University School of Medicine, New York, New York, USA
| | - Brian S. Kim
- Center for the Study of Itch
- Department of Medicine
- Department of Anesthesiology
- Department of Pathology, and
- Department of Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Aaron D. Laposky
- National Center on Sleep Disorders Research, Division of Lung Diseases, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Yvonne C. Lee
- Division of Rheumatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Emmanuel Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Aric A. Prather
- Department of Psychiatry, UCSF, San Francisco, California, USA
| | - Brian J. Prendergast
- Department of Psychology and Committee on Neurobiology, University of Chicago, Chicago, Illinois, USA
| | - Colin Reardon
- Department, of Anatomy, Physiology, and Cell Biology, UCD School of Veterinary Medicine, Davis, California, USA
| | - Albert C. Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Shaon Sengupta
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Éva Szentirmai
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Mahesh Thakkar
- Harry S. Truman Memorial Veterans Hospital, Columbia, Missouri, USA
- Department of Neurology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Wendy E. Walker
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Health Sciences Center, Texas Tech University, El Paso, Texas, USA
| | - Laura A. Solt
- Department of Immunology and Microbiology, Scripps Research Institute, Jupiter, Florida, USA
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112
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Abstract
Circadian clocks are endogenous oscillators that control 24-h physiological and behavioral processes. The central circadian clock exerts control over myriad aspects of mammalian physiology, including the regulation of sleep, metabolism, and the immune system. Here, we review advances in understanding the genetic regulation of sleep through the circadian system, as well as the impact of dysregulated gene expression on metabolic function. We also review recent studies that have begun to unravel the circadian clock’s role in controlling the cardiovascular and nervous systems, gut microbiota, cancer, and aging. Such circadian control of these systems relies, in part, on transcriptional regulation, with recent evidence for genome-wide regulation of the clock through circadian chromosome organization. These novel insights into the genomic regulation of human physiology provide opportunities for the discovery of improved treatment strategies and new understanding of the biological underpinnings of human disease.
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113
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Brown LS, Klerman EB, Doyle FJ. Compensating for Sensor Error in the Model Predictive Control of Circadian Clock Phase. IEEE CONTROL SYSTEMS LETTERS 2019; 3:853-858. [PMID: 33748651 PMCID: PMC7970662 DOI: 10.1109/lcsys.2019.2919438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The circadian oscillator regulates many critical biological functions; misalignment between the phase of this oscillator and the environment has been linked to adverse health outcomes. Thus, shifting the circadian phase of the oscillator to align with the environment using either light or small molecule pharmaceuticals as control inputs is desired. One challenge to controlling circadian phase is that the magnitude and direction of the phase shift caused by these inputs is dependent on the phase at which the input is delivered. Simulations show that model predictive control (MPC) can successfully shift the phase of the circadian clock using perfect knowledge of the current phase of the system. However, methods to assess circadian phase continuously in real time, as would be needed to implement MPC in vivo, are limited in their accuracy. Here, we explore the impact of imperfect sensing on our ability to control circadian phase. While some pathological patterns of sensor error can make control impossible, we show that by assuming errors in the phase sensor are bounded to be sufficiently small, we can bound the error of our MPC algorithm. We propose using the expected phase response curve to improve control when sensor error is present.
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Affiliation(s)
- Lindsey S Brown
- Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS), Cambridge, MA 02138, USA
| | - Elizabeth B Klerman
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Womens Hospital, Boston, MA 02115 and the Division of Sleep Medicine, Harvard Medical School (HMS), Boston, MA 02115, USA
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114
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Porcu A, Gonzalez R, McCarthy MJ. Pharmacological Manipulation of the Circadian Clock: A Possible Approach to the Management of Bipolar Disorder. CNS Drugs 2019; 33:981-999. [PMID: 31625128 DOI: 10.1007/s40263-019-00673-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bipolar disorder (BD) is a mood disorder with genetic and neurobiological underpinnings, characterized primarily by recurrent episodes of mania and depression, with notable disruptions in rhythmic behaviors such as sleep, energy, appetite and attention. The chronobiological links to BD are further supported by the effectiveness of various treatment modalities such as bright light, circadian phase advance, and mood-stabilizing drugs such as lithium that have effects on the circadian clock. Over the past 30 years, the neurobiology of the circadian clock has been exquisitely described and there now exists a detailed knowledge of key signaling pathways, neurotransmitters and signaling mechanisms that regulate various dimensions of circadian clock function. With this new wealth of information, it is becoming increasingly plausible that new drugs for BD could be made by targeting molecular elements of the circadian clock. However, circadian rhythms are multidimensional and complex, involving unique, time-dependent factors that are not typically considered in drug development. We review the organization of the circadian clock in the central nervous system and briefly summarize data implicating the circadian clock in BD. We then consider some of the unique aspects of the circadian clock as a drug target in BD, discuss key methodological considerations and evaluate some of the candidate clock pathways and systems that could serve as potential targets for novel mood stabilizers. We expect this work will serve as a roadmap to facilitate the development of compounds acting on the circadian clock for the treatment of BD.
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Affiliation(s)
- Alessandra Porcu
- Department of Psychiatry and Center for Circadian Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Robert Gonzalez
- Department of Psychiatry, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, 17033-0850, USA
| | - Michael J McCarthy
- Department of Psychiatry and Center for Circadian Biology, University of California San Diego, La Jolla, CA, 92093, USA. .,Psychiatry Service, VA San Diego Healthcare System, 3350 La Jolla Village Dr MC116A, San Diego, CA, 92161, USA.
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115
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Cederroth CR, Albrecht U, Bass J, Brown SA, Dyhrfjeld-Johnsen J, Gachon F, Green CB, Hastings MH, Helfrich-Förster C, Hogenesch JB, Lévi F, Loudon A, Lundkvist GB, Meijer JH, Rosbash M, Takahashi JS, Young M, Canlon B. Medicine in the Fourth Dimension. Cell Metab 2019; 30:238-250. [PMID: 31390550 PMCID: PMC6881776 DOI: 10.1016/j.cmet.2019.06.019] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/08/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022]
Abstract
The importance of circadian biology has rarely been considered in pre-clinical studies, and even more when translating to the bedside. Circadian biology is becoming a critical factor for improving drug efficacy and diminishing drug toxicity. Indeed, there is emerging evidence showing that some drugs are more effective at nighttime than daytime, whereas for others it is the opposite. This suggests that the biology of the target cell will determine how an organ will respond to a drug at a specific time of the day, thus modulating pharmacodynamics. Thus, it is now time that circadian factors become an integral part of translational research.
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Affiliation(s)
- Christopher R Cederroth
- Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Urs Albrecht
- Department of Biology, Unit of Biochemistry, University of Fribourg, Fribourg, Switzerland
| | - Joseph Bass
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Steven A Brown
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | | | - Frederic Gachon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Michael H Hastings
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | - Charlotte Helfrich-Förster
- Neurobiology and Genetics, Biocenter, Theodor-Boveri Institute, University of Würzburg, Würzburg, Germany
| | - John B Hogenesch
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Francis Lévi
- Cancer Chronotherapy Team, School of Medicine, University of Warwick, Coventry, UK; Warwick University on "Personalized Cancer Chronotherapeutics through System Medicine" (C2SysMed), European Associated Laboratory of the Unité Mixte de Recherche Scientifique 935, Institut National de la Santé et de la Recherche Médicale and Paris-Sud University, Villejuif, France; Department of Medical Oncology, Paul Brousse Hospital, Assistance Publique-Hopitaux de Paris, 94800 Villejuif, France
| | - Andrew Loudon
- School of Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | | | - Johanna H Meijer
- Department of Neurophysiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, the Netherlands
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Joseph S Takahashi
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Young
- Laboratory of Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Barbara Canlon
- Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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116
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Sulli G, Lam MTY, Panda S. Interplay between Circadian Clock and Cancer: New Frontiers for Cancer Treatment. Trends Cancer 2019; 5:475-494. [PMID: 31421905 DOI: 10.1016/j.trecan.2019.07.002] [Citation(s) in RCA: 244] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 07/07/2019] [Accepted: 07/08/2019] [Indexed: 12/23/2022]
Abstract
Circadian clocks constitute the evolutionary molecular machinery that dictates the temporal regulation of physiology to maintain homeostasis. Disruption of the circadian rhythm plays a key role in tumorigenesis and facilitates the establishment of cancer hallmarks. Conversely, oncogenic processes directly weaken circadian rhythms. Pharmacological modulation of core clock genes is a new approach in cancer therapy. The integration of circadian biology into cancer research offers new options for making cancer treatment more effective, encompassing the prevention, diagnosis, and treatment of this devastating disease. This review highlights the role of the circadian clock in tumorigenesis and cancer hallmarks, and discusses how pharmacological modulation of circadian clock genes can lead to new therapeutic options.
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Affiliation(s)
- Gabriele Sulli
- The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Medicine, Division of Regenerative Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; Scintillon Institute, San Diego, CA 92121, USA.
| | - Michael Tun Yin Lam
- The Salk Institute for Biological Studies, La Jolla, CA, USA; Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, 9300 Campus Point Drive, La Jolla, CA 92037, USA
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117
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Li X, Shi L, Zhang K, Wei W, Liu Q, Mao F, Li J, Cai W, Chen H, Teng H, Li J, Sun Z. CirGRDB: a database for the genome-wide deciphering circadian genes and regulators. Nucleic Acids Res 2019; 46:D64-D70. [PMID: 29059379 PMCID: PMC5753205 DOI: 10.1093/nar/gkx944] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/03/2017] [Indexed: 01/16/2023] Open
Abstract
Circadian rhythms govern various kinds of physiological and behavioral functions of the living organisms, and disruptions of the rhythms are highly detrimental to health. Although several databases have been built for circadian genes, a resource for comprehensive post-transcriptional regulatory information of circadian RNAs and expression patterns of disease-related circadian RNAs is still lacking. Here, we developed CirGRDB (http://cirgrdb.biols.ac.cn) by integrating more than 4936 genome-wide assays, with the aim of fulfilling the growing need to understand the rhythms of life. CirGRDB presents a friendly web interface that allows users to search and browse temporal expression patterns of interested genes in 37 human/mouse tissues or cell lines, and three clinical disorders including sleep disorder, aging and tumor. More importantly, eight kinds of potential transcriptional and post-transcriptional regulators involved in the rhythmic expression of the specific genes, including transcription factors, histone modifications, chromatin accessibility, enhancer RNAs, miRNAs, RNA-binding proteins, RNA editing and RNA methylation, can also be retrieved. Furthermore, a regulatory network could be generated based on the regulatory information. In summary, CirGRDB offers a useful repository for exploring disease-related circadian RNAs, and deciphering the transcriptional and post-transcriptional regulation of circadian rhythms.
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Affiliation(s)
- Xianfeng Li
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Leisheng Shi
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Kun Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Wenqing Wei
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jinchen Li
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Wanshi Cai
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Huiqian Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiada Li
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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118
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Abstract
Fundamental aspects of neurobiology are time-of-day regulated. Therefore, it is not surprising that neurodegenerative and psychiatric diseases are accompanied by sleep and circadian rhythm disruption. Although the direction of causation remains unclear, abnormal sleep-wake patterns often occur early in disease, exacerbate progression, and are a common primary complaint from patients. Circadian medicine incorporates knowledge of 24-hour biological rhythms to improve treatment. This article highlights how research and technologic advances in circadian biology might translate to improved patient care.
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119
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Shafi AA, Knudsen KE. Cancer and the Circadian Clock. Cancer Res 2019; 79:3806-3814. [PMID: 31300477 DOI: 10.1158/0008-5472.can-19-0566] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 12/31/2022]
Abstract
The circadian clock is a master regulator of mammalian physiology, regulating daily oscillations of crucial biological processes and behaviors. Notably, circadian disruption has recently been identified as an independent risk factor for cancer and classified as a carcinogen. As such, it is imperative to discern the underpinning mechanisms by which circadian disruption alters cancer risk. Emergent data, reviewed herein, demonstrate that circadian regulatory functions play critical roles in several hallmarks of cancer, including control of cell proliferation, cell death, DNA repair, and metabolic alteration. Developing a deeper understanding of circadian-cancer regulation cross-talk holds promise for developing new strategies for cancer interception, prevention, and management.
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Affiliation(s)
- Ayesha A Shafi
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. .,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Medical Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Urology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
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120
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Clarke R, Tyson JJ, Tan M, Baumann WT, Jin L, Xuan J, Wang Y. Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers. Endocr Relat Cancer 2019; 26:R345-R368. [PMID: 30965282 PMCID: PMC7045974 DOI: 10.1530/erc-18-0309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022]
Abstract
Drawing on concepts from experimental biology, computer science, informatics, mathematics and statistics, systems biologists integrate data across diverse platforms and scales of time and space to create computational and mathematical models of the integrative, holistic functions of living systems. Endocrine-related cancers are well suited to study from a systems perspective because of the signaling complexities arising from the roles of growth factors, hormones and their receptors as critical regulators of cancer cell biology and from the interactions among cancer cells, normal cells and signaling molecules in the tumor microenvironment. Moreover, growth factors, hormones and their receptors are often effective targets for therapeutic intervention, such as estrogen biosynthesis, estrogen receptors or HER2 in breast cancer and androgen receptors in prostate cancer. Given the complexity underlying the molecular control networks in these cancers, a simple, intuitive understanding of how endocrine-related cancers respond to therapeutic protocols has proved incomplete and unsatisfactory. Systems biology offers an alternative paradigm for understanding these cancers and their treatment. To correctly interpret the results of systems-based studies requires some knowledge of how in silico models are built, and how they are used to describe a system and to predict the effects of perturbations on system function. In this review, we provide a general perspective on the field of cancer systems biology, and we explore some of the advantages, limitations and pitfalls associated with using predictive multiscale modeling to study endocrine-related cancers.
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Affiliation(s)
- Robert Clarke
- Department of Oncology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - John J Tyson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Ming Tan
- Department of Biostatistics, Bioinformatics & Biomathematics, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - William T Baumann
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Lu Jin
- Department of Oncology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Jianhua Xuan
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, USA
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, USA
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121
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Oster H. Circadian enhancer profiling in diet-induced obese mice reveals a critical time window for lipid-lowering therapies. Hepatobiliary Surg Nutr 2019; 8:280-282. [PMID: 31245414 DOI: 10.21037/hbsn.2019.01.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Henrik Oster
- Institute of Neurobiology, University of Lübeck, Lübeck, Germany
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122
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Zhang Z, Hunter L, Wu G, Maidstone R, Mizoro Y, Vonslow R, Fife M, Hopwood T, Begley N, Saer B, Wang P, Cunningham P, Baxter M, Durrington H, Blaikley JF, Hussell T, Rattray M, Hogenesch JB, Gibbs J, Ray DW, Loudon ASI. Genome-wide effect of pulmonary airway epithelial cell-specific Bmal1 deletion. FASEB J 2019; 33:6226-6238. [PMID: 30794439 PMCID: PMC6463917 DOI: 10.1096/fj.201801682r] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 01/22/2019] [Indexed: 12/16/2022]
Abstract
Pulmonary airway epithelial cells (AECs) form a critical interface between host and environment. We investigated the role of the circadian clock using mice bearing targeted deletion of the circadian gene brain and muscle ARNT-like 1 (Bmal1) in AECs. Pulmonary neutrophil infiltration, biomechanical function, and responses to influenza infection were all disrupted. A circadian time-series RNA sequencing study of laser-captured AECs revealed widespread disruption in genes of the core circadian clock and output pathways regulating cell metabolism (lipids and xenobiotics), extracellular matrix, and chemokine signaling, but strikingly also the gain of a novel rhythmic transcriptome in Bmal1-targeted cells. Many of the rhythmic components were replicated in primary AECs cultured in air-liquid interface, indicating significant cell autonomy for control of pulmonary circadian physiology. Finally, we found that metabolic cues dictate phasing of the pulmonary clock and circadian responses to immunologic challenges. Thus, the local circadian clock in AECs is vital in lung health by coordinating major cell processes such as metabolism and immunity.-Zhang, Z. Hunter, L., Wu, G., Maidstone, R., Mizoro, Y., Vonslow, R., Fife, M., Hopwood, T., Begley, N., Saer, B., Wang, P., Cunningham, P., Baxter, M., Durrington, H., Blaikley, J. F., Hussell, T., Rattray, M., Hogenesch, J. B., Gibbs, J., Ray, D. W., Loudon, A. S. I. Genome-wide effect of pulmonary airway epithelial cell-specific Bmal1 deletion.
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Affiliation(s)
- Zhenguang Zhang
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Louise Hunter
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Gang Wu
- Division of Human Genetics, Department of Pediatrics, Center for Chronobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Division of Immunobiology, Department of Pediatrics, Center for Chronobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Robert Maidstone
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom; and
| | - Yasutaka Mizoro
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Ryan Vonslow
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Mark Fife
- Manchester Center for Collaborative Inflammation Research, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, United Kingdom
| | - Thomas Hopwood
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Nicola Begley
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Ben Saer
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Ping Wang
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom; and
| | - Peter Cunningham
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Matthew Baxter
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Hannah Durrington
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - John F. Blaikley
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Tracy Hussell
- Manchester Center for Collaborative Inflammation Research, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, United Kingdom
| | - Magnus Rattray
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom; and
| | - John B. Hogenesch
- Division of Human Genetics, Department of Pediatrics, Center for Chronobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Julie Gibbs
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - David W. Ray
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Andrew S. I. Loudon
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
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123
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Adeola HA, Papagerakis S, Papagerakis P. Systems Biology Approaches and Precision Oral Health: A Circadian Clock Perspective. Front Physiol 2019; 10:399. [PMID: 31040792 PMCID: PMC6476986 DOI: 10.3389/fphys.2019.00399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/22/2019] [Indexed: 12/20/2022] Open
Abstract
A vast majority of the pathophysiological and metabolic processes in humans are temporally controlled by a master circadian clock located centrally in the hypothalamic suprachiasmatic nucleus of the brain, as well as by specialized peripheral oscillators located in other body tissues. This circadian clock system generates a rhythmical diurnal transcriptional-translational cycle in clock genes and protein expression and activities regulating numerous downstream target genes. Clock genes as key regulators of physiological function and dysfunction of the circadian clock have been linked to various diseases and multiple morbidities. Emerging omics technologies permits largescale multi-dimensional investigations of the molecular landscape of a given disease and the comprehensive characterization of its underlying cellular components (e.g., proteins, genes, lipids, metabolites), their mechanism of actions, functional networks and regulatory systems. Ultimately, they can be used to better understand disease and interpatient heterogeneity, individual profile, identify personalized targetable key molecules and pathways, discover novel biomarkers and genetic alterations, which collectively can allow for a better patient stratification into clinically relevant subgroups to improve disease prediction and prevention, early diagnostic, clinical outcomes, therapeutic benefits, patient's quality of life and survival. The use of “omics” technologies has allowed for recent breakthroughs in several scientific domains, including in the field of circadian clock biology. Although studies have explored the role of clock genes using circadiOmics (which integrates circadian omics, such as genomics, transcriptomics, proteomics and metabolomics) in human disease, no such studies have investigated the implications of circadian disruption in oral, head and neck pathologies using multi-omics approaches and linking the omics data to patient-specific circadian profiles. There is a burgeoning body of evidence that circadian clock controls the development and homeostasis of oral and maxillofacial structures, such as salivary glands, teeth and oral epithelium. Hence, in the current era of precision medicine and dentistry and patient-centered health care, it is becoming evident that a multi-omics approach is needed to improve our understanding of the role of circadian clock-controlled key players in the regulation of head and neck pathologies. This review discusses current knowledge on the role of the circadian clock and the contribution of omics-based approaches toward a novel precision health era for diagnosing and treating head and neck pathologies, with an emphasis on oral, head and neck cancer and Sjögren's syndrome.
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Affiliation(s)
- Henry A Adeola
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, University of the Western Cape and Tygerberg Hospital, Cape Town, South Africa
| | - Silvana Papagerakis
- Laboratory of Oral, Head & Neck Cancer-Personalized Diagnostics and Therapeutics, Division of Head and Neck Surgery, Department of Surgery, University of Saskatchewan, Saskatoon, SK, Canada
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124
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Enhancing Therapy: It's about Time. Cell 2019; 174:771-772. [PMID: 30096305 DOI: 10.1016/j.cell.2018.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
How diet and obesity impact diurnal changes in physiology remains unclear. In this issue of Cell, Guan et al. report that diet-induced obesity modulates the activity of circadian gene enhancers including those regulating lipid metabolism and show that the efficacy of lipid-lowering drugs depends on the time of administration.
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125
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SMOLENSKY MH, REINBERG AE, FISCHER FM. Working Time Society consensus statements: Circadian time structure impacts vulnerability to xenobiotics-relevance to industrial toxicology and nonstandard work schedules. INDUSTRIAL HEALTH 2019; 57:158-174. [PMID: 30700669 PMCID: PMC6449632 DOI: 10.2486/indhealth.sw-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/27/2018] [Indexed: 05/13/2023]
Abstract
The circadian time structure (CTS) has long been the subject of research in occupational medicine, but not to industrial toxicology, including methods of setting threshold limit values (TLVs) and employee biological monitoring. Numerous animal and human investigations document vulnerability to chemical, contagion, and other xenobiotics varies according to the circadian time of encounter. Permanent and rotating nightshift personnel are exposed to industrial contaminants in the same or higher concentration as dayshift personnel, and because of incomplete CTS adjustment to night work, contact with contaminants occurs during a different biological time than day workers. Thus, the amount of protection afforded by certain TLVs, especially for employees of high-risk settings who work night and other nonstandard shift schedules, might be inadequate. The CTS seems additionally germane to procedures of employee biological monitoring in that high-amplitude 24 h rhythms in biomarkers indicative of xenobiotic exposure may result in misjudgment of health risks when data are not gathered in sufficient frequency over time and properly interpreted. Biological reference values time-qualified for their rhythmic variation, currently of interest to laboratory medicine practice, are seemingly important to industrial medicine as circadian time and work-shift specific biological exposure indices to improve surveillance of personnel, particularly those working nonstandard shift schedules.
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Affiliation(s)
- Michael H. SMOLENSKY
- Department of Biomedical Engineering, Cockrell School of
Engineering, The University of Texas at Austin, USA
| | | | - Frida Marina FISCHER
- Department of Environmental Health, School of Public Health,
University of São Paulo, Brazil
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126
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Asgari-Targhi A, Klerman EB. Mathematical modeling of circadian rhythms. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2019; 11:e1439. [PMID: 30328684 PMCID: PMC6375788 DOI: 10.1002/wsbm.1439] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/22/2022]
Abstract
Circadian rhythms are endogenous ~24-hr oscillations usually entrained to daily environmental cycles of light/dark. Many biological processes and physiological functions including mammalian body temperature, the cell cycle, sleep/wake cycles, neurobehavioral performance, and a wide range of diseases including metabolic, cardiovascular, and psychiatric disorders are impacted by these rhythms. Circadian clocks are present within individual cells and at tissue and organismal levels as emergent properties from the interaction of cellular oscillators. Mathematical models of circadian rhythms have been proposed to provide a better understanding of and to predict aspects of this complex physiological system. These models can be used to: (a) manipulate the system in silico with specificity that cannot be easily achieved using in vivo and in vitro experimental methods and at lower cost, (b) resolve apparently contradictory empirical results, (c) generate hypotheses, (d) design new experiments, and (e) to design interventions for altering circadian rhythms. Mathematical models differ in structure, the underlying assumptions, the number of parameters and variables, and constraints on variables. Models representing circadian rhythms at different physiologic scales and in different species are reviewed to promote understanding of these models and facilitate their use. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models.
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127
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Kervezee L, Cuesta M, Cermakian N, Boivin DB. The Phase-Shifting Effect of Bright Light Exposure on Circadian Rhythmicity in the Human Transcriptome. J Biol Rhythms 2019; 34:84-97. [DOI: 10.1177/0748730418821776] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Laura Kervezee
- Centre for Study and Treatment of Circadian Rhythms, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Canada
- Laboratory of Molecular Chronobiology, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Canada
| | - Marc Cuesta
- Centre for Study and Treatment of Circadian Rhythms, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Canada
- Laboratory of Molecular Chronobiology, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Canada
| | - Nicolas Cermakian
- Laboratory of Molecular Chronobiology, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Canada
| | - Diane B. Boivin
- Centre for Study and Treatment of Circadian Rhythms, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Canada
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128
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Kervezee L, Kosmadopoulos A, Boivin DB. Metabolic and cardiovascular consequences of shift work: The role of circadian disruption and sleep disturbances. Eur J Neurosci 2018; 51:396-412. [PMID: 30357975 DOI: 10.1111/ejn.14216] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/25/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022]
Abstract
Shift work, defined as work occurring outside typical daytime working hours, is associated with an increased risk of various non-communicable diseases, including diabetes and cardiovascular disease. Disruption of the internal circadian timing system and concomitant sleep disturbances is thought to play a critical role in the development of these health problems. Indeed, controlled laboratory studies have shown that short-term circadian misalignment and sleep restriction independently impair physiological processes, including insulin sensitivity, energy expenditure, immune function, blood pressure and cardiac modulation by the autonomous nervous system. If allowed to persist, these acute effects may lead to the development of cardiometabolic diseases in the long term. Here, we discuss the evidence for the contributions of circadian disruption and associated sleep disturbances to the risk of metabolic and cardiovascular health problems in shift workers. Improving the understanding of the physiological mechanisms affected by circadian misalignment and sleep disturbance will contribute to the development and implementation of strategies that prevent or mitigate the cardiometabolic impact of shift work.
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Affiliation(s)
- Laura Kervezee
- Centre for Study and Treatment of Circadian Rhythms, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
| | - Anastasi Kosmadopoulos
- Centre for Study and Treatment of Circadian Rhythms, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
| | - Diane B Boivin
- Centre for Study and Treatment of Circadian Rhythms, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
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129
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Singer JM, Hughey JJ. LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data. J Biol Rhythms 2018; 34:5-18. [PMID: 30472909 PMCID: PMC6376636 DOI: 10.1177/0748730418813785] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Unraveling the effects of genetic or environmental perturbations on biological rhythms requires detecting changes in rhythmicity across multiple conditions. Although methods to detect rhythmicity in genome-scale data are well established, methods to detect changes in rhythmicity or changes in average expression between experimental conditions are often ad hoc and statistically unreliable. Here we present LimoRhyde (linear models for rhythmicity, design), a flexible approach for analyzing transcriptome data from circadian systems. Borrowing from cosinor regression, LimoRhyde decomposes circadian or zeitgeber time into multiple components to fit a linear model to the expression of each gene. The linear model can accommodate any number of additional experimental variables, whether discrete or continuous, making it straightforward to detect differential rhythmicity and differential expression using state-of-the-art methods for analyzing microarray and RNA-seq data. In this approach, differential rhythmicity corresponds to a statistical interaction between an experimental variable and circadian time, whereas differential expression corresponds to the main effect of an experimental variable while accounting for circadian time. To validate LimoRhyde’s performance, we applied it to simulated data. To demonstrate LimoRhyde’s versatility, we applied it to murine and human circadian transcriptome datasets acquired under various experimental designs. Our results show how LimoRhyde systematizes the analysis of such data, and suggest that LimoRhyde could prove valuable for assessing how circadian systems respond to perturbations.
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Affiliation(s)
- Jordan M Singer
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jacob J Hughey
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
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130
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Population-level rhythms in human skin with implications for circadian medicine. Proc Natl Acad Sci U S A 2018; 115:12313-12318. [PMID: 30377266 DOI: 10.1073/pnas.1809442115] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Skin is the largest organ in the body and serves important barrier, regulatory, and sensory functions. The epidermal layer shows rhythmic physiological responses to daily environmental variation (e.g., DNA repair). We investigated the role of the circadian clock in the transcriptional regulation of epidermis using a hybrid experimental design, in which a limited set of human subjects (n = 20) were sampled throughout the 24-h cycle and a larger population (n = 219) were sampled once. We found a robust circadian oscillator in human epidermis at the population level using pairwise correlations of clock and clock-associated genes in 298 epidermis samples. We then used CYCLOPS to reconstruct the temporal order of all samples, and identified hundreds of rhythmically expressed genes at the population level in human epidermis. We compared these results with published time-series skin data from mice and found a strong concordance in circadian phase across species for both transcripts and pathways. Furthermore, like blood, epidermis is readily accessible and a potential source of biomarkers. Using ZeitZeiger, we identified a biomarker set for human epidermis that is capable of reporting circadian phase to within 3 hours from a single sample. In summary, we show rhythms in human epidermis that persist at the population scale and describe a path to develop robust single-sample circadian biomarkers.
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131
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Shrestha TC, Šuchmanová K, Houdek P, Sumová A, Ralph MR. Implicit time-place conditioning alters Per2 mRNA expression selectively in striatum without shifting its circadian clocks. Sci Rep 2018; 8:15547. [PMID: 30341352 PMCID: PMC6195625 DOI: 10.1038/s41598-018-33637-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/02/2018] [Indexed: 11/30/2022] Open
Abstract
Animals create implicit memories of the time of day that significant events occur then anticipate the recurrence of those conditions at the same time on subsequent days. We tested the hypothesis that implicit time memory for daily encounters relies on the setting of the canonical circadian clockwork in brain areas involved in the formation or expression of context memories. We conditioned mice to avoid locations paired with a mild foot shock at one of two Zeitgeber times set 8 hours apart. Place avoidance was exhibited only when testing time matched the prior training time. The suprachiasmatic nucleus, dorsal striatum, nucleus accumbens, cingulate cortex, hippocampal complex, and amygdala were assessed for clock gene expression. Baseline phase dependent differences in clock gene expression were found in most tissues. Evidence for conditioned resetting of a molecular circadian oscillation was found only in the striatum (dorsal striatum and nucleus accumbens shell), and specifically for Per2 expression. There was no evidence of glucocorticoid stress response in any tissue. The results are consistent with a model where temporal conditioning promotes a selective Per2 response in dopamine-targeted brain regions responsible for sensorimotor integration, without resetting the entire circadian clockwork.
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Affiliation(s)
- Tenjin C Shrestha
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Karolína Šuchmanová
- Department of Neurohumoral Regulations, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Houdek
- Department of Neurohumoral Regulations, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alena Sumová
- Department of Neurohumoral Regulations, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin R Ralph
- Department of Psychology, University of Toronto, Toronto, Ontario, Canada.
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132
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Yeung J, Naef F. Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior. Trends Genet 2018; 34:915-926. [PMID: 30309754 DOI: 10.1016/j.tig.2018.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/31/2018] [Accepted: 09/10/2018] [Indexed: 11/18/2022]
Abstract
Circadian rhythms in physiology and behavior evolved to resonate with daily cycles in the external environment. In mammals, organs orchestrate temporal physiology over the 24-h day, which requires extensive gene expression rhythms targeted to the right tissue. Although a core set of gene products oscillates across virtually all cell types, gene expression profiling across tissues over the 24-h day showed that rhythmic gene expression programs are tissue specific. We highlight recent progress in uncovering how the circadian clock interweaves with tissue-specific gene regulatory networks involving functions such as xenobiotic metabolism, glucose homeostasis, and sleep. This progress hinges on not only comprehensive experimental approaches but also computational methods for multivariate analysis of periodic functional genomics data. We emphasize dynamic chromatin interactions as a novel regulatory layer underlying circadian gene transcription, core clock functions, and ultimately behavior. Finally, we discuss perspectives on extending the knowledge of the circadian clock in animals to human chronobiology.
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Affiliation(s)
- Jake Yeung
- The Institute of Bioengineering (IBI), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Felix Naef
- The Institute of Bioengineering (IBI), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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133
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Olsen LR, Leipold MD, Pedersen CB, Maecker HT. The anatomy of single cell mass cytometry data. Cytometry A 2018; 95:156-172. [DOI: 10.1002/cyto.a.23621] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Lars R. Olsen
- Department of Bio and Health InformaticsTechnical University of Denmark Copenhagen Denmark
- Center for Genomic MedicineCopenhagen University Hospital Copenhagen Denmark
| | - Michael D. Leipold
- Institute for Immunity, Transplantation, and InfectionStanford University School of Medicine Stanford CA
| | - Christina B. Pedersen
- Department of Bio and Health InformaticsTechnical University of Denmark Copenhagen Denmark
- Center for Genomic MedicineCopenhagen University Hospital Copenhagen Denmark
| | - Holden Terry Maecker
- Institute for Immunity, Transplantation, and InfectionStanford University School of Medicine Stanford CA
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134
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Wong DCS, O’Neill JS. Non-transcriptional processes in circadian rhythm generation. CURRENT OPINION IN PHYSIOLOGY 2018; 5:117-132. [PMID: 30596188 PMCID: PMC6302373 DOI: 10.1016/j.cophys.2018.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
'Biological clocks' orchestrate mammalian biology to a daily rhythm. Whilst 'clock gene' transcriptional circuits impart rhythmic regulation to myriad cellular systems, our picture of the biochemical mechanisms that determine their circadian (∼24 hour) period is incomplete. Here we consider the evidence supporting different models for circadian rhythm generation in mammalian cells in light of evolutionary factors. We find it plausible that the circadian timekeeping mechanism in mammalian cells is primarily protein-based, signalling biological timing information to the nucleus by the post-translational regulation of transcription factor activity, with transcriptional feedback imparting robustness to the oscillation via hysteresis. We conclude by suggesting experiments that might distinguish this model from competing paradigms.
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135
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Lung physiology and defense. CURRENT OPINION IN PHYSIOLOGY 2018. [DOI: 10.1016/j.cophys.2018.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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136
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Braun R, Kath WL, Iwanaszko M, Kula-Eversole E, Abbott SM, Reid KJ, Zee PC, Allada R. Universal method for robust detection of circadian state from gene expression. Proc Natl Acad Sci U S A 2018; 115:E9247-E9256. [PMID: 30201705 PMCID: PMC6166804 DOI: 10.1073/pnas.1800314115] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Circadian clocks play a key role in regulating a vast array of biological processes, with significant implications for human health. Accurate assessment of physiological time using transcriptional biomarkers found in human blood can significantly improve diagnosis of circadian disorders and optimize the delivery time of therapeutic treatments. To be useful, such a test must be accurate, minimally burdensome to the patient, and readily generalizable to new data. A major obstacle in development of gene expression biomarker tests is the diversity of measurement platforms and the inherent variability of the data, often resulting in predictors that perform well in the original datasets but cannot be universally applied to new samples collected in other settings. Here, we introduce TimeSignature, an algorithm that robustly infers circadian time from gene expression. We demonstrate its application in data from three independent studies using distinct microarrays and further validate it against a new set of samples profiled by RNA-sequencing. Our results show that TimeSignature is more accurate and efficient than competing methods, estimating circadian time to within 2 h for the majority of samples. Importantly, we demonstrate that once trained on data from a single study, the resulting predictor can be universally applied to yield highly accurate results in new data from other studies independent of differences in study population, patient protocol, or assay platform without renormalizing the data or retraining. This feature is unique among expression-based predictors and addresses a major challenge in the development of generalizable, clinically useful tests.
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Affiliation(s)
- Rosemary Braun
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611;
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208
| | - William L Kath
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208
- Department of Neurobiology, Northwestern University, Evanston, IL 60208
| | - Marta Iwanaszko
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208
| | | | - Sabra M Abbott
- Department of Neurology, Northwestern University, Chicago, IL 60611
- the Center for Circadian and Sleep Medicine, Northwestern University, Chicago, IL 60611
| | - Kathryn J Reid
- Department of Neurology, Northwestern University, Chicago, IL 60611
- the Center for Circadian and Sleep Medicine, Northwestern University, Chicago, IL 60611
| | - Phyllis C Zee
- Department of Neurobiology, Northwestern University, Evanston, IL 60208
- Department of Neurology, Northwestern University, Chicago, IL 60611
| | - Ravi Allada
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208
- Department of Neurobiology, Northwestern University, Evanston, IL 60208
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137
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Ruben MD, Wu G, Smith DF, Schmidt RE, Francey LJ, Lee YY, Anafi RC, Hogenesch JB. A database of tissue-specific rhythmically expressed human genes has potential applications in circadian medicine. Sci Transl Med 2018; 10:10/458/eaat8806. [PMID: 30209245 PMCID: PMC8961342 DOI: 10.1126/scitranslmed.aat8806] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/23/2018] [Indexed: 12/14/2022]
Abstract
The discovery that half of the mammalian protein-coding genome is regulated by the circadian clock has clear implications for medicine. Recent studies demonstrated that the circadian clock influences therapeutic outcomes in human heart disease and cancer. However, biological time is rarely given clinical consideration. A key barrier is the absence of information on tissue-specific molecular rhythms in the human body. We have applied the cyclic ordering by periodic structure (CYCLOPS) algorithm, designed to reconstruct sample temporal order in the absence of time-of-day information, to the gene expression collection of 13 tissues from 632 human donors. We identified rhythms in gene expression across the body; nearly half of protein-coding genes were shown to be cycling in at least 1 of the 13 tissues analyzed. One thousand of these cycling genes encode proteins that either transport or metabolize drugs or are themselves drug targets. These results provide a useful resource for studying the role of circadian rhythms in medicine and support the idea that biological time might play a role in determining drug response.
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Affiliation(s)
- Marc D. Ruben
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert, Sabin Way, Cincinnati, OH 45229, USA
| | - Gang Wu
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert, Sabin Way, Cincinnati, OH 45229, USA
| | - David F. Smith
- Divisions of Pediatric Otolaryngology and Pulmonary and Sleep Medicine, Cincinnati Children’s Hospital Medical Center, 3333, Burnet Avenue, Cincinnati, OH 45229, USA.,Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati School of Medicine, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
| | - Robert E. Schmidt
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert, Sabin Way, Cincinnati, OH 45229, USA
| | - Lauren J. Francey
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert, Sabin Way, Cincinnati, OH 45229, USA
| | - Yin Yeng Lee
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert, Sabin Way, Cincinnati, OH 45229, USA
| | - Ron C. Anafi
- Department of Medicine, Center for Sleep and Circadian, Neurobiology, Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - John B. Hogenesch
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert, Sabin Way, Cincinnati, OH 45229, USA.,Corresponding author.
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138
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von Allmen DC, Francey LJ, Rogers GM, Ruben MD, Cohen AP, Wu G, Schmidt RE, Ishman SL, Amin RS, Hogenesch JB, Smith DF. Circadian Dysregulation: The Next Frontier in Obstructive Sleep Apnea Research. Otolaryngol Head Neck Surg 2018; 159:948-955. [PMID: 30200807 DOI: 10.1177/0194599818797311] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To review the effects of the circadian clock on homeostasis, the functional interaction between the circadian clock and hypoxia-inducible factors, and the role of circadian dysregulation in the progression of cardiopulmonary disease in obstructive sleep apnea (OSA). DATA SOURCES The MEDLINE database was accessed through PubMed. REVIEW METHODS A general review is presented on molecular pathways disrupted in OSA, circadian rhythms and the role of the circadian clock, hypoxia signaling, crosstalk between the circadian and hypoxia systems, the role of the circadian clock in cardiovascular disease, and implications for practice. Studies included in this State of the Art Review demonstrate the potential contribution of the circadian clock and hypoxia in animal models or human disease. CONCLUSIONS Molecular crosstalk between the circadian clock and hypoxia-inducible factors has not been evaluated in disease models of OSA. IMPLICATIONS FOR PRACTICE Pediatric OSA is highly prevalent and, if left untreated, may lead to cardiopulmonary sequelae. Changes in inflammatory markers that normally demonstrate circadian rhythmicity are also seen among patients with OSA. Hypoxia-inducible transcription factors interact with core circadian clock transcription factors; however, the interplay between these pathways has not been elucidated in the cardiopulmonary system. This gap in knowledge hinders our ability to identify potential biomarkers of OSA and develop alternative therapeutic strategies. A deeper understanding of the mechanisms by which OSA impinges on clock function and the impact of clock dysregulation on the cardiopulmonary system may lead to future advancements for the care of patients with OSA. The aim of this review is to shed light on this important clinical topic.
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Affiliation(s)
- Douglas C von Allmen
- 1 Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Lauren J Francey
- 2 Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Garrett M Rogers
- 3 College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Marc D Ruben
- 2 Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Aliza P Cohen
- 4 Division of Pediatric Otolaryngology-Head and Neck Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Gang Wu
- 2 Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Robert E Schmidt
- 2 Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Stacey L Ishman
- 1 Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- 4 Division of Pediatric Otolaryngology-Head and Neck Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- 5 Division of Pulmonary and Sleep Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Raouf S Amin
- 5 Division of Pulmonary and Sleep Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- 6 Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - John B Hogenesch
- 2 Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- 6 Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - David F Smith
- 1 Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- 4 Division of Pediatric Otolaryngology-Head and Neck Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- 5 Division of Pulmonary and Sleep Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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139
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Guan D, Xiong Y, Borck PC, Jang C, Doulias PT, Papazyan R, Fang B, Jiang C, Zhang Y, Briggs ER, Hu W, Steger D, Ischiropoulos H, Rabinowitz JD, Lazar MA. Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes. Cell 2018; 174:831-842.e12. [PMID: 30057115 PMCID: PMC6086765 DOI: 10.1016/j.cell.2018.06.031] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/23/2018] [Accepted: 06/13/2018] [Indexed: 12/11/2022]
Abstract
Overnutrition disrupts circadian metabolic rhythms by mechanisms that are not well understood. Here, we show that diet-induced obesity (DIO) causes massive remodeling of circadian enhancer activity in mouse liver, triggering synchronous high-amplitude circadian rhythms of both fatty acid (FA) synthesis and oxidation. SREBP expression was rhythmically induced by DIO, leading to circadian FA synthesis and, surprisingly, FA oxidation (FAO). DIO similarly caused a high-amplitude circadian rhythm of PPARα, which was also required for FAO. Provision of a pharmacological activator of PPARα abrogated the requirement of SREBP for FAO (but not FA synthesis), suggesting that SREBP indirectly controls FAO via production of endogenous PPARα ligands. The high-amplitude rhythm of PPARα imparted time-of-day-dependent responsiveness to lipid-lowering drugs. Thus, acquisition of rhythmicity for non-core clock components PPARα and SREBP1 remodels metabolic gene transcription in response to overnutrition and enables a chronopharmacological approach to metabolic disorders.
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Affiliation(s)
- Dongyin Guan
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ying Xiong
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Patricia C Borck
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cholsoon Jang
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Paschalis-Thomas Doulias
- Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and Systems Pharmacology & Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Romeo Papazyan
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bin Fang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chunjie Jiang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuxiang Zhang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erika R Briggs
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenxiang Hu
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David Steger
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and Systems Pharmacology & Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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140
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Wittenbrink N, Ananthasubramaniam B, Münch M, Koller B, Maier B, Weschke C, Bes F, de Zeeuw J, Nowozin C, Wahnschaffe A, Wisniewski S, Zaleska M, Bartok O, Ashwal-Fluss R, Lammert H, Herzel H, Hummel M, Kadener S, Kunz D, Kramer A. High-accuracy determination of internal circadian time from a single blood sample. J Clin Invest 2018; 128:3826-3839. [PMID: 29953415 DOI: 10.1172/jci120874] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/20/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The circadian clock is a fundamental and pervasive biological program that coordinates 24-hour rhythms in physiology, metabolism, and behavior, and it is essential to health. Whereas therapy adapted to time of day is increasingly reported to be highly successful, it needs to be personalized, since internal circadian time is different for each individual. In addition, internal time is not a stable trait, but is influenced by many factors, including genetic predisposition, age, sex, environmental light levels, and season. An easy and convenient diagnostic tool is currently missing. METHODS To establish a validated test, we followed a 3-stage biomarker development strategy: (a) using circadian transcriptomics of blood monocytes from 12 individuals in a constant routine protocol combined with machine learning approaches, we identified biomarkers for internal time; and these biomarkers (b) were migrated to a clinically relevant gene expression profiling platform (NanoString) and (c) were externally validated using an independent study with 28 early or late chronotypes. RESULTS We developed a highly accurate and simple assay (BodyTime) to estimate the internal circadian time in humans from a single blood sample. Our assay needs only a small set of blood-based transcript biomarkers and is as accurate as the current gold standard method, dim-light melatonin onset, at smaller monetary, time, and sample-number cost. CONCLUSION The BodyTime assay provides a new diagnostic tool for personalization of health care according to the patient's circadian clock. FUNDING This study was supported by the Bundesministerium für Bildung und Forschung, Germany (FKZ: 13N13160 and 13N13162) and Intellux GmbH, Germany.
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Affiliation(s)
- Nicole Wittenbrink
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany.,Humboldt-Universität zu Berlin, Department of Biology, Systems Immunology Lab, Berlin, Germany
| | - Bharath Ananthasubramaniam
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany.,Humboldt-Universität zu Berlin, Institute for Theoretical Biology, Berlin, Germany
| | - Mirjam Münch
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany.,St-Hedwig-Krankenhaus, Clinic for Sleep and Chronomedicine, Berlin, Germany.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Physiology, Group Sleep Research and Clinical Chronobiology, Berlin, Germany
| | - Barbara Koller
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Bert Maier
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Charlotte Weschke
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Frederik Bes
- St-Hedwig-Krankenhaus, Clinic for Sleep and Chronomedicine, Berlin, Germany.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Physiology, Group Sleep Research and Clinical Chronobiology, Berlin, Germany
| | - Jan de Zeeuw
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Physiology, Group Sleep Research and Clinical Chronobiology, Berlin, Germany.,Intellux Berlin GmbH, Berlin, Germany
| | - Claudia Nowozin
- St-Hedwig-Krankenhaus, Clinic for Sleep and Chronomedicine, Berlin, Germany.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Physiology, Group Sleep Research and Clinical Chronobiology, Berlin, Germany
| | - Amely Wahnschaffe
- St-Hedwig-Krankenhaus, Clinic for Sleep and Chronomedicine, Berlin, Germany.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Physiology, Group Sleep Research and Clinical Chronobiology, Berlin, Germany
| | - Sophia Wisniewski
- St-Hedwig-Krankenhaus, Clinic for Sleep and Chronomedicine, Berlin, Germany.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Physiology, Group Sleep Research and Clinical Chronobiology, Berlin, Germany
| | | | - Osnat Bartok
- The Hebrew University, Biological Chemistry Department, Jerusalem, Israel
| | - Reut Ashwal-Fluss
- The Hebrew University, Biological Chemistry Department, Jerusalem, Israel
| | - Hedwig Lammert
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Hanspeter Herzel
- Humboldt-Universität zu Berlin, Institute for Theoretical Biology, Berlin, Germany
| | - Michael Hummel
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Sebastian Kadener
- The Hebrew University, Biological Chemistry Department, Jerusalem, Israel.,Brandeis University, Department of Biology, Waltham, Massachusetts, USA
| | - Dieter Kunz
- St-Hedwig-Krankenhaus, Clinic for Sleep and Chronomedicine, Berlin, Germany.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Physiology, Group Sleep Research and Clinical Chronobiology, Berlin, Germany.,Intellux Berlin GmbH, Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
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141
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Archer SN, Schmidt C, Vandewalle G, Dijk DJ. Phenotyping of PER3 variants reveals widespread effects on circadian preference, sleep regulation, and health. Sleep Med Rev 2018; 40:109-126. [PMID: 29248294 DOI: 10.1016/j.smrv.2017.10.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/16/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022]
Abstract
Period3 (Per3) is one of the most robustly rhythmic genes in humans and animals. It plays a significant role in temporal organisation in peripheral tissues. The effects of PER3 variants on many phenotypes have been investigated in targeted and genome-wide studies. PER3 variants, especially the human variable number tandem repeat (VNTR), associate with diurnal preference, mental disorders, non-visual responses to light, brain and cognitive responses to sleep loss/circadian misalignment. Introducing the VNTR into mice alters responses to sleep loss and expression of sleep homeostasis-related genes. Several studies were limited in size and some findings were not replicated. Nevertheless, the data indicate a significant contribution of PER3 to sleep and circadian phenotypes and diseases, which may be connected by common pathways. Thus, PER3-dependent altered light sensitivity could relate to high retinal PER3 expression and may contribute to altered brain response to light, diurnal preference and seasonal mood. Altered cognitive responses during sleep loss/circadian misalignment and changes to slow wave sleep may relate to changes in wake/activity-dependent patterns of hypothalamic gene expression involved in sleep homeostasis and neural network plasticity. Comprehensive characterisation of effects of clock gene variants may provide new insights into the role of circadian processes in health and disease.
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Affiliation(s)
- Simon N Archer
- Sleep Research Centre, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XP, UK.
| | - Christina Schmidt
- GIGA-Research, Cyclotron Research Centre-In Vivo Imaging Unit, University of Liège, Belgium; Psychology and Neuroscience of Cognition Research Unit (PsyNCog), Faculty of Psychology and Educational Sciences, University of Liège, Belgium
| | - Gilles Vandewalle
- GIGA-Research, Cyclotron Research Centre-In Vivo Imaging Unit, University of Liège, Belgium
| | - Derk-Jan Dijk
- Sleep Research Centre, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XP, UK
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142
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Sulli G, Manoogian ENC, Taub PR, Panda S. Training the Circadian Clock, Clocking the Drugs, and Drugging the Clock to Prevent, Manage, and Treat Chronic Diseases. Trends Pharmacol Sci 2018; 39:812-827. [PMID: 30060890 DOI: 10.1016/j.tips.2018.07.003] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/05/2018] [Accepted: 07/07/2018] [Indexed: 12/09/2022]
Abstract
Daily rhythms in behavior, physiology, and metabolism are an integral part of homeostasis. These rhythms emerge from interactions between endogenous circadian clocks and ambient light-dark cycles, sleep-activity cycles, and eating-fasting cycles. Nearly the entire primate genome shows daily rhythms in expression in tissue- and locus-specific manners. These molecular rhythms modulate several key aspects of cellular and tissue function with profound implications in public health, disease prevention, and disease management. In modern societies light at night disrupts circadian rhythms, leading to further disruption of sleep-activity and eating-fasting cycles. While acute circadian disruption may cause transient discomfort or exacerbate chronic diseases, chronic circadian disruption can enhance risks for numerous diseases. The molecular understanding of circadian rhythms is opening new therapeutic frontiers placing the circadian clock in a central role. Here, we review recent advancements on how to enhance our circadian clock through behavioral interventions, timing of drug administration, and pharmacological targeting of circadian clock components that are already providing new preventive and therapeutic strategies for several diseases, including metabolic syndrome and cancer.
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Affiliation(s)
- Gabriele Sulli
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Pam R Taub
- Division of Cardiovascular Medicine, Department of Medicine, University of California, San Diego, CA 92037, USA
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Zhu B, Dacso CC, O’Malley BW. Unveiling "Musica Universalis" of the Cell: A Brief History of Biological 12-Hour Rhythms. J Endocr Soc 2018; 2:727-752. [PMID: 29978151 PMCID: PMC6025213 DOI: 10.1210/js.2018-00113] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/01/2018] [Indexed: 12/18/2022] Open
Abstract
"Musica universalis" is an ancient philosophical concept claiming the movements of celestial bodies follow mathematical equations and resonate to produce an inaudible harmony of music, and the harmonious sounds that humans make were an approximation of this larger harmony of the universe. Besides music, electromagnetic waves such as light and electric signals also are presented as harmonic resonances. Despite the seemingly universal theme of harmonic resonance in various disciplines, it was not until recently that the same harmonic resonance was discovered also to exist in biological systems. Contrary to traditional belief that a biological system is either at stead-state or cycles with a single frequency, it is now appreciated that most biological systems have no homeostatic "set point," but rather oscillate as composite rhythms consisting of superimposed oscillations. These oscillations often cycle at different harmonics of the circadian rhythm, and among these, the ~12-hour oscillation is most prevalent. In this review, we focus on these 12-hour oscillations, with special attention to their evolutionary origin, regulation, and functions in mammals, as well as their relationship to the circadian rhythm. We further discuss the potential roles of the 12-hour clock in regulating hepatic steatosis, aging, and the possibility of 12-hour clock-based chronotherapy. Finally, we posit that biological rhythms are also musica universalis: whereas the circadian rhythm is synchronized to the 24-hour light/dark cycle coinciding with the Earth's rotation, the mammalian 12-hour clock may have evolved from the circatidal clock, which is entrained by the 12-hour tidal cues orchestrated by the moon.
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Affiliation(s)
- Bokai Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Clifford C Dacso
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Bert W O’Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
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Haspel J. An "eye" for rhythm. Sci Transl Med 2018; 9:9/390/eaan4288. [PMID: 28515338 DOI: 10.1126/scitranslmed.aan4288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A new analytical method allows reconstruction of circadian gene expression in human biopsy samples.
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Affiliation(s)
- Jeffrey Haspel
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63130, USA.
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Shilts J, Chen G, Hughey JJ. Evidence for widespread dysregulation of circadian clock progression in human cancer. PeerJ 2018; 6:e4327. [PMID: 29404219 PMCID: PMC5797448 DOI: 10.7717/peerj.4327] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
The ubiquitous daily rhythms in mammalian physiology are guided by progression of the circadian clock. In mice, systemic disruption of the clock can promote tumor growth. In vitro, multiple oncogenes can disrupt the clock. However, due to the difficulties of studying circadian rhythms in solid tissues in humans, whether the clock is disrupted within human tumors has remained unknown. We sought to determine the state of the circadian clock in human cancer using publicly available transcriptome data. We developed a method, called the clock correlation distance (CCD), to infer circadian clock progression in a group of samples based on the co-expression of 12 clock genes. Our method can be applied to modestly sized datasets in which samples are not labeled with time of day and coverage of the circadian cycle is incomplete. We used the method to define a signature of clock gene co-expression in healthy mouse organs, then validated the signature in healthy human tissues. By then comparing human tumor and non-tumor samples from twenty datasets of a range of cancer types, we discovered that clock gene co-expression in tumors is consistently perturbed. Subsequent analysis of data from clock gene knockouts in mice suggested that perturbed clock gene co-expression in human cancer is not caused solely by the inactivation of clock genes. Furthermore, focusing on lung cancer, we found that human lung tumors showed systematic changes in expression in a large set of genes previously inferred to be rhythmic in healthy lung. Our findings suggest that clock progression is dysregulated in many solid human cancers and that this dysregulation could have broad effects on circadian physiology within tumors. In addition, our approach opens the door to using publicly available data to infer circadian clock progression in a multitude of human phenotypes.
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Affiliation(s)
- Jarrod Shilts
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Guanhua Chen
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Jacob J Hughey
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, United States of America.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
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Palli R, Thakar J. Developing Network Models of Multiscale Host Responses Involved in Infections and Diseases. Methods Mol Biol 2018; 1819:385-402. [PMID: 30421414 DOI: 10.1007/978-1-4939-8618-7_18] [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] [Indexed: 06/09/2023]
Abstract
Complex interactions involved in host response to infections and diseases require advanced analytical tools to infer drivers of the response in order to develop strategies for intervention. This chapter discusses approaches to assemble interactions ranging from molecular to cellular levels and their analysis to investigate the cross talk between immune pathways. Particularly, construction of immune networks by either data-driven or literature-driven methods is explained. Next, graph theoretic approaches for probing static network properties as well as visualization of networks are discussed. Finally, development of Boolean models for simulation of network dynamics to investigate cross talk and emergent properties are considered along with Boolean-like models that may compensate for some of the limitations encountered in Boolean simulations. In conclusion, the chapter will allow readers to construct and analyze multiscale networks involved in immune responses.
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Affiliation(s)
- Rohith Palli
- Medical Scientist Training Program and Biophysics, Structural & Computational Biology graduate program, Rochester, NY, USA
| | - Juilee Thakar
- Departments of Microbiology and Immunology, Rochester, NY, USA.
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Molecular Aspects of Circadian Pharmacology and Relevance for Cancer Chronotherapy. Int J Mol Sci 2017; 18:ijms18102168. [PMID: 29039812 PMCID: PMC5666849 DOI: 10.3390/ijms18102168] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/13/2017] [Accepted: 10/14/2017] [Indexed: 02/01/2023] Open
Abstract
The circadian timing system (CTS) controls various biological functions in mammals including xenobiotic metabolism and detoxification, immune functions, cell cycle events, apoptosis and angiogenesis. Although the importance of the CTS is well known in the pharmacology of drugs, it is less appreciated at the clinical level. Genome-wide studies highlighted that the majority of drug target genes are controlled by CTS. This suggests that chronotherapeutic approaches should be taken for many drugs to enhance their effectiveness. Currently chronotherapeutic approaches are successfully applied in the treatment of different types of cancers. The chronotherapy approach has improved the tolerability and antitumor efficacy of anticancer drugs both in experimental animals and in cancer patients. Thus, chronobiological studies have been of importance in determining the most appropriate time of administration of anticancer agents to minimize their side effects or toxicity and enhance treatment efficacy, so as to optimize the therapeutic ratio. This review focuses on the underlying mechanisms of the circadian pharmacology i.e., chronopharmacokinetics and chronopharmacodynamics of anticancer agents with the molecular aspects, and provides an overview of chronotherapy in cancer and some of the recent advances in the development of chronopharmaceutics.
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Affiliation(s)
- Zheng Chen
- a Department of Biochemistry and Molecular Biology , The University of Texas Health Science Center at Houston , Houston , TX , USA
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