1
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Larriba Y, Mason IC, Saxena R, Scheer FAJL, Rueda C. CIRCUST: A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans. PLoS Comput Biol 2023; 19:e1011510. [PMID: 37769026 PMCID: PMC10564179 DOI: 10.1371/journal.pcbi.1011510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 10/10/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023] Open
Abstract
The circadian system drives near-24-h oscillations in behaviors and biological processes. The underlying core molecular clock regulates the expression of other genes, and it has been shown that the expression of more than 50 percent of genes in mammals displays 24-h rhythmic patterns, with the specific genes that cycle varying from one tissue to another. Determining rhythmic gene expression patterns in human tissues sampled as single timepoints has several challenges, including the reconstruction of temporal order of highly noisy data. Previous methodologies have attempted to address these challenges in one or a small number of tissues for which rhythmic gene evolutionary conservation is assumed to be preserved. Here we introduce CIRCUST, a novel CIRCular-robUST methodology for analyzing molecular rhythms, that relies on circular statistics, is robust against noise, and requires fewer assumptions than existing methodologies. Next, we validated the method against four controlled experiments in which sampling times were known, and finally, CIRCUST was applied to 34 tissues from the Genotype-Tissue Expression (GTEx) dataset with the aim towards building a comprehensive daily rhythm gene expression atlas in humans. The validation and application shown here indicate that CIRCUST provides a flexible framework to formulate and solve the issues related to the analysis of molecular rhythms in human tissues. CIRCUST methodology is publicly available at https://github.com/yolandalago/CIRCUST/.
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Affiliation(s)
- Yolanda Larriba
- Department of Statistics and Operational Research, University of Valladolid, Valladolid, Spain
- Mathematics Research Institute of the University of Valladolid, University of Valladolid, Valladolid, Spain
| | - Ivy C. Mason
- Medical Chronobiology Program, Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richa Saxena
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Genomic Medicine and Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Division of Anesthesia, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Frank A. J. L. Scheer
- Medical Chronobiology Program, Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Cristina Rueda
- Department of Statistics and Operational Research, University of Valladolid, Valladolid, Spain
- Mathematics Research Institute of the University of Valladolid, University of Valladolid, Valladolid, Spain
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2
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Zong W, Seney ML, Ketchesin KD, Gorczyca MT, Liu AC, Esser KA, Tseng GC, McClung CA, Huo Z. Experimental design and power calculation in omics circadian rhythmicity detection using the cosinor model. Stat Med 2023; 42:3236-3258. [PMID: 37265194 PMCID: PMC10425922 DOI: 10.1002/sim.9803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/27/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Circadian clocks are 24-h endogenous oscillators in physiological and behavioral processes. Though recent transcriptomic studies have been successful in revealing the circadian rhythmicity in gene expression, the power calculation for omics circadian analysis have not been fully explored. In this paper, we develop a statistical method, namely CircaPower, to perform power calculation for circadian pattern detection. Our theoretical framework is determined by three key factors in circadian gene detection: sample size, intrinsic effect size and sampling design. Via simulations, we systematically investigate the impact of these key factors on circadian power calculation. We not only demonstrate that CircaPower is fast and accurate, but also show its underlying cosinor model is robust against variety of violations of model assumptions. In real applications, we demonstrate the performance of CircaPower using mouse pan-tissue data and human post-mortem brain data, and illustrate how to perform circadian power calculation using mouse skeleton muscle RNA-Seq pilot as case study. Our method CircaPower has been implemented in an R package, which is made publicly available on GitHub ( https://github.com/circaPower/circaPower).
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Affiliation(s)
- Wei Zong
- Department of Biostatistics, University of Pittsburgh, PA, USA
| | - Marianne L. Seney
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Kyle D. Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Michael T. Gorczyca
- Department of Computational and Systems Biology, University of Pittsburgh, PA, USA
| | - Andrew C. Liu
- Department of Physiology and Aging, University of Florida, FL, USA
| | - Karyn A. Esser
- Department of Physiology and Aging, University of Florida, FL, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, PA, USA
| | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, FL, USA
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3
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Yeung CYC, Svensson RB, Yurchenko K, Malmgaard-Clausen NM, Tryggedsson I, Lendal M, Jokipii-Utzon A, Olesen JL, Lu Y, Kadler KE, Schjerling P, Kjaer M. Disruption of day-to-night changes in circadian gene expression with chronic tendinopathy. J Physiol 2023. [PMID: 36810732 DOI: 10.1113/jp284083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
Overuse injury in tendon tissue (tendinopathy) is a frequent and costly musculoskeletal disorder and represents a major clinical problem with unsolved pathogenesis. Studies in mice have demonstrated that circadian clock-controlled genes are vital for protein homeostasis and important in the development of tendinopathy. We performed RNA sequencing, collagen content and ultrastructural analyses on human tendon biopsies obtained 12 h apart in healthy individuals to establish whether human tendon is a peripheral clock tissue and we performed RNA sequencing on patients with chronic tendinopathy to examine the expression of circadian clock genes in tendinopathic tissues. We found time-dependent expression of 280 RNAs including 11 conserved circadian clock genes in healthy tendons and markedly fewer (23) differential RNAs with chronic tendinopathy. Further, the expression of COL1A1 and COL1A2 was reduced at night but was not circadian rhythmic in synchronised human tenocyte cultures. In conclusion, day-to-night changes in gene expression in healthy human patellar tendons indicate a conserved circadian clock as well as the existence of a night reduction in collagen I expression. KEY POINTS: Tendinopathy is a major clinical problem with unsolved pathogenesis. Previous work in mice has shown that a robust circadian rhythm is required for collagen homeostasis in tendons. The use of circadian medicine in the diagnosis and treatment of tendinopathy has been stifled by the lack of studies on human tissue. Here, we establish that the expression of circadian clock genes in human tendons is time dependent, and now we have data to corroborate that circadian output is reduced in diseased tendon tissues. We consider our findings to be of significance in advancing the use of the tendon circadian clock as a therapeutic target or preclinical biomarker for tendinopathy.
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Affiliation(s)
- Ching-Yan Chloé Yeung
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Center for Healthy Aging, Department of Clinical Medicine, University of Copenhagen, Denmark
| | - René B Svensson
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Center for Healthy Aging, Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Kateryna Yurchenko
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Center for Healthy Aging, Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Nikolaj M Malmgaard-Clausen
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Center for Healthy Aging, Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Ida Tryggedsson
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Center for Healthy Aging, Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Marius Lendal
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Center for Healthy Aging, Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Anja Jokipii-Utzon
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Center for Healthy Aging, Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Jens L Olesen
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Center for Healthy Aging, Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Yinhui Lu
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Karl E Kadler
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Peter Schjerling
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Center for Healthy Aging, Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Michael Kjaer
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Center for Healthy Aging, Department of Clinical Medicine, University of Copenhagen, Denmark
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4
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Dose B, Yalçin M, Dries SPM, Relógio A. TimeTeller for timing health: The potential of circadian medicine to improve performance, prevent disease and optimize treatment. Front Digit Health 2023; 5:1157654. [PMID: 37153516 PMCID: PMC10155816 DOI: 10.3389/fdgth.2023.1157654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Circadian medicine, the study of the effects of time on health and disease has seen an uprising in recent years as a means to enhance health and performance, and optimize treatment timing. Our endogenous time generating system -the circadian clock- regulates behavioural, physiological and cellular processes. Disruptions of the clock, via external factors like shift work or jet lag, or internal perturbations such as genetic alterations, are linked to an increased risk of various diseases like obesity, diabetes, cardiovascular diseases and cancer. By aligning an individual's circadian clock with optimal times for performing daily routines, physical and mental performance, and also the effectiveness of certain therapies can be improved. Despite the benefits of circadian medicine, the lack of non-invasive tools for characterizing the clock limits the potential of the field. TimeTeller is a non-invasive molecular/digital tool for the characterization of circadian rhythms and prediction of daily routines, including treatment timing, to unlock the potential of circadian medicine and implementing it in various settings. Given the multiple known and potentially yet unknown dependent health factors of individual circadian rhythms, the utility of this emerging biomarker is best exploited in data driven, personalized medicine use cases, using health information across lifestyle, care, and research settings.
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Affiliation(s)
| | - Müge Yalçin
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, Germany
| | | | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, Germany
- Correspondence: Angela Relógio
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5
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Möller-Levet CS, Laing EE, Archer SN, Dijk DJ. Diurnal and circadian rhythmicity of the human blood transcriptome overlaps with organ- and tissue-specific expression of a non-human primate. BMC Biol 2022; 20:63. [PMID: 35264172 PMCID: PMC8905855 DOI: 10.1186/s12915-022-01258-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/18/2022] [Indexed: 12/14/2022] Open
Abstract
Background Twenty-four-hour rhythmicity in mammalian tissues and organs is driven by local circadian oscillators, systemic factors, the central circadian pacemaker and light-dark cycles. At the physiological level, the neural and endocrine systems synchronise gene expression in peripheral tissues and organs to the 24-h-day cycle, and disruption of such regulation has been shown to lead to pathological conditions. Thus, monitoring rhythmicity in tissues/organs holds promise for circadian medicine; however, most tissues and organs are not easily accessible in humans and alternative approaches to quantify circadian rhythmicity are needed. We investigated the overlap between rhythmic transcripts in human blood and transcripts shown to be rhythmic in 64 tissues/organs of the baboon, how these rhythms are aligned with light-dark cycles and each other, and whether timing of tissue-specific rhythmicity can be predicted from a blood sample. Results We compared rhythmicity in transcriptomic time series collected from humans and baboons using set logic, circular cross-correlation, circular clustering, functional enrichment analyses, and least squares regression. Of the 759 orthologous genes that were rhythmic in human blood, 652 (86%) were also rhythmic in at least one baboon tissue and most of these genes were associated with basic processes such as transcription and protein homeostasis. In total, 109 (17%) of the 652 overlapping rhythmic genes were reported as rhythmic in only one baboon tissue or organ and several of these genes have tissue/organ-specific functions. The timing of human and baboon rhythmic transcripts displayed prominent ‘night’ and ‘day’ clusters, with genes in the dark cluster associated with translation. Alignment between baboon rhythmic transcriptomes and the overlapping human blood transcriptome was significantly closer when light onset, rather than midpoint of light, or end of light period, was used as phase reference point. The timing of overlapping human and baboon rhythmic transcriptomes was significantly correlated in 25 tissue/organs with an average earlier timing of 3.21 h (SD 2.47 h) in human blood. Conclusions The human blood transcriptome contains sets of rhythmic genes that overlap with rhythmic genes of tissues/organs in baboon. The rhythmic sets vary across tissues/organs, but the timing of most rhythmic genes is similar in human blood and baboon tissues/organs. These results have implications for development of blood transcriptome-based biomarkers for circadian rhythmicity in tissues and organs. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01258-7.
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Affiliation(s)
- Carla S Möller-Levet
- Bioinformatics Core Facility, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.
| | - Emma E Laing
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Simon N Archer
- Surrey Sleep Research Centre, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Derk-Jan Dijk
- Surrey Sleep Research Centre, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK. .,UK Dementia Research Institute, Care Research and Technology Centre at Imperial College, London and the University of Surrey, Guildford, UK.
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6
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Song H, Cheng Y, Fan L, Sun H. Expression patterns of clock genes in the kidney of two Lasiopodomys species. ANIM BIOL 2022. [DOI: 10.1163/15707563-bja10067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Previous studies showed that the kidney has its own molecular circadian clock expression regulation that maintains the homeostasis of physiological processes. However, limited information is available on the molecular mechanisms of the kidney circadian rhythm in subterranean rodents. Here, we report circadian gene expression in the kidney of subterranean Mandarin voles and the related aboveground Brandt’s voles, reared under 12L:12D (LD) or dark (DD) conditions, respectively. The results showed that the rhythmic genes were represented in Brandt’s voles in higher numbers under LD than DD conditions, but the number of rhythmic genes in Mandarin voles was similar between the two treatment conditions. The gene expression levels at different timepoints all showed reduced results under DD conditions compared with those in the LD cycle in Brandt’s voles, whereas the expression levels of the tested genes at certain Zeitgeber timepoints showed higher results than in the LD cycle in Mandarin voles. The gene expression peak showed chaotic resetting under DD conditions in both voles. We thus suggest that Mandarin and Brandt’s voles have different molecular circadian clock expression adjustment patterns in the kidney as an adaptation to different living environments. Mandarin voles seem to be more adapted to the dark environment, while Brandt’s voles are more dependent on external light conditions.
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Affiliation(s)
- Hongjie Song
- Centre for Nutritional Ecology, Centre for Sport Nutrition and Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yuyang Cheng
- Centre for Nutritional Ecology, Centre for Sport Nutrition and Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Linchao Fan
- Centre for Nutritional Ecology, Centre for Sport Nutrition and Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Hong Sun
- Centre for Nutritional Ecology, Centre for Sport Nutrition and Health, Zhengzhou University, Zhengzhou, 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
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7
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Kawakami S, Yoshitane H, Morimura T, Kimura W, Fukada Y. Diurnal shift of mouse activity by the deficiency of an aging-related gene Lmna. J Biochem 2022; 171:509-518. [PMID: 35137145 DOI: 10.1093/jb/mvac015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 02/02/2022] [Indexed: 11/13/2022] Open
Abstract
Nuclear lamina is a fundamental structure of the cell nucleus and regulates a wide range of molecular pathways. Defects of components of the nuclear lamina cause aging-like physiological disorders, called laminopathy. Generally, aging and diseases are often associated with perturbation of various time-of-day-dependent regulations, but it remains still elusive whether laminopathy induces any changes of the circadian clock and physiological rhythms. Here we demonstrated that deficiency of Lmna gene in mice caused an obvious shift of locomotor activities to the daytime. The abnormal activity profile was accompanied by a remarkable change in phase-angle between the central clock in the suprachiasmatic nucleus (SCN) and lung peripheral clocks, leaving the phase of the SCN clock unaffected by the mutation. These observations suggest that Lmna deficiency causes a change of the habitat from nocturnal to diurnal behaviors. On the other hand, molecular oscillation and its phase resetting mechanism were intact in both the Lmna-deficient cells and progeria-mimicking cells. Intriguingly, high-fat diet feeding extended the short lifespan and ameliorated the abnormalities of the behaviors and the phase of the peripheral clock in the Lmna-deficient mice. The present study supports the important contribution of the energy conditions to a shift between the diurnal and nocturnal activities.
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Affiliation(s)
- Satoshi Kawakami
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Circadian Clock Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa 2-1-6, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hikari Yoshitane
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Circadian Clock Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa 2-1-6, Setagaya-ku, Tokyo 156-8506, Japan
| | - Taiki Morimura
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Circadian Clock Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa 2-1-6, Setagaya-ku, Tokyo 156-8506, Japan
| | - Wataru Kimura
- RIKEN Center for Biosystems Dynamics Research, Minatojima-minamimachi 2-2-3, Chuo-ku, Kobe, Hyogo 650-0043, Japan
| | - Yoshitaka Fukada
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Circadian Clock Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa 2-1-6, Setagaya-ku, Tokyo 156-8506, Japan.,Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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8
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Ding H, Meng L, Liu AC, Gumz ML, Bryant AJ, Mcclung CA, Tseng GC, Esser KA, Huo Z. Likelihood-based tests for detecting circadian rhythmicity and differential circadian patterns in transcriptomic applications. Brief Bioinform 2021; 22:bbab224. [PMID: 34117739 PMCID: PMC8575021 DOI: 10.1093/bib/bbab224] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/06/2021] [Accepted: 05/22/2021] [Indexed: 01/08/2023] Open
Abstract
Circadian rhythmicity in transcriptomic profiles has been shown in many physiological processes, and the disruption of circadian patterns has been found to associate with several diseases. In this paper, we developed a series of likelihood-based methods to detect (i) circadian rhythmicity (denoted as LR_rhythmicity) and (ii) differential circadian patterns comparing two experimental conditions (denoted as LR_diff). In terms of circadian rhythmicity detection, we demonstrated that our proposed LR_rhythmicity could better control the type I error rate compared to existing methods under a wide variety of simulation settings. In terms of differential circadian patterns, we developed methods in detecting differential amplitude, differential phase, differential basal level and differential fit, which also successfully controlled the type I error rate. In addition, we demonstrated that the proposed LR_diff could achieve higher statistical power in detecting differential fit, compared to existing methods. The superior performance of LR_rhythmicity and LR_diff was demonstrated in four real data applications, including a brain aging data (gene expression microarray data of human postmortem brain), a time-restricted feeding data (RNA sequencing data of human skeletal muscles) and a scRNAseq data (single cell RNA sequencing data of mouse suprachiasmatic nucleus). An R package for our methods is publicly available on GitHub https://github.com/diffCircadian/diffCircadian.
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Affiliation(s)
- Haocheng Ding
- Department of Biostatistics at the University of Florida, Gainesville, FL, 32608, USA
| | - Lingsong Meng
- Department of Biostatistics at the University of Florida, Gainesville, FL, 32608, USA
| | - Andrew C Liu
- Department of Physiology and Functional Genomics at the University of Florida College of Medicine, Gainesville, FL, 32608, USA
| | - Michelle L Gumz
- Department of Medicine at the University of Florida, Gainesville, FL, 32608, USA
| | - Andrew J Bryant
- Department of Medicine at the University of Florida, Gainesville, FL, 32608, USA
| | - Colleen A Mcclung
- Psychiatry and Clinical and Translational Science at the University of Pittsburgh, Gainesville, FL, 32608, USA
| | - George C Tseng
- Department of Biostatistics at the University of Pittsburgh, Gainesville, FL, 32608, USA
| | - Karyn A Esser
- Department of Physiology and Functional Genomics at the University of Florida College of Medicine, Gainesville, FL, 32608, USA
| | - Zhiguang Huo
- Department of Biostatistics at the University of Florida, Gainesville, FL, 32608, USA
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9
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Tabibzadeh S. CircadiOmic medicine and aging. Ageing Res Rev 2021; 71:101424. [PMID: 34389481 DOI: 10.1016/j.arr.2021.101424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/22/2021] [Accepted: 08/05/2021] [Indexed: 01/15/2023]
Abstract
The earth displays daily, seasonal and annual environmental cycles that have led to evolutionarily adapted ultradian, circadian and infradian rhythmicities in the entire biosphere. All biological organisms must adapt to these cycles that synchronize the function of their circadiome. The objective of this review is to discuss the latest knowledge regarding the role of circadiomics in health and aging. The biological timekeepers are responsive to the environmental cues at microsecond to seasonal time-scales and act with precision of a clock machinery. The robustness of these rhythms is essential to normal daily function of cells, tissues and organs. Mis-alignment of circadian rhythms makes the individual prone to aging, sleep disorders, cancer, diabetes, and neuro-degenerative diseases. Circadian and CircadiOmic medicine are emerging fields that leverage our in-depth understanding of health issues, that arise as a result of disturbances in circadian rhythms, towards establishing better therapeutic approaches in personalized medicine and for geroprotection.
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Affiliation(s)
- Siamak Tabibzadeh
- Frontiers in Bioscience Research Institute in Aging and Cancer, 16471 Scientific Way, Irvine, CA 92618, United States.
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10
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Genes Relevant to Tissue Response to Cancer Therapy Display Diurnal Variation in mRNA Expression in Human Oral Mucosa. J Circadian Rhythms 2021; 19:8. [PMID: 34221066 PMCID: PMC8231453 DOI: 10.5334/jcr.213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background: To address a critical gap for application of cancer chronotherapy of when would be the best time(s) for treating an individual cancer patient, we conducted a pilot study to characterize diurnal variations of gene expression in oral mucosal tissue, which is vulnerable to damage from cancer therapies. Methods: We conducted RNA-seq assay on individual oral mucosal samples collected from 11 healthy volunteers every 4 hours (6 time points). Using a cosine-based method, we estimated the individual and average values of peak-time and amplitude for each gene. Correlations between gene expression peak-times and age was examined, adjusting for individual’s sleep timing. Results: Among candidate gene pathways that are relevant to treatment response, 7 of 16 genes (PER3, CIART, TEF, PER1, PER2, CRY2, ARNTL) involved in circadian regulation and 1 of 118 genes (WEE1) involved in cell cycle regulation achieved p-value ≤ 0.1 and relative amplitude>0.1. The average peak times were approximately 10:15 for PER3, CIART and TEF, 10:45 for PER1, 13:00 for WEE1, PER2 and CRY2, and 19:30 for ARNTL. Ranges in peak times across individuals differed by gene (e.g., 8 hours for PER1; 16.7 hours for WEE1). Older people had later peak times for PER1 (r = 0.77, p = 0.03) and PER3 (r = 0.69, p-value = 0.06). Conclusion: In oral mucosa, expression of some genes relevant to treatment response displayed diurnal variation. These genes may be candidates for development of biomarkers for optimizing individual timing of cancer therapy using non-invasively collected oral mucosa.
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11
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Meléndez-Fernández OH, Walton JC, DeVries AC, Nelson RJ. Clocks, Rhythms, Sex, and Hearts: How Disrupted Circadian Rhythms, Time-of-Day, and Sex Influence Cardiovascular Health. Biomolecules 2021; 11:883. [PMID: 34198706 PMCID: PMC8232105 DOI: 10.3390/biom11060883] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular diseases are the top cause of mortality in the United States, and ischemic heart disease accounts for 16% of all deaths around the world. Modifiable risk factors such as diet and exercise have often been primary targets in addressing these conditions. However, mounting evidence suggests that environmental factors that disrupt physiological rhythms might contribute to the development of these diseases, as well as contribute to increasing other risk factors that are typically associated with cardiovascular disease. Exposure to light at night, transmeridian travel, and social jetlag disrupt endogenous circadian rhythms, which, in turn, alter carefully orchestrated bodily functioning, and elevate the risk of disease and injury. Research into how disrupted circadian rhythms affect physiology and behavior has begun to reveal the intricacies of how seemingly innocuous environmental and social factors have dramatic consequences on mammalian physiology and behavior. Despite the new focus on the importance of circadian rhythms, and how disrupted circadian rhythms contribute to cardiovascular diseases, many questions in this field remain unanswered. Further, neither time-of-day nor sex as a biological variable have been consistently and thoroughly taken into account in previous studies of circadian rhythm disruption and cardiovascular disease. In this review, we will first discuss biological rhythms and the master temporal regulator that controls these rhythms, focusing on the cardiovascular system, its rhythms, and the pathology associated with its disruption, while emphasizing the importance of the time-of-day as a variable that directly affects outcomes in controlled studies, and how temporal data will inform clinical practice and influence personalized medicine. Finally, we will discuss evidence supporting the existence of sex differences in cardiovascular function and outcomes following an injury, and highlight the need for consistent inclusion of both sexes in studies that aim to understand cardiovascular function and improve cardiovascular health.
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Affiliation(s)
- O. Hecmarie Meléndez-Fernández
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV 26505, USA; (J.C.W.); (R.J.N.)
| | - James C. Walton
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV 26505, USA; (J.C.W.); (R.J.N.)
| | - A. Courtney DeVries
- Department of Medicine, Division of Oncology/Hematology, West Virginia University, Morgantown, WV 26505, USA;
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26505, USA
| | - Randy J. Nelson
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV 26505, USA; (J.C.W.); (R.J.N.)
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12
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Litovchenko M, Meireles-Filho ACA, Frochaux MV, Bevers RPJ, Prunotto A, Anduaga AM, Hollis B, Gardeux V, Braman VS, Russeil JMC, Kadener S, Dal Peraro M, Deplancke B. Extensive tissue-specific expression variation and novel regulators underlying circadian behavior. SCIENCE ADVANCES 2021; 7:eabc3781. [PMID: 33514540 PMCID: PMC7846174 DOI: 10.1126/sciadv.abc3781] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/10/2020] [Indexed: 05/10/2023]
Abstract
Natural genetic variation affects circadian rhythms across the evolutionary tree, but the underlying molecular mechanisms are poorly understood. We investigated population-level, molecular circadian clock variation by generating >700 tissue-specific transcriptomes of Drosophila melanogaster (w1118 ) and 141 Drosophila Genetic Reference Panel (DGRP) lines. This comprehensive circadian gene expression atlas contains >1700 cycling genes including previously unknown central circadian clock components and tissue-specific regulators. Furthermore, >30% of DGRP lines exhibited aberrant circadian gene expression, revealing abundant genetic variation-mediated, intertissue circadian expression desynchrony. Genetic analysis of one line with the strongest deviating circadian expression uncovered a novel cry mutation that, as shown by protein structural modeling and brain immunohistochemistry, disrupts the light-driven flavin adenine dinucleotide cofactor photoreduction, providing in vivo support for the importance of this conserved photoentrainment mechanism. Together, our study revealed pervasive tissue-specific circadian expression variation with genetic variants acting upon tissue-specific regulatory networks to generate local gene expression oscillations.
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Affiliation(s)
- Maria Litovchenko
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Antonio C A Meireles-Filho
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Michael V Frochaux
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Roel P J Bevers
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Alessio Prunotto
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | | | - Brian Hollis
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Vincent Gardeux
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Virginie S Braman
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Julie M C Russeil
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | | | - Matteo Dal Peraro
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Bart Deplancke
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
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13
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Crnko S, Schutte H, Doevendans PA, Sluijter JPG, van Laake LW. Minimally Invasive Ways of Determining Circadian Rhythms in Humans. Physiology (Bethesda) 2021; 36:7-20. [DOI: 10.1152/physiol.00018.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Circadian rhythm exerts a critical role in mammalian health and disease. A malfunctioning circadian clock can be a consequence, as well as the cause of several pathophysiologies. Clinical therapies and research may also be influenced by the clock. Since the most suitable manner of revealing this rhythm in humans is not yet established, we discuss existing methods and seek to determine the most feasible ones.
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Affiliation(s)
- Sandra Crnko
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, Circulatory Health Laboratory, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Hilde Schutte
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Pieter A. Doevendans
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
- Central Military Hospital, Utrecht, The Netherlands
| | - Joost P. G. Sluijter
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, Circulatory Health Laboratory, University Medical Centre Utrecht, Utrecht, The Netherlands
- Utrecht University, Utrecht, The Netherlands
| | - Linda W. van Laake
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, Circulatory Health Laboratory, University Medical Centre Utrecht, Utrecht, The Netherlands
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14
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Luo PH, Shu YM, Ni RJ, Liu YJ, Zhou JN. A Characteristic Expression Pattern of Core Circadian Genes in the Diurnal Tree Shrew. Neuroscience 2020; 437:145-160. [PMID: 32339628 DOI: 10.1016/j.neuroscience.2020.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 02/08/2023]
Abstract
The day-active tree shrew may serve as an animal model of human-like diurnal rhythms. However, the molecular basis for circadian rhythms in this species has remained unclear. In the present study, we investigated the expression patterns of core circadian genes involved in transcriptional/translational feedback loops (TTFLs) in both central and peripheral tissues of the tree shrew. The expression of 12 core circadian genes exhibited similar rhythmic patterns in the olfactory bulb, prefrontal cortex, hippocampus, and cerebellum, while the hypothalamus exhibited the weakest oscillations. The rhythms in peripheral tissues, especially the liver, were much more robust than those in brain tissues. ARNTL and NPAS2 were weakly rhythmic in brain tissues but exhibited almost the strongest rhythmicity in peripheral tissues. CLOCK and CRY2 exhibited the weakest rhythms in both central and peripheral tissues, while NR1D1 and CIART exhibited robust rhythms in both tissues. Most of these circadian genes were highly expressed at light/dark transitions in both brain and peripheral tissues, such as ARNTL and NPAS2 peaking at dusk while PERs peaking at dawn. Additionally, the peripheral clock was phase-advanced relative to the brain clock, as there was a significant advance (2-4 h) for PER3, DBP, NR1D1 and NR1D2. Furthermore, these genes exhibited an anti-phasic relationship between the diurnal tree shrew and the nocturnal mouse (i.e., 12-h phasing differential). Collectively, our findings demonstrate a characteristic expression pattern of core circadian genes in the tree shrew, which may provide a means for elucidating molecular mechanisms of diurnal rhythms.
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Affiliation(s)
- Peng-Hao Luo
- CAS Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yu-Mian Shu
- CAS Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China; School of Architecture and Civil Engineering, Chengdu University, Chengdu, China
| | - Rong-Jun Ni
- CAS Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China; Psychiatric Laboratory and Mental Health Center, West China Hospital of Sichuan University, Chengdu, China
| | - Ya-Jing Liu
- CAS Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China; Department of Obstetrics and Gynecology, Center for Reproductive Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jiang-Ning Zhou
- CAS Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China.
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15
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Zhang CZ, Sun HZ, Zhang CH, Jin L, Sang D, Li SL. Effects of photoperiod on circadian clock genes in skin contribute to the regulation of hair follicle cycling of Inner Mongolia white cashmere goats. Anim Sci J 2019; 91:e13320. [PMID: 31845459 DOI: 10.1111/asj.13320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 08/03/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022]
Abstract
This study investigated how the effects of photoperiod on circadian clock genes in the skin contribute to the regulation of hair follicle cycling of Inner Mongolia white cashmere goats. Twenty-four female (non-pregnant) Inner Mongolia white cashmere goats aged 1 - 1.5 years old with similar live weights (mean, 20.36 ± 2.63 kg) were randomly allocated into two groups: a natural daily photoperiod group (NDPP group:10 - 16 hr Light, n = 12) and a short daily photoperiod group (SDPP group: 7 hr Light:17 hr Dark, n = 12). All goats were housed in individual pens from May 15 to October 15, 2015 and were fed the same diets. We detected the mRNA expression of brain and muscle arnt-like protein-1 (Bmal1), circadian locomotor output control kaput (Clock), cryptochrome-1 (Cry1), period homolog-1 (Per1) and Rev-erbα genes in the goat skin. ANOVA revealed a significant 24 hr (10:00 hr, 14:00 hr, 18:00 hr, 22:00 hr, 02:00 hr, 06:00 hr, 10:00 hr) variation between the SDPP and NDPP groups for three months (July, September, and October). In summary, the current results confirm that an intrinsic oscillating molecular clock exists in goat skin, and that the clock is important for potential timing mechanisms at the anagen phase of hair follicles, which would contribute to the regulation mechanisms of hair follicle cell proliferation.
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Affiliation(s)
- Chong Zhi Zhang
- Institute for Animal Nutrition and Feed Research, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hai Zhou Sun
- Institute for Animal Nutrition and Feed Research, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Chun Hua Zhang
- Institute for Animal Nutrition and Feed Research, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Lu Jin
- Institute for Animal Nutrition and Feed Research, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Dan Sang
- Institute for Animal Nutrition and Feed Research, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Sheng Li Li
- Institute for Animal Nutrition and Feed Research, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
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16
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Ten-Second Electrophysiology: Evaluation of the 3DEP Platform for high-speed, high-accuracy cell analysis. Sci Rep 2019; 9:19153. [PMID: 31844107 PMCID: PMC6915758 DOI: 10.1038/s41598-019-55579-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/18/2019] [Indexed: 01/08/2023] Open
Abstract
Electrical correlates of the physiological state of a cell, such as membrane conductance and capacitance, as well as cytoplasm conductivity, contain vital information about cellular function, ion transport across the membrane, and propagation of electrical signals. They are, however, difficult to measure; gold-standard techniques are typically unable to measure more than a few cells per day, making widespread adoption difficult and limiting statistical reproducibility. We have developed a dielectrophoretic platform using a disposable 3D electrode geometry that accurately (r2 > 0.99) measures mean electrical properties of populations of ~20,000 cells, by taking parallel ensemble measurements of cells at 20 frequencies up to 45 MHz, in (typically) ten seconds. This allows acquisition of ultra-high-resolution (100-point) DEP spectra in under two minutes. Data acquired from a wide range of cells – from platelets to large cardiac cells - benchmark well with patch-clamp-data. These advantages are collectively demonstrated in a longitudinal (same-animal) study of rapidly-changing phenomena such as ultradian (2–3 hour) rhythmicity in whole blood samples of the common vole (Microtus arvalis), taken from 10 µl tail-nick blood samples and avoiding sacrifice of the animal that is typically required in these studies.
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17
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Gaspar LS, Álvaro AR, Carmo‐Silva S, Mendes AF, Relógio A, Cavadas C. The importance of determining circadian parameters in pharmacological studies. Br J Pharmacol 2019; 176:2827-2847. [PMID: 31099023 PMCID: PMC6637036 DOI: 10.1111/bph.14712] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/26/2019] [Accepted: 04/01/2019] [Indexed: 12/25/2022] Open
Abstract
In mammals, most molecular and cellular processes show circadian changes, leading to daily variations in physiology and ultimately in behaviour. Such daily variations induce a temporal coordination of processes that is essential to ensure homeostasis and health. Thus, it is of no surprise that pharmacokinetics (PK) and pharmacodynamics (PD) of many drugs are also subject to circadian variations, profoundly affecting their efficacy and tolerability. Understanding how circadian rhythms influence drug PK, PD, and toxicity might significantly improve treatment efficacy and decrease related side effects. Therefore, it is essential to take circadian variations into account and to determine circadian parameters in pharmacological studies, especially when drugs have a short half-life or target rhythmic processes. This review provides an overview of the current knowledge on circadian rhythms and their relevance to the field of pharmacology. Methodologies to evaluate circadian rhythms in vitro, in rodent models and in humans, from experimental to computational approaches, are described and discussed. Lastly, we aim at alerting the scientific, medical, and regulatory communities to the relevance of the physiological time, as a key parameter to be considered when designing pharmacological studies. This will eventually lead to more successful preclinical and clinical trials and pave the way to a more personalized treatment to the benefit of the patients.
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Affiliation(s)
- Laetitia S. Gaspar
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Institute for Interdisciplinary Research (IIIUC)University of CoimbraCoimbraPortugal
| | - Ana Rita Álvaro
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
| | - Sara Carmo‐Silva
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
| | - Alexandrina Ferreira Mendes
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Faculty of PharmacyUniversity of CoimbraCoimbraPortugal
| | - Angela Relógio
- Institute for Theoretical BiologyCharité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt—Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Medical Department of Hematology, Oncology, and Tumor Immunology, Molecular Cancer Research CenterCharité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt—Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Cláudia Cavadas
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Faculty of PharmacyUniversity of CoimbraCoimbraPortugal
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18
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Kim P, Oster H, Lehnert H, Schmid SM, Salamat N, Barclay JL, Maronde E, Inder W, Rawashdeh O. Coupling the Circadian Clock to Homeostasis: The Role of Period in Timing Physiology. Endocr Rev 2019; 40:66-95. [PMID: 30169559 DOI: 10.1210/er.2018-00049] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
Abstract
A plethora of physiological processes show stable and synchronized daily oscillations that are either driven or modulated by biological clocks. A circadian pacemaker located in the suprachiasmatic nucleus of the ventral hypothalamus coordinates 24-hour oscillations of central and peripheral physiology with the environment. The circadian clockwork involved in driving rhythmic physiology is composed of various clock genes that are interlocked via a complex feedback loop to generate precise yet plastic oscillations of ∼24 hours. This review focuses on the specific role of the core clockwork gene Period1 and its paralogs on intra-oscillator and extra-oscillator functions, including, but not limited to, hippocampus-dependent processes, cardiovascular function, appetite control, as well as glucose and lipid homeostasis. Alterations in Period gene function have been implicated in a wide range of physical and mental disorders. At the same time, a variety of conditions including metabolic disorders also impact clock gene expression, resulting in circadian disruptions, which in turn often exacerbates the disease state.
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Affiliation(s)
- Pureum Kim
- School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Henrik Oster
- Institute of Neurobiology, University of Lübeck, Lübeck, Germany
| | - Hendrik Lehnert
- Department of Internal Medicine 1, University of Lübeck, Lübeck, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Sebastian M Schmid
- Department of Internal Medicine 1, University of Lübeck, Lübeck, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Nicole Salamat
- School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Johanna L Barclay
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Erik Maronde
- Department of Anatomy, Goethe University Frankfurt, Frankfurt, Germany
| | - Warrick Inder
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Department of Diabetes and Endocrinology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Oliver Rawashdeh
- School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
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19
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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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20
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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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21
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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: 173] [Impact Index Per Article: 28.8] [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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Allison KC, Goel N. Timing of eating in adults across the weight spectrum: Metabolic factors and potential circadian mechanisms. Physiol Behav 2018; 192:158-166. [PMID: 29486170 PMCID: PMC6019166 DOI: 10.1016/j.physbeh.2018.02.047] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 12/21/2022]
Abstract
Timing of eating is recognized as a significant contributor to body weight regulation. Disruption of sleep-wake cycles from a predominantly diurnal (daytime) to a delayed (evening) lifestyle leads to altered circadian rhythms and metabolic dysfunction. This article reviews current evidence for timed and delayed eating in individuals of normal weight and those with overweight or obesity: although some findings indicate a benefit of eating earlier in the daytime on weight and/or metabolic outcomes, results have not been uniformly consistent, and more rigorous and longer-duration studies are needed. We also review potential circadian mechanisms underlying the metabolic- and weight-related changes resulting from timed and delayed eating. Further identification of such mechanisms using deep phenotyping is required to determine targets for medical interventions for obesity and for prevention of metabolic syndrome and diabetes, and to inform clinical guidelines regarding eating schedules for management of weight and metabolic disease.
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Affiliation(s)
- Kelly C Allison
- Center for Weight and Eating Disorders, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Namni Goel
- Division of Sleep and Chronobiology, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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23
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Aitken S, Semple CA. The circadian dynamics of small nucleolar RNA in the mouse liver. J R Soc Interface 2018; 14:rsif.2017.0034. [PMID: 28468917 PMCID: PMC5454292 DOI: 10.1098/rsif.2017.0034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/12/2017] [Indexed: 12/30/2022] Open
Abstract
The circadian regulation of gene expression allows plants and animals to anticipate predictable environmental changes. While the influence of the circadian clock has recently been shown to extend to ribosome biogenesis, the dynamics and regulation of the many small nucleolar RNA that are required in pre-ribosomal RNA folding and modification are unknown. Using a novel computational method, we show that 18S and 28S pre-rRNA are subject to circadian regulation in a nuclear RNA sequencing time course. A population of snoRNA with circadian expression is identified that is functionally associated with rRNA modification. More generally, we find the abundance of snoRNA known to modify 18S and 28S to be inversely correlated with the abundance of their target. Cyclic patterns in the expression of a number of snoRNA indicate a coordination with rRNA maturation, potentially through an upregulation in their biogenesis, or their release from mature rRNA at the end of the previous cycle of rRNA maturation, in antiphase with the diurnal peak in pre-rRNA. Few cyclic snoRNA have cyclic host genes, indicating the action of regulatory mechanisms in addition to transcriptional activation of the host gene. For highly expressed independently transcribed snoRNA, we find a characteristic RNA polymerase II and H3K4me3 signature that correlates with mean snoRNA expression over the day.
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Affiliation(s)
- Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Colin A Semple
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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24
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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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25
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Gliniak CM, Brown JM, Noy N. The retinol-binding protein receptor STRA6 regulates diurnal insulin responses. J Biol Chem 2017; 292:15080-15093. [PMID: 28733465 DOI: 10.1074/jbc.m117.782334] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/17/2017] [Indexed: 01/06/2023] Open
Abstract
It has long been appreciated that insulin action is closely tied to circadian rhythms. However, the mechanisms that dictate diurnal insulin sensitivity in metabolic tissues are not well understood. Retinol-binding protein 4 (RBP4) has been implicated as a driver of insulin resistance in rodents and humans, and it has become an attractive drug target in type II diabetes. RBP4 is synthesized primarily in the liver where it binds retinol and transports it to tissues throughout the body. The retinol-RBP4 complex (holo-RBP) can be recognized by a cell-surface receptor known as stimulated by retinoic acid 6 (STRA6), which transports retinol into cells. Coupled to retinol transport, holo-RBP can activate STRA6-driven Janus kinase (JAK) signaling and downstream induction of signal transducer and activator of transcription (STAT) target genes. STRA6 signaling in white adipose tissue has been shown to inhibit insulin receptor responses. Here, we examined diurnal rhythmicity of the RBP4/STRA6 signaling axis and investigated whether STRA6 is necessary for diurnal variations in insulin sensitivity. We show that adipose tissue STRA6 undergoes circadian patterning driven in part by the nuclear transcription factor REV-ERBα. Furthermore, STRA6 is necessary for diurnal rhythmicity of insulin action and JAK/STAT signaling in adipose tissue. These findings establish that holo-RBP and its receptor STRA6 are potent regulators of diurnal insulin responses and suggest that the holo-RBP/STRA6 signaling axis may represent a novel therapeutic target in type II diabetes.
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Affiliation(s)
- Christy M Gliniak
- From the Department of Cellular and Molecular Medicine and.,the Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106
| | - J Mark Brown
- From the Department of Cellular and Molecular Medicine and .,the Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106.,the Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio 44195 and
| | - Noa Noy
- From the Department of Cellular and Molecular Medicine and
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26
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Hughey JJ. Machine learning identifies a compact gene set for monitoring the circadian clock in human blood. Genome Med 2017; 9:19. [PMID: 28241858 PMCID: PMC5329904 DOI: 10.1186/s13073-017-0406-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/19/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The circadian clock and the daily rhythms it produces are crucial for human health, but are often disrupted by the modern environment. At the same time, circadian rhythms may influence the efficacy and toxicity of therapeutics and the metabolic response to food intake. Developing treatments for circadian dysfunction, as well as optimizing the daily timing of treatments for other health conditions, will require a simple and accurate method to monitor the molecular state of the circadian clock. METHODS Here we used a recently developed method called ZeitZeiger to predict circadian time (CT, time of day according to the circadian clock) from genome-wide gene expression in human blood. RESULTS In cross-validation on 498 samples from 60 individuals across three publicly available datasets, ZeitZeiger predicted CT in single samples with a median absolute error of 2.1 h. The predictor trained on all 498 samples used 15 genes, only two of which are part of the core circadian clock. By then applying ZeitZeiger to 475 additional samples from the same three datasets, we quantified how the circadian clock in the blood was affected by various perturbations to the sleep-wake and light-dark cycles. Finally, we extended ZeitZeiger (1) to handle intra-individual variation by making predictions based on multiple samples taken a known time apart, and (2) to handle inter-individual variation by personalizing predictions based on samples from the respective individual. Each of these strategies improved prediction of CT by ~20%. CONCLUSIONS Our results are an important step towards precision circadian medicine. In addition, our generalizable extensions to ZeitZeiger may be applicable to the growing number of biological datasets that contain multiple observations per individual.
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Affiliation(s)
- Jacob J Hughey
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.
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27
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Boyle G, Richter K, Priest HD, Traver D, Mockler TC, Chang JT, Kay SA, Breton G. Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes. PLoS One 2017; 12:e0169923. [PMID: 28076377 PMCID: PMC5226840 DOI: 10.1371/journal.pone.0169923] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/23/2016] [Indexed: 11/18/2022] Open
Abstract
From photosynthetic bacteria to mammals, the circadian clock evolved to track diurnal rhythms and enable organisms to anticipate daily recurring changes such as temperature and light. It orchestrates a broad spectrum of physiology such as the sleep/wake and eating/fasting cycles. While we have made tremendous advances in our understanding of the molecular details of the circadian clock mechanism and how it is synchronized with the environment, we still have rudimentary knowledge regarding its connection to help regulate diurnal physiology. One potential reason is the sheer size of the output network. Diurnal/circadian transcriptomic studies are reporting that around 10% of the expressed genome is rhythmically controlled. Zebrafish is an important model system for the study of the core circadian mechanism in vertebrate. As Zebrafish share more than 70% of its genes with human, it could also be an additional model in addition to rodent for exploring the diurnal/circadian output with potential for translational relevance. Here we performed comparative diurnal/circadian transcriptome analysis with established mouse liver and other tissue datasets. First, by combining liver tissue sampling in a 48h time series, transcription profiling using oligonucleotide arrays and bioinformatics analysis, we profiled rhythmic transcripts and identified 2609 rhythmic genes. The comparative analysis revealed interesting features of the output network regarding number of rhythmic genes, proportion of tissue specific genes and the extent of transcription factor family expression. Undoubtedly, the Zebrafish model system will help identify new vertebrate outputs and their regulators and provides leads for further characterization of the diurnal cis-regulatory network.
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Affiliation(s)
- Greg Boyle
- Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, Texas, United States of America
| | - Kerstin Richter
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Henry D. Priest
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - David Traver
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Jeffrey T. Chang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, Texas, United States of America
| | - Steve A. Kay
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ghislain Breton
- Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, Texas, United States of America
- * E-mail:
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