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Santovito LS, Shaikh M, Sharma D, Forsyth CB, Voigt RM, Keshavarzian A, Bishehsari F. Effect of Alcohol on Clock Synchrony and Tissue Circadian Homeostasis in Mice. Mol Nutr Food Res 2024; 68:e2400234. [PMID: 39126133 DOI: 10.1002/mnfr.202400234] [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: 03/28/2024] [Revised: 06/28/2024] [Indexed: 08/12/2024]
Abstract
Alcohol use disorder accounts for a growing worldwide health system concern. Alcohol causes damages to various organs, including intestine and liver, primarily involved in its absorption and metabolism. However, alcohol-related organ damage risk varies significantly among individuals, even when they report consuming comparable dosages of alcohol. Factor(s) that may modulate the risk of organ injuries from alcohol consumption could be responsible for inter-individual variations in susceptibility to alcohol-related organ damages. Accumulating evidence suggests disruptions in circadian rhythm can exacerbate alcohol-related organ damages. Here we investigated the interplay between alcohol, circadian rhythm, and key tissue cellular processes at baseline, after a regular and a shift in the light/dark cycle (LCD) in mice. Central/peripheral clock expression of core clock genes (CoClGs) was analyzed. We also studied circadian homeostasis of tissue cellular processes that are involved in damages from alcohol. These experiments reveal that alcohol affects the expression of CoClGs causing a central-peripheral dyssynchrony, amplified by shift in LCD. The observed circadian clock dyssynchrony was linked to circadian disorganization of key processes involved in the alcohol-related damages, particularly when alcohol was combined with LCD. These results offer insights into the mechanisms by which alcohol interacts with circadian rhythm disruption to promote organ injury.
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Affiliation(s)
- Luca S Santovito
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Maliha Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Deepak Sharma
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Christopher B Forsyth
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, 60612, USA
- Departments of Medicine, Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Robin M Voigt
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, 60612, USA
- Departments of Medicine, Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, 60612, USA
- Departments of Medicine, Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, 60612, USA
- Department of Physiology, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Faraz Bishehsari
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, 60612, USA
- MD Anderson Cancer Center-UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Internal Medicine, Gastroenterology Research Center, University of Texas, Houston, TX, 77030, USA
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2
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Zhang X, Jie Y. Importance of Circadian Rhythms in the Ocular Surface. Biomolecules 2024; 14:796. [PMID: 39062510 PMCID: PMC11274730 DOI: 10.3390/biom14070796] [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: 05/28/2024] [Revised: 06/22/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Circadian rhythms are a ubiquitous feature throughout the organism. Accumulating evidence suggests that the dysfunction of circadian rhythms due to genetic mutations or environmental factors contributes to the genesis and progress of multiple diseases. The physiological homeostasis of the ocular surface, like any other tissue or organ, is also orchestrated by circadian rhythms. In this review, we summarize the molecular clocks and the expression of clock-controlled genes in the mammalian ocular surface. Based on the circadian expression of these genes, we conclude the diurnal oscillations of cellular biological activities in the mammalian ocular surface. Moreover, we evaluate the factors entraining circadian oscillators in the ocular surface. Finally, we further discuss the latest development of the close correlation between circadian rhythms and ocular health. Briefly, this review aimed to synthesize the previous studies to aid in understanding the importance of circadian rhythms in the ocular surface and the possible opportunities for circadian rhythm-based interventional strategies to restore the homeostasis of the ocular surface.
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Affiliation(s)
| | - Ying Jie
- Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, No. 1 Dong Jiao Min Xiang, Dong Cheng District, Beijing 100730, China;
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3
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Hibberd TJ, Ramsay S, Spencer-Merris P, Dinning PG, Zagorodnyuk VP, Spencer NJ. Circadian rhythms in colonic function. Front Physiol 2023; 14:1239278. [PMID: 37711458 PMCID: PMC10498548 DOI: 10.3389/fphys.2023.1239278] [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: 06/13/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023] Open
Abstract
A rhythmic expression of clock genes occurs within the cells of multiple organs and tissues throughout the body, termed "peripheral clocks." Peripheral clocks are subject to entrainment by a multitude of factors, many of which are directly or indirectly controlled by the light-entrainable clock located in the suprachiasmatic nucleus of the hypothalamus. Peripheral clocks occur in the gastrointestinal tract, notably the epithelia whose functions include regulation of absorption, permeability, and secretion of hormones; and in the myenteric plexus, which is the intrinsic neural network principally responsible for the coordination of muscular activity in the gut. This review focuses on the physiological circadian variation of major colonic functions and their entraining mechanisms, including colonic motility, absorption, hormone secretion, permeability, and pain signalling. Pathophysiological states such as irritable bowel syndrome and ulcerative colitis and their interactions with circadian rhythmicity are also described. Finally, the classic circadian hormone melatonin is discussed, which is expressed in the gut in greater quantities than the pineal gland, and whose exogenous use has been of therapeutic interest in treating colonic pathophysiological states, including those exacerbated by chronic circadian disruption.
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Affiliation(s)
- Timothy J. Hibberd
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Stewart Ramsay
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | | | - Phil G. Dinning
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
- Colorectal Surgical Unit, Division of Surgery, Flinders Medical Centre, Adelaide, SA, Australia
| | | | - Nick J. Spencer
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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4
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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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5
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Obodo D, Outland EH, Hughey JJ. Sex Inclusion in Transcriptome Studies of Daily Rhythms. J Biol Rhythms 2023; 38:3-14. [PMID: 36419398 PMCID: PMC9903005 DOI: 10.1177/07487304221134160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Biomedical research on mammals has traditionally neglected females, raising the concern that some scientific findings may generalize poorly to half the population. Although this lack of sex inclusion has been broadly documented, its extent within circadian genomics remains undescribed. To address this gap, we examined sex inclusion practices in a comprehensive collection of publicly available transcriptome studies on daily rhythms. Among 148 studies having samples from mammals in vivo, we found strong underrepresentation of females across organisms and tissues. Overall, only 23 of 123 studies in mice, 0 of 10 studies in rats, and 9 of 15 studies in humans included samples from females. In addition, studies having samples from both sexes tended to have more samples from males than from females. These trends appear to have changed little over time, including since 2016, when the US National Institutes of Health began requiring investigators to consider sex as a biological variable. Our findings highlight an opportunity to dramatically improve representation of females in circadian research and to explore sex differences in daily rhythms at the genome level.
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Affiliation(s)
- Dora Obodo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Elliot H. Outland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jacob J. Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee,Jacob J. Hughey, Department of Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End Ave., Suite 1475, Nashville, TN 37232, USA; e-mail:
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6
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Ratiner K, Fachler-Sharp T, Elinav E. Small Intestinal Microbiota Oscillations, Host Effects and Regulation-A Zoom into Three Key Effector Molecules. BIOLOGY 2023; 12:142. [PMID: 36671834 PMCID: PMC9855434 DOI: 10.3390/biology12010142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
The gut microbiota features a unique diurnal rhythmicity which contributes to modulation of host physiology and homeostasis. The composition and activity of the microbiota and its secreted molecules influence the intestinal milieu and neighboring organs, such as the liver. Multiple immune-related molecules have been linked to the diurnal microbiota-host interaction, including Reg3γ, IgA, and MHCII, which are secreted or expressed on the gut surface and directly interact with intestinal bacteria. These molecules are also strongly influenced by dietary patterns, such as high-fat diet and time-restricted feeding, which are already known to modulate microbial rhythms and peripheral clocks. Herein, we use Reg3γ, IgA, and MHCII as test cases to highlight the divergent effects mediated by the diurnal activity of the gut microbiota and their downstream host effects. We further highlight current challenges and conflicts, remaining questions, and perspectives toward a holistic understanding of the microbiome's impacts on circadian human behavior.
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Affiliation(s)
- Karina Ratiner
- Systems Immunology Department, Weisman Institute of Science, Rehovot 7610001, Israel
| | - Tahel Fachler-Sharp
- Systems Immunology Department, Weisman Institute of Science, Rehovot 7610001, Israel
- Department of Dermatology, Hadassah-Hebrew University Medical Center, Jerusalem 9987500, Israel
| | - Eran Elinav
- Systems Immunology Department, Weisman Institute of Science, Rehovot 7610001, Israel
- Microbiota & Cancer Division, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
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7
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Desmet L, Thijs T, Segers A, Depoortere I. Chronic jetlag reprograms gene expression in the colonic smooth muscle layer inducing diurnal rhythmicity in the effect of bile acids on colonic contractility. Neurogastroenterol Motil 2023; 35:e14487. [PMID: 36264144 DOI: 10.1111/nmo.14487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 09/14/2022] [Accepted: 09/27/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Secondary bile acids entrain peripheral circadian clocks and inhibit colonic motility via the bile acid receptor GPBAR1. We aimed to investigate whether chronodisruption affected the rhythm in serum bile acid levels and whether this was associated with alterations in clock gene and Gpbar1 mRNA expression in the colonic smooth muscle layer. We hypothesized that this in turn may affect the rhythm in the inhibitory effect of secondary bile acids on colonic contractility. METHODS Mice were exposed to 4 weeks of chronic jetlag induction. The expression of Gpbar1 and clock genes was measured in colonic smooth muscle tissue using RT-qPCR over 24 h (4 h time interval). The effect of secondary bile acids on electrical field-induced neural contractions was measured isometrically in colonic smooth muscle strips. KEY RESULTS Chronic jetlag abolished the rhythmicity in serum bile acid levels. This was associated with a phase-shift in diurnal clock gene mRNA fluctuations in smooth muscle tissue. Chronic jetlag induced a rhythm in Gpbar1 expression in the colonic smooth muscle layer. In parallel, a rhythm was induced in the inhibitory effect of taurodeoxycholic acid (TDCA), but not deoxycholic acid, on neural colonic contractions that peaked together with Gpbar1 expression. CONCLUSIONS & INFERENCES Chronodisruption abolished the rhythm in bile acid levels which might contribute to a shift in smooth muscle clock gene expression. Our findings suggest that chronodisruption caused a transcriptional reprogramming in the colonic smooth layer thereby inducing a rhythm in the expression of Gpbar1 and in the inhibitory effect of TDCA on colonic contractility.
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Affiliation(s)
- Louis Desmet
- Translational Research Center for Gastrointestinal Disorders, Gut Peptide Research Lab, University of Leuven, Leuven, Belgium
| | - Theo Thijs
- Translational Research Center for Gastrointestinal Disorders, Gut Peptide Research Lab, University of Leuven, Leuven, Belgium
| | - Anneleen Segers
- Translational Research Center for Gastrointestinal Disorders, Gut Peptide Research Lab, University of Leuven, Leuven, Belgium
| | - Inge Depoortere
- Translational Research Center for Gastrointestinal Disorders, Gut Peptide Research Lab, University of Leuven, Leuven, Belgium
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8
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Taleb Z, Karpowicz P. Circadian regulation of digestive and metabolic tissues. Am J Physiol Cell Physiol 2022; 323:C306-C321. [PMID: 35675638 DOI: 10.1152/ajpcell.00166.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The circadian clock is a self-sustained molecular timekeeper that drives 24-h (circadian) rhythms in animals. The clock governs important aspects of behavior and physiology including wake/sleep activity cycles that regulate the activity of metabolic and digestive systems. Light/dark cycles (photoperiod) and cycles in the time of feeding synchronize the circadian clock to the surrounding environment, providing an anticipatory benefit that promotes digestive health. The availability of animal models targeting the genetic components of the circadian clock has made it possible to investigate the circadian clock's role in cellular functions. Circadian clock genes have been shown to regulate the physiological function of hepatocytes, gastrointestinal cells, and adipocytes; disruption of the circadian clock leads to the exacerbation of liver diseases and liver cancer, inflammatory bowel disease and colorectal cancer, and obesity. Previous findings provide strong evidence that the circadian clock plays an integral role in digestive/metabolic disease pathogenesis, hence, the circadian clock is a necessary component in metabolic and digestive health and homeostasis. Circadian rhythms and circadian clock function provide an opportunity to improve the prevention and treatment of digestive and metabolic diseases by aligning digestive system tissue with the 24-h day.
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Affiliation(s)
- Zainab Taleb
- Department of Biomedical Sciences, University of Windsor, Windsor, Ontario, Canada
| | - Phillip Karpowicz
- Department of Biomedical Sciences, University of Windsor, Windsor, Ontario, Canada
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9
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Kobayashi Y, Takemi S, Sakai T, Shibata C, Sakata I. Diurnal changes of colonic motility and regulatory factors for colonic motility in Suncus murinus. Neurogastroenterol Motil 2022; 34:e14302. [PMID: 34846085 DOI: 10.1111/nmo.14302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND The aim of this study was to investigate the fundamental mechanisms of colonic motility in the house musk suncus (Suncus murinus) as an established animal model of gut motility. METHODS To measure gut motility in free-moving conscious suncus, strain gauge force transducers were implanted on the serosa of the colon and gastric body. KEY RESULTS We recorded diurnal changes in colonic motility and observed the relationship between feeding and colonic motility. Giant migrating contractions (GMCs) of the colon were invariably detected during defecation and tended to increase during the dark period, thereby indicating that colonic motility has a circadian rhythm. Given that GMCs in the suncus were observed immediately after feeding during the dark period, we assume the occurrence of a gastrocolic reflex in suncus, similar to that observed in humans and dogs. We also examined the factors that regulate suncus GMCs. Intravenous administration of 5-HT (100 µg/kg), substance P (10 and 100 µg/kg), calcitonin gene-related peptide (10 µg/kg), and α2 adrenergic receptor antagonist yohimbine (0.5, 1, and 3 mg/kg) induced GMC-like contractions, as did intragastric and intracolonic administration of the transient receptor potential vanilloid 1 agonist, capsaicin (1 mg/kg). CONCLUSIONS & INFERENCES These results indicate that the fundamental mechanisms of colonic motility in suncus are similar to those in humans and dogs, and we thus propose that suncus could serve as a novel small animal model for studying colonic motility.
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Affiliation(s)
- Yuki Kobayashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Shota Takemi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takafumi Sakai
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Chikashi Shibata
- Division of Faculty of Medicine, Department of Gastroenterologic Surgery, Tohoku Medical and Pharmacological University, Sendai, Japan
| | - Ichiro Sakata
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan.,Division of Strategy Research, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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10
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Taleb Z, Carmona-Alcocer V, Stokes K, Haireek M, Wang H, Collins SM, Khan WI, Karpowicz P. BMAL1 Regulates the Daily Timing of Colitis. Front Cell Infect Microbiol 2022; 12:773413. [PMID: 35223537 PMCID: PMC8863668 DOI: 10.3389/fcimb.2022.773413] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
Many physiological functions exhibit circadian rhythms: oscillations in biological processes that occur in a 24-hour period. These daily rhythms are maintained through a highly conserved molecular pacemaker known as the circadian clock. Circadian disruption has been proposed to cause increased risk of Inflammatory Bowel Disease (IBD) but the underlying mechanisms remain unclear. Patients with IBD experience chronic inflammation and impaired regeneration of intestinal epithelial cells. Previous animal-based studies have revealed that colitis models of IBD are more severe in mice without a circadian clock but the timing of colitis, and whether its inflammatory and regenerative processes have daily rhythms, remains poorly characterized. We tested circadian disruption using Bmal1-/- mutant mice that have a non-functional circadian clock and thus no circadian rhythms. Dextran Sulfate Sodium (DSS) was used to induce colitis. The disease activity of colitis was found to exhibit time-dependent variation in Bmal1+/+ control mice but is constant and elevated in Bmal1-/- mutants, who exhibit poor recovery. Histological analyses indicate worsened colitis severity in Bmal1-/- mutant colon, and colon infiltration of immune system cells shows a daily rhythm that is lost in the Bmal1-/- mutant. Similarly, epithelial proliferation in the colon has a daily rhythm in Bmal1+/+ controls but not in Bmal1-/- mutants. Our results support a critical role of a functional circadian clock in the colon which drives 24-hour rhythms in inflammation and healing, and whose disruption impairs colitis recovery. This indicates that weakening circadian rhythms not only worsens colitis, but delays healing and should be taken into account in the management of IBD. Recognition of this is important in the management of IBD patients required to do shift work.
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Affiliation(s)
- Zainab Taleb
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | | | - Kyle Stokes
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Marta Haireek
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Huaqing Wang
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Stephen M. Collins
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Waliul I. Khan
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Phillip Karpowicz
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
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11
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Lidington D, Wan H, Dinh DD, Ng C, Bolz SS. Circadian Rhythmicity in Cerebral Microvascular Tone Influences Subarachnoid Hemorrhage-Induced Injury. Stroke 2021; 53:249-259. [PMID: 34905942 PMCID: PMC8700310 DOI: 10.1161/strokeaha.121.036950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Supplemental Digital Content is available in the text. Circadian rhythms influence the extent of brain injury following subarachnoid hemorrhage (SAH), but the mechanism is unknown. We hypothesized that cerebrovascular myogenic reactivity is rhythmic and explains the circadian variation in SAH-induced injury.
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Affiliation(s)
- Darcy Lidington
- Department of Physiology (D.L., H.W., D.D.D., C.N., S.-S.B.), University of Toronto, Canada.,Toronto Centre for Microvascular Medicine at The Ted Rogers Centre for Heart Research Translational Biology and Engineering Program (D.L., H.W., D.D.D., C.N., S-S.B.), University of Toronto, Canada
| | - Hoyee Wan
- Department of Physiology (D.L., H.W., D.D.D., C.N., S.-S.B.), University of Toronto, Canada.,Toronto Centre for Microvascular Medicine at The Ted Rogers Centre for Heart Research Translational Biology and Engineering Program (D.L., H.W., D.D.D., C.N., S-S.B.), University of Toronto, Canada
| | - Danny D Dinh
- Department of Physiology (D.L., H.W., D.D.D., C.N., S.-S.B.), University of Toronto, Canada.,Toronto Centre for Microvascular Medicine at The Ted Rogers Centre for Heart Research Translational Biology and Engineering Program (D.L., H.W., D.D.D., C.N., S-S.B.), University of Toronto, Canada
| | - Chloe Ng
- Department of Physiology (D.L., H.W., D.D.D., C.N., S.-S.B.), University of Toronto, Canada.,Toronto Centre for Microvascular Medicine at The Ted Rogers Centre for Heart Research Translational Biology and Engineering Program (D.L., H.W., D.D.D., C.N., S-S.B.), University of Toronto, Canada
| | - Steffen-Sebastian Bolz
- Department of Physiology (D.L., H.W., D.D.D., C.N., S.-S.B.), University of Toronto, Canada.,Toronto Centre for Microvascular Medicine at The Ted Rogers Centre for Heart Research Translational Biology and Engineering Program (D.L., H.W., D.D.D., C.N., S-S.B.), University of Toronto, Canada.,Heart & Stroke/Richard Lewar Centre of Excellence for Cardiovascular Research (S-S.B.), University of Toronto, Canada
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12
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Guido ME, Monjes NM, Wagner PM, Salvador GA. Circadian Regulation and Clock-Controlled Mechanisms of Glycerophospholipid Metabolism from Neuronal Cells and Tissues to Fibroblasts. Mol Neurobiol 2021; 59:326-353. [PMID: 34697790 DOI: 10.1007/s12035-021-02595-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022]
Abstract
Along evolution, living organisms developed a precise timekeeping system, circadian clocks, to adapt life to the 24-h light/dark cycle and temporally regulate physiology and behavior. The transcriptional molecular circadian clock and metabolic/redox oscillator conforming these clocks are present in organs, tissues, and even in individual cells, where they exert circadian control over cellular metabolism. Disruption of the molecular clock may cause metabolic disorders and higher cancer risk. The synthesis and degradation of glycerophospholipids (GPLs) is one of the most highly regulated metabolisms across the 24-h cycle in terms of total lipid content and enzyme expression and activity in the nervous system and individual cells. Lipids play a plethora of roles (membrane biogenesis, energy sourcing, signaling, and the regulation of protein-chromatin interaction, among others), making control of their metabolism a vital checkpoint in the cellular organization of physiology. An increasing body of evidence clearly demonstrates an orchestrated and sequential series of events occurring in GPL metabolism across the 24-h day in diverse retinal cell layers, immortalized fibroblasts, and glioma cells. Moreover, the clock gene Per1 and other circadian-related genes are tightly involved in the regulation of GPL synthesis in quiescent cells. However, under proliferation, the metabolic oscillator continues to control GPL metabolism of brain cancer cells even after molecular circadian clock disruption, reflecting the crucial role of the temporal metabolism organization in cell preservation. The aim of this review is to examine the control exerted by circadian clocks over GPL metabolism, their synthesizing enzyme expression and activities in normal and tumorous cells of the nervous system and in immortalized fibroblasts.
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Affiliation(s)
- Mario E Guido
- CIQUIBIC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina.
- Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina.
| | - Natalia M Monjes
- CIQUIBIC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
- Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
| | - Paula M Wagner
- CIQUIBIC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
- Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
| | - Gabriela A Salvador
- INIBIBB-UNS-CONICET, Departamento de Biología, Bioquímica y Farmacia, UNS, Bahía Blanca, Argentina
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13
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Stokes K, Nunes M, Trombley C, Flôres DEFL, Wu G, Taleb Z, Alkhateeb A, Banskota S, Harris C, Love OP, Khan WI, Rueda L, Hogenesch JB, Karpowicz P. The Circadian Clock Gene, Bmal1, Regulates Intestinal Stem Cell Signaling and Represses Tumor Initiation. Cell Mol Gastroenterol Hepatol 2021; 12:1847-1872.e0. [PMID: 34534703 PMCID: PMC8591196 DOI: 10.1016/j.jcmgh.2021.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Circadian rhythms are daily physiological oscillations driven by the circadian clock: a 24-hour transcriptional timekeeper that regulates hormones, inflammation, and metabolism. Circadian rhythms are known to be important for health, but whether their loss contributes to colorectal cancer is not known. We tested the nonredundant clock gene Bmal1 in intestinal homeostasis and tumorigenesis, using the Apcmin model of colorectal cancer. METHODS Bmal1 mutant, epithelium-conditional Bmal1 mutant, and photoperiod (day/night cycle) disrupted mice bearing the Apcmin allele were assessed for tumorigenesis. Tumors and normal nontransformed tissue were characterized. Intestinal organoids were assessed for circadian transcription rhythms by RNA sequencing, and in vivo and organoid assays were used to test Bmal1-dependent proliferation and self-renewal. RESULTS Loss of Bmal1 or circadian photoperiod increases tumor initiation. In the intestinal epithelium the clock regulates transcripts involved in regeneration and intestinal stem cell signaling. Tumors have no self-autonomous clock function and only weak clock function in vivo. Apcmin clock-disrupted tumors show high Yes-associated protein 1 (Hippo signaling) activity but show low Wnt (Wingless and Int-1) activity. Intestinal organoid assays show that loss of Bmal1 increases self-renewal in a Yes-associated protein 1-dependent manner. CONCLUSIONS Bmal1 regulates intestinal stem cell pathways, including Hippo signaling, and the loss of circadian rhythms potentiates tumor initiation. Transcript profiling: GEO accession number: GSE157357.
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Affiliation(s)
- Kyle Stokes
- Department of Biomedical Sciences, Windsor, Ontario, Canada
| | - Malika Nunes
- Department of Biomedical Sciences, Windsor, Ontario, Canada
| | | | - Danilo E F L Flôres
- Division of Human Genetics and Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Gang Wu
- Division of Human Genetics and Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Zainab Taleb
- Department of Biomedical Sciences, Windsor, Ontario, Canada
| | | | - Suhrid Banskota
- Department of Pathology and Molecular Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Chris Harris
- Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| | - Oliver P Love
- Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| | - Waliul I Khan
- Department of Pathology and Molecular Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Luis Rueda
- School of Computer Science, Windsor, Ontario, Canada
| | - John B Hogenesch
- Division of Human Genetics and Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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14
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Ruby CL, Major RJ, Hinrichsen RD. Regulation of tissue regeneration by the circadian clock. Eur J Neurosci 2021; 53:3576-3597. [PMID: 33893679 DOI: 10.1111/ejn.15244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/31/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022]
Abstract
Circadian rhythms are regulated by a highly conserved transcriptional/translational feedback loop that maintains approximately 24-hr periodicity from cellular to organismal levels. Much research effort is being devoted to understanding how the outputs of the master clock affect peripheral oscillators, and in turn, numerous biological processes. Recent studies have revealed roles for circadian timing in the regulation of numerous cellular behaviours in support of complex tissue regeneration. One such role involves the interaction between the circadian clockwork and the cell cycle. The molecular mechanisms that control the cell cycle create a system of regulation that allows for high fidelity DNA synthesis, mitosis and apoptosis. In recent years, it has become clear that clock gene products are required for proper DNA synthesis and cell cycle progression, and conversely, elements of the cell cycle cascade feedback to influence molecular circadian timing mechanisms. It is through this crosstalk that the circadian system orchestrates stem cell proliferation, niche exit and control of the signalling pathways that govern differentiation and self-renewal. In this review, we discuss the evidence for circadian control of tissue homeostasis and repair and suggest new avenues for research.
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Affiliation(s)
- Christina L Ruby
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
| | - Robert J Major
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
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15
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Koritala BSC, Porter KI, Arshad OA, Gajula RP, Mitchell HD, Arman T, Manjanatha MG, Teeguarden J, Van Dongen HPA, McDermott JE, Gaddameedhi S. Night shift schedule causes circadian dysregulation of DNA repair genes and elevated DNA damage in humans. J Pineal Res 2021; 70:e12726. [PMID: 33638890 PMCID: PMC8011353 DOI: 10.1111/jpi.12726] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/22/2021] [Indexed: 12/21/2022]
Abstract
Circadian disruption has been identified as a risk factor for health disorders such as obesity, cardiovascular disease, and cancer. Although epidemiological studies suggest an increased risk of various cancers associated with circadian misalignment due to night shift work, the underlying mechanisms have yet to be elucidated. We sought to investigate the potential mechanistic role that circadian disruption of cancer hallmark pathway genes may play in the increased cancer risk in shift workers. In a controlled laboratory study, we investigated the circadian transcriptome of cancer hallmark pathway genes and associated biological pathways in circulating leukocytes obtained from healthy young adults during a 24-hour constant routine protocol following 3 days of simulated day shift or night shift. The simulated night shift schedule significantly altered the normal circadian rhythmicity of genes involved in cancer hallmark pathways. A DNA repair pathway showed significant enrichment of rhythmic genes following the simulated day shift schedule, but not following the simulated night shift schedule. In functional assessments, we demonstrated that there was an increased sensitivity to both endogenous and exogenous sources of DNA damage after exposure to simulated night shift. Our results suggest that circadian dysregulation of DNA repair may increase DNA damage and potentiate elevated cancer risk in night shift workers.
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Affiliation(s)
- Bala S. C. Koritala
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
- Sleep and Performance Research Center, Washington State University, Spokane, WA, USA
- Division of Pediatric Otolaryngology-Head and Neck Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Kenneth I. Porter
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
- Sleep and Performance Research Center, Washington State University, Spokane, WA, USA
| | - Osama A. Arshad
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rajendra P. Gajula
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
- Sleep and Performance Research Center, Washington State University, Spokane, WA, USA
| | - Hugh D. Mitchell
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tarana Arman
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Mugimane G. Manjanatha
- Division of Genetic and Molecular Toxicology, National Center for Toxicology Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Justin Teeguarden
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Hans P. A. Van Dongen
- Sleep and Performance Research Center, Washington State University, Spokane, WA, USA
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Jason E. McDermott
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Shobhan Gaddameedhi
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
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16
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Abstract
Many molecular, physiological and behavioural processes display distinct 24-hour rhythms that are directed by the circadian system. The master clock, located in the suprachiasmatic nucleus region of the hypothalamus, is synchronized or entrained by the light-dark cycle and, in turn, synchronizes clocks present in peripheral tissues and organs. Other environmental cues, most importantly feeding time, also synchronize peripheral clocks. In this way, the circadian system can prepare the body for predictable environmental changes such as the availability of nutrients during the normal feeding period. This Review summarizes existing knowledge about the diurnal regulation of gastrointestinal processes by circadian clocks present in the digestive tract and its accessory organs. The circadian control of gastrointestinal digestion, motility, hormones and barrier function as well as of the gut microbiota are discussed. An overview is given of the interplay between different circadian clocks in the digestive system that regulate glucose homeostasis and lipid and bile acid metabolism. Additionally, the bidirectional interaction between the master clock and peripheral clocks in the digestive system, encompassing different entraining factors, is described. Finally, the possible behavioural adjustments or pharmacological strategies for the prevention and treatment of the adverse effects of chronodisruption are outlined.
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17
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Cheng WY, Lam KL, Pik-Shan Kong A, Chi-Keung Cheung P. Prebiotic supplementation (beta-glucan and inulin) attenuates circadian misalignment induced by shifted light-dark cycle in mice by modulating circadian gene expression. Food Res Int 2020; 137:109437. [PMID: 33233118 DOI: 10.1016/j.foodres.2020.109437] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/13/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022]
Abstract
Circadian rhythm governs multiple behavioural and physiological processes and its disruption is closely associated with various pathological conditions. In this study, the effects of dietary intervention by prebiotics including beta-glucan and inulin on attenuating circadian desynchrony in C57BL/6J mice subjected to weekly shifted light-dark cycle under a high fat diet was investigated. Using RT-qPCR and rhythmicity analysis, our study revealed that beta-glucan (0.2 g/day) and inulin (0.2 g/day) modulated the expression and phase of circadian-clock genes, explicitly reversed the phase delay of Period 1 and Period 3 in the hypothalamus, and reversed the phase delay of Period 2 in the liver of the mice. In the shifted mouse group, inulin also exhibited its reversal effects on the phase advance of Brain and muscle-Arnt-like 1 in the hypothalamus. These findings indicated that prebiotic supplementation can be a novel dietary approach for attenuating circadian misalignment.
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Affiliation(s)
- Wai-Yin Cheng
- Food and Nutritional Sciences, School of Life Sciences, The Chinese University of Hong Kong, University Science Centre, Shatin, New Territory, Hong Kong Special Administrative Region
| | - Ka-Lung Lam
- Food and Nutritional Sciences, School of Life Sciences, The Chinese University of Hong Kong, University Science Centre, Shatin, New Territory, Hong Kong Special Administrative Region
| | - Alice Pik-Shan Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong Special Administrative Region
| | - Peter Chi-Keung Cheung
- Food and Nutritional Sciences, School of Life Sciences, The Chinese University of Hong Kong, University Science Centre, Shatin, New Territory, Hong Kong Special Administrative Region.
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18
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Bishehsari F, Moossavi S, Engen PA, Liu X, Zhang Y. Abnormal Food Timing Promotes Alcohol-Associated Dysbiosis and Colon Carcinogenesis Pathways. Front Oncol 2020; 10:1029. [PMID: 32850307 PMCID: PMC7396506 DOI: 10.3389/fonc.2020.01029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/26/2020] [Indexed: 12/21/2022] Open
Abstract
Background: Alcohol consumption is an established risk factor for colorectal cancer (CRC). Identifying cofactor(s) that modulate the effect of alcohol on colon inflammation and carcinogenesis could help risk stratification for CRC. Disruption of circadian rhythm by light/dark shift promotes alcohol-induced colonic inflammation and cancer. More recently, we found that abnormal food timing causes circadian rhythm disruption and promotes alcohol associated colon carcinogenesis. In this study, we examined the interaction of wrong-time feeding (WTF) and alcohol on CRC-related pathways, in relation to changes in microbial community structure. Methods: Polyposis mice (TS4Cre ×cAPC Δ468) underwent four conditions: alcohol or water and feeding during the light (wrong-time fed/WTF) or during the dark (right-time fed). Colonic cecum mucosal gene expression was analyzed by RNA-seq. Microbiota 16S ribosomal RNA sequencing analysis was used to examine colonic feces. Modeling was used to estimate the extent of the gene expression changes that could be related to the changes in the colonic microbial composition. Results: The circadian rhythm pathway was the most altered pathway by the WTF treatment, indicating that WTF is disruptive to the colonic circadian rhythm. Pathway analysis revealed interaction of WTF with alcohol in dysregulating pathways related to colon carcinogenesis. Similarly, the interaction of alcohol and WTF was detected at multiple parameters of the colonic microbiota including α and β diversity, as well as the community structure. Our modeling revealed that almost a third of total gene alterations induced by our treatments could be related to alterations in the abundance of the microbial taxa. Conclusion: These data support the promoting effect of abnormal food timing alcohol-associated CRC-related pathways in the colon and suggest colon dysbiosis as a targetable mechanism.
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Affiliation(s)
- Faraz Bishehsari
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL, United States
| | - Shirin Moossavi
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Phillip A. Engen
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL, United States
| | - Xiaohan Liu
- Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, IL, United States
| | - Yue Zhang
- Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, IL, United States
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19
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Parasram K, Karpowicz P. Time after time: circadian clock regulation of intestinal stem cells. Cell Mol Life Sci 2020; 77:1267-1288. [PMID: 31586240 PMCID: PMC11105114 DOI: 10.1007/s00018-019-03323-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/16/2019] [Accepted: 09/25/2019] [Indexed: 12/22/2022]
Abstract
Daily fluctuations in animal physiology, known as circadian rhythms, are orchestrated by a conserved molecular timekeeper, known as the circadian clock. The circadian clock forms a transcription-translation feedback loop that has emerged as a central biological regulator of many 24-h processes. Early studies of the intestine discovered that many digestive functions have a daily rhythm and that intestinal cell production was similarly time-dependent. As genetic methods in model organisms have become available, it has become apparent that the circadian clock regulates many basic cellular functions, including growth, proliferation, and differentiation, as well as cell signalling and stem cell self-renewal. Recent connections between circadian rhythms and immune system function, and between circadian rhythms and microbiome dynamics, have also been revealed in the intestine. These processes are highly relevant in understanding intestinal stem cell biology. Here we describe the circadian clock regulation of intestinal stem cells primarily in two model organisms: Drosophila melanogaster and mice. Like all cells in the body, intestinal stem cells are subject to circadian timing, and both cell-intrinsic and cell-extrinsic circadian processes contribute to their function.
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Affiliation(s)
- Kathyani Parasram
- Department of Biological Sciences, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
| | - Phillip Karpowicz
- Department of Biological Sciences, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada.
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20
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Chang ML, Moussette S, Gamero-Estevez E, Gálvez JH, Chiwara V, Gupta IR, Ryan AK, Naumova AK. Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock. PLoS One 2019; 14:e0223212. [PMID: 31560728 PMCID: PMC6764692 DOI: 10.1371/journal.pone.0223212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/15/2019] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association study (GWAS) loci for several immunity-mediated diseases (early onset asthma, inflammatory bowel disease (IBD), primary biliary cholangitis, and rheumatoid arthritis) map to chromosomal region 17q12-q21. The predominant view is that association between 17q12-q21 alleles and increased risk of developing asthma or IBD is due to regulatory variants. ORM sphingolipid biosynthesis regulator (ORMDL3) residing in this region is the most promising gene candidate for explaining association with disease. However, the relationship between 17q12-q21 alleles and disease is complex suggesting contributions from other factors, such as trans-acting genetic and environmental modifiers or circadian rhythms. Circadian rhythms regulate expression levels of thousands of genes and their dysregulation is implicated in the etiology of several common chronic inflammatory diseases. However, their role in the regulation of the 17q12-q21 genes has not been investigated. Moreover, the core clock gene nuclear receptor subfamily 1, group D, member 1 (NR1D1) resides about 200 kb distal to the GWAS region. We hypothesized that circadian rhythms influenced gene expression levels in 17q12-q21 region and conversely, regulatory elements in this region influenced transcription of the core clock gene NR1D1 in cis. To test these hypotheses, we examined the diurnal expression profiles of zona pellucida binding protein 2 (ZPBP2/Zpbp2), gasdermin B (GSDMB), and ORMDL3/Ormdl3 in human and mouse tissues and analyzed the impact of genetic variation in the ZPBP2/Zpbp2 region on NR1D1/Nr1d1 expression. We found that Ormdl3 and Zpbp2 were controlled by the circadian clock in a tissue-specific fashion. We also report that deletion of the Zpbp2 region altered the expression profile of Nr1d1 in lungs and ileum in a time-dependent manner. In liver, the deletion was associated with enhanced expression of Ormdl3. We provide the first evidence that disease-associated genes Zpbp2 and Ormdl3 are regulated by circadian rhythms and the Zpbp2 region influences expression of the core clock gene Nr1d1.
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Affiliation(s)
- Matthew L. Chang
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Sanny Moussette
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | | | | | - Victoria Chiwara
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Indra R. Gupta
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Paediatrics, McGill University, Montreal, Quebec, Canada
| | - Aimee K. Ryan
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Paediatrics, McGill University, Montreal, Quebec, Canada
| | - Anna K. Naumova
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Obstetrics and Gynecology, McGill University, Montreal, Quebec, Canada
- * E-mail:
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21
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Paulose JK, Cassone CV, Graniczkowska KB, Cassone VM. Entrainment of the Circadian Clock of the Enteric Bacterium Klebsiella aerogenes by Temperature Cycles. iScience 2019; 19:1202-1213. [PMID: 31551197 PMCID: PMC6831877 DOI: 10.1016/j.isci.2019.09.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/22/2019] [Accepted: 09/04/2019] [Indexed: 01/20/2023] Open
Abstract
The gastrointestinal bacterium Klebsiella (née Enterobacter) aerogenes expresses an endogenously generated, temperature-compensated circadian rhythm in swarming motility. We hypothesized that this rhythm may be synchronized/entrained in vivo by body temperature (TB). To determine entrainment, cultures expressing bioluminescence were exposed to temperature cycles of 1°C (35°C-36°C) or 3°C (34°C-37°C) in amplitude at periods (T-cycles) of T = 22, T = 24, or T = 28 h. Bacteria entrained to all T-cycles at both amplitudes and with stable phase relationships. A high-amplitude phase response curve (PRC) in response to 1-h pulses of 3°C temperature spike (34°C-37°C) at different circadian phases was constructed, revealing a Type-0 phase resetting paradigm. Furthermore, real-time bioluminescence imaging revealed a spatiotemporal pattern to the circadian rhythm. These data are consistent with the hypothesis that the K. aerogenes circadian clock entrains to its host via detection of and phase shifting to the daily pattern of TB.
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Affiliation(s)
- Jiffin K Paulose
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Charles V Cassone
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | | | - Vincent M Cassone
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA.
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22
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Intestinal Stem Cells Exhibit Conditional Circadian Clock Function. Stem Cell Reports 2019; 11:1287-1301. [PMID: 30428387 PMCID: PMC6235668 DOI: 10.1016/j.stemcr.2018.10.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
The circadian clock is a molecular pacemaker that produces 24-hr physiological cycles known as circadian rhythms. How the clock regulates stem cells is an emerging area of research with many outstanding questions. We tested clock function in vivo at the single cell resolution in the Drosophila intestine, a tissue that is exquisitely sensitive to environmental cues and has circadian rhythms in regeneration. Our results indicate that circadian clocks function in intestinal stem cells and enterocytes but are downregulated during enteroendocrine cell differentiation. Drosophila intestinal cells are principally synchronized by the photoperiod, but intestinal stem cell clocks are highly responsive to signaling pathways that comprise their niche, and we find that the Wnt and Hippo signaling pathways positively regulate stem cell circadian clock function. These data reveal that intestinal stem cell circadian rhythms are regulated by cellular signaling and provide insight as to how clocks may be altered during physiological changes such as regeneration and aging. Intestinal epithelial cells have circadian clock function but enteroendocrine cells do not Restricted feeding can entrain circadian clocks in the absence of photoperiod Circadian clock communication exists between intestinal stem cells and enterocytes Notch, Wnt, and Hippo signaling regulate stem cell clock function
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23
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Bishehsari F, Zhang L, Voigt RM, Maltby N, Semsarieh B, Zorub E, Shaikh M, Wilber S, Armstrong AR, Mirbagheri SS, Preite NZ, Song P, Stornetta A, Balbo S, Forsyth CB, Keshavarzian A. Alcohol Effects on Colon Epithelium are Time-Dependent. Alcohol Clin Exp Res 2019; 43:1898-1908. [PMID: 31237690 PMCID: PMC6722020 DOI: 10.1111/acer.14141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/20/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Alcohol intake increases the risk of developing colon cancer. Circadian disruption promotes alcohol's effect on colon carcinogenesis through unknown mechanisms. Alcohol's metabolites induce DNA damage, an early step in carcinogenesis. We assessed the effect of time of alcohol consumption on markers of tissue damage in the colonic epithelium. METHODS Mice were treated by alcohol or phosphate-buffered saline (PBS), at 4-hour intervals for 3 days, and their colons were analyzed for (i) proliferation (Ki67) and antiapoptosis (Bcl-2) markers, (ii) DNA damage (γ-H2AX), and (iii) the major acetaldehyde (AcH)-DNA adduct, N2 -ethylidene-dG. To model circadian disruption, mice were shifted once weekly for 12 h and then were sacrificed at 4-hour intervals. Samples of mice with a dysfunctional molecular clock were analyzed. The dynamics of DNA damage repair from AcH treatment as well as role of xeroderma pigmentosum, complementation group A (XPA) in their repair were studied in vitro. RESULTS Proliferation and survival of colonic epithelium have daily rhythmicity. Alcohol induced colonic epithelium proliferation in a time-dependent manner, with a stronger effect during the light/rest period. Alcohol-associated DNA damage also occurred more when alcohol was given at light. Levels of DNA adduct did not vary by time, suggesting rather lower repair efficiency during the light versus dark. XPA gene expression, a key excision repair gene, was time-dependent, peaking at the beginning of the dark. XPA knockout colon epithelial cells were inefficient in repair of the DNA damage induced by alcohol's metabolite. CONCLUSIONS Time of day of alcohol intake may be an important determinant of colon tissue damage and carcinogenicity.
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Affiliation(s)
- Faraz Bishehsari
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Lijuan Zhang
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Robin M. Voigt
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Natalie Maltby
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Bita Semsarieh
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Eyas Zorub
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Maliha Shaikh
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Sherry Wilber
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Andrew R Armstrong
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Seyed Sina Mirbagheri
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Nailliw Z. Preite
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Peter Song
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Alessia Stornetta
- Masonic Cancer Center, University of Minnesota, Minneapolis MN 55455
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis MN 55455
| | - Christopher B. Forsyth
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
| | - Ali Keshavarzian
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL USA
- Department of Physiology, Rush University Medical Center, Chicago, IL USA
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht Netherlands
- Department of Pharmacology, Rush University Medical Center, Chicago, IL USA
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24
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Jiao X, Wu M, Lu D, Gu J, Li Z. Transcriptional Profiling of Daily Patterns of mRNA Expression in the C57BL/6J Mouse Cornea. Curr Eye Res 2019; 44:1054-1066. [PMID: 31136724 DOI: 10.1080/02713683.2019.1625408] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Purpose: The purpose of this study was to determine how the transcriptome of the murine cornea adapts to diurnal changes in physiology. Methods: C57BL/6J mice were maintained under a 12-h light/12-h dark (LD) cycle for two weeks. Corneas were collected from euthanized mice at Zeitgeber time (ZT) 0, 3, 6, 9, 12, 15, 18, and 21. Total RNA was extracted and subjected to RNA sequencing (RNA-Seq). A JTK_CYCLE algoithm and other software tools were used to analyze the transcriptional data to determine the periodicity, rhythmicity, and amplitude of the transcripts. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the enrichment of cycling transcripts. Results: Approximately 24% of the total transcripts from the murine corneal genome were rhythmically expressed over an LD cycle. GO analysis showed that these cycling genes are primarily involved in cellular and metabolic processes. A KEGG pathway analysis identified 6 branches and 44 pathways that encode the gene outputs necessary for basic cellular functions and processes. More importantly, most of the rhythmic genes between the day and night are enriched in their own unique pathways in addition to some common pathways. Furthermore, most of the rhythmic gene expression was concentrated in the 12-h and 24-h periods. A comparative analysis of GO and KEGG showed large differences in metabolic processes, but not cellular processes. Finally, the murine cornea also rhythmically expressed 11 canonical components of circadian clock genes over an LD cycle at the transcriptional level. Conclusions: One fourth of the corneal transcriptome follows a rhythmic expression pattern involved in basic molecular and cellular mechanisms. This implies that the time of day contributes significantly to the overall temporal organization of the corneal transcriptome.
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Affiliation(s)
- Xinwei Jiao
- Henan Provincial People's Hospital and People's Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital , Zhengzhou , China
| | - Mingjuan Wu
- International Ocular Surface Research Center and Institute of Ophthalmology, Key Laboratory for Regenerative Medicine, Jinan University Medical School , Guangzhou , China
| | - Dingli Lu
- Henan Provincial People's Hospital and People's Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital , Zhengzhou , China
| | - Jianqin Gu
- Henan Provincial People's Hospital and People's Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital , Zhengzhou , China
| | - Zhijie Li
- Henan Provincial People's Hospital and People's Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital , Zhengzhou , China.,International Ocular Surface Research Center and Institute of Ophthalmology, Key Laboratory for Regenerative Medicine, Jinan University Medical School , Guangzhou , China
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25
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Föh B, Schröder T, Oster H, Derer S, Sina C. Seasonal Clock Changes Are Underappreciated Health Risks-Also in IBD? Front Med (Lausanne) 2019; 6:103. [PMID: 31143764 PMCID: PMC6521728 DOI: 10.3389/fmed.2019.00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 04/26/2019] [Indexed: 12/19/2022] Open
Abstract
Today, daylight saving time is observed in nearly 80 countries around the world, including the European Union, the USA, Canada, and Russia. The benefits of daylight saving time in energy management have been questioned since it was first introduced during World War I and the latest research has led to varying results. Meanwhile, adverse effects of seasonal time shifts on human biology have been postulated and the European Union is planning to abandon the biannual clock change completely. Medical studies have revealed a correlation of seasonal time shifts with increased incidences of several diseases including stroke, myocardial infarction, and unipolar depressive episodes. Moreover, studies in mice have provided convincing evidence, that circadian rhythm disruption may be involved in the pathogenesis of inflammatory bowel diseases, mainly by disturbing the intestinal barrier integrity. Here, we present previously unpublished data from a large German cohort indicating a correlation of seasonal clock changes and medical leaves due to ulcerative colitis and Crohn's disease. Furthermore, we discuss the health risks of clock changes and the current attempts on reforming daylight saving time from a medical perspective.
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Affiliation(s)
- Bandik Föh
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Torsten Schröder
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Henrik Oster
- Institute of Neurobiology, University of Lübeck, Lübeck, Germany
| | - Stefanie Derer
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Christian Sina
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Lübeck, Germany
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26
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Segers A, Desmet L, Thijs T, Verbeke K, Tack J, Depoortere I. The circadian clock regulates the diurnal levels of microbial short-chain fatty acids and their rhythmic effects on colon contractility in mice. Acta Physiol (Oxf) 2019; 225:e13193. [PMID: 30269420 DOI: 10.1111/apha.13193] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/11/2018] [Accepted: 09/26/2018] [Indexed: 12/14/2022]
Abstract
AIM The microbiota shows diurnal oscillations that are synchronized by the host's circadian clock and feeding rhythms. Short-chain fatty acids (SCFAs) produced by the microbiota are possible synchronizers of peripheral circadian clocks. We aimed to investigate whether faecal SCFAs show a diurnal rhythm that regulates the rhythm of SCFA receptor expression (FFAR2/3, OLFR78, HCAR2) and SCFA-induced colonic contractility. The role of the circadian clock was studied in mice lacking the core clock gene Bmal1. METHODS Mice were sacrificed at 4-hour intervals. Faecal SCFA concentrations and SCFA receptor expression were determined. The effect of increasing concentrations of a SCFA mix on electrical field-induced neural responses in colon strips was measured isometrically. RESULTS Diurnal fluctuations in faecal SCFA concentrations (peak 4 hours after lights on) were observed that were in phase with the rhythm of Ffar2/3 expression in the colonic muscle layer. Olfr78 expression was not diurnal and Hcar2 was not detectable. The inhibitory effect of a SCFA mix on neural contractions in colonic smooth muscle strips showed a diurnal rhythm and oscillated in phase with faecal SCFA concentrations and Ffar2/3 expression. In contrast, neither excitatory neural responses nor acetylcholine-induced smooth muscle contractions showed a diurnal rhythm. In Bmal1-/- mice, no fluctuations in faecal SCFA levels, Ffar3 expression and neural responses to SCFAs were observed. CONCLUSION Diurnal microbial SCFA levels regulate the rhythm of Ffar3 expression in the colonic myenteric plexus, which causes rhythmicity in SCFA-induced colonic motility. Deletion of Bmal1 abolishes rhythmicity of SCFA levels and their downstream effects.
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Affiliation(s)
- Anneleen Segers
- Translational Research Center for Gastrointestinal Disorders KU Leuven Leuven Belgium
| | - Louis Desmet
- Translational Research Center for Gastrointestinal Disorders KU Leuven Leuven Belgium
| | - Theo Thijs
- Translational Research Center for Gastrointestinal Disorders KU Leuven Leuven Belgium
| | - Kristin Verbeke
- Translational Research Center for Gastrointestinal Disorders KU Leuven Leuven Belgium
| | - Jan Tack
- Translational Research Center for Gastrointestinal Disorders KU Leuven Leuven Belgium
| | - Inge Depoortere
- Translational Research Center for Gastrointestinal Disorders KU Leuven Leuven Belgium
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27
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Paulose JK, Cassone CV, Cassone VM. Aging, melatonin biosynthesis, and circadian clockworks in the gastrointestinal system of the laboratory mouse. Physiol Genomics 2018; 51:1-9. [PMID: 30444453 DOI: 10.1152/physiolgenomics.00095.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The gastrointestinal (GI) system is vital in its capacities for nutrient and water uptake, immune function, metabolism and detoxification, and stem-cell derived regeneration. Of significance to human health are a myriad of GI disorders associated with aging that integrate with the circadian clock. Here we present data from three groups of mice: young (3 mo old), middle aged (12 mo old), and old aged (24 mo old). Small intestine and colon samples taken every 4 h under light-dark (LD) conditions were assayed for gene expression related to molecular circadian rhythmicity, transcription, cell signaling, and immune function. Transcripts related to melatonin biosynthesis and signaling, as well as melatonin content from stool, were also included, as GI melatonin and aging have been associated in contexts outside of the circadian clock. With respect to circadian genes, the data here are congruent with data from other peripheral tissues: age does not affect the rhythmic expression of core clock genes in the gut. The same can be said for several clock-controlled transcripts. In contrast, diurnal patterns in the expression of nitric oxide synthase 1 and of immune factors irak4 and interleukin-8 were observed in the colon of young mice that were lost in middle-aged and aged animals. Furthermore, the diurnal pattern of melatonin synthesis genes was altered by age, and stool melatonin levels showed significant decline between young mice and aged cohorts. These data expand the evidence for the persistence of the circadian clock throughout the aging process and highlight its importance to health.
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Affiliation(s)
- Jiffin K Paulose
- Department of Biology, University of Kentucky , Lexington, Kentucky
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28
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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: 63] [Impact Index Per Article: 10.5] [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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29
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Landgraf D, Neumann AM, Oster H. Circadian clock-gastrointestinal peptide interaction in peripheral tissues and the brain. Best Pract Res Clin Endocrinol Metab 2017; 31:561-571. [PMID: 29224668 DOI: 10.1016/j.beem.2017.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Food intake and sleep are two mutually exclusive behaviors and both are normally confined to opposing phases of the diurnal cycle. The temporal coordination of behavior and physiology along the 24-h day-night cycle is organized by a network of circadian clocks that orchestrate transcriptional programs controlling cellular physiology. Many of the peptide hormones of the gastrointestinal tract are not only secreted in a circadian fashion, they can also affect circadian clock function in peripheral metabolic tissues and the brain, thus providing metabolic feedback to metabolic and neurobehavioral circuits. In this review, we summarize the current knowledge on this gastrointestinal peptide crosstalk and its potential role in the coordination of nutrition and the maintenance of metabolic homeostasis.
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Affiliation(s)
- Dominic Landgraf
- Department of Psychiatry, Ludwig Maximilian University of Munich, Germany
| | - Anne-Marie Neumann
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism, University of Lübeck, Germany
| | - Henrik Oster
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism, University of Lübeck, Germany.
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30
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Uetani N, Hardy S, Gravel SP, Kiessling S, Pietrobon A, Wong NN, Chénard V, Cermakian N, St-Pierre J, Tremblay ML. PRL2 links magnesium flux and sex-dependent circadian metabolic rhythms. JCI Insight 2017; 2:91722. [PMID: 28679948 DOI: 10.1172/jci.insight.91722] [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: 11/14/2016] [Accepted: 05/23/2017] [Indexed: 11/17/2022] Open
Abstract
Magnesium (Mg2+) plays pleiotropic roles in cellular biology, and it is essentially required for all living organisms. Although previous studies demonstrated intracellular Mg2+ levels were regulated by the complex of phosphatase of regenerating liver 2 (PRL2) and Mg2+ transporter of cyclin M (CNNMs), physiological functions of PRL2 in whole animals remain unclear. Interestingly, Mg2+ was recently identified as a regulator of circadian rhythm-dependent metabolism; however, no mechanism was found to explain the clock-dependent Mg2+ oscillation. Herein, we report PRL2 as a missing link between sex and metabolism, as well as clock genes and daily cycles of Mg2+ fluxes. Our results unveil that PRL2-null animals displayed sex-dependent alterations in body composition, and expression of PRLs and CNNMs were sex- and circadian time-dependently regulated in brown adipose tissues. Consistently, PRL2-KO mice showed sex-dependent alterations in thermogenesis and in circadian energy metabolism. These physiological changes were associated with an increased rate of uncoupled respiration with lower intracellular Mg2+ in PRL2-KO cells. Moreover, PRL2 deficiency causes inhibition of the ATP citrate lyase axis, which is involved in fatty acid synthesis. Overall, our findings support that sex- and circadian-dependent PRL2 expression alter intracellular Mg2+ levels, which accordingly controls energy metabolism status.
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Affiliation(s)
| | - Serge Hardy
- Rosalind and Morris Goodman Cancer Research Centre
| | | | - Silke Kiessling
- Laboratory of Molecular Chronobiology, Douglas Mental Health University Institute, and
| | | | - Nau Nau Wong
- Rosalind and Morris Goodman Cancer Research Centre
| | | | - Nicolas Cermakian
- Laboratory of Molecular Chronobiology, Douglas Mental Health University Institute, and
| | - Julie St-Pierre
- Rosalind and Morris Goodman Cancer Research Centre.,Department of Biochemistry
| | - Michel L Tremblay
- Rosalind and Morris Goodman Cancer Research Centre.,Department of Biochemistry.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
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31
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Zhu B, Zhang Q, Pan Y, Mace EM, York B, Antoulas AC, Dacso CC, O'Malley BW. A Cell-Autonomous Mammalian 12 hr Clock Coordinates Metabolic and Stress Rhythms. Cell Metab 2017; 25:1305-1319.e9. [PMID: 28591634 PMCID: PMC5526350 DOI: 10.1016/j.cmet.2017.05.004] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/11/2016] [Accepted: 05/18/2017] [Indexed: 02/08/2023]
Abstract
Besides circadian rhythms, oscillations cycling with a 12 hr period exist. However, the prevalence, origin, regulation, and function of mammalian 12 hr rhythms remain elusive. Utilizing an unbiased mathematical approach identifying all superimposed oscillations, we uncovered prevalent 12 hr gene expression and metabolic rhythms in mouse liver, coupled with a physiological 12 hr unfolded protein response oscillation. The mammalian 12 hr rhythm is cell autonomous, driven by a dedicated 12 hr pacemaker distinct from the circadian clock, and can be entrained in vitro by metabolic and ER stress cues. Mechanistically, we identified XBP1s as a transcriptional regulator of the mammalian 12 hr clock. Downregulation of the 12 hr gene expression strongly correlates with human hepatic steatosis and steatohepatitis, implying its importance in maintaining metabolic homeostasis. The mammalian 12 hr rhythm of gene expression also is conserved in nematodes and crustaceans, indicating an ancient origin of the 12 hr clock. Our work sheds new light on how perturbed biological rhythms contribute to human disease.
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Affiliation(s)
- Bokai Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiang Zhang
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Yinghong Pan
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
| | - Emily M Mace
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Athanasios C Antoulas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA; Max Planck Fellow Group for Data-Driven System Reduction and Identification, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg 39106, Germany
| | - Clifford C Dacso
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
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32
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Dierickx P, Vermunt MW, Muraro MJ, Creyghton MP, Doevendans PA, van Oudenaarden A, Geijsen N, Van Laake LW. Circadian networks in human embryonic stem cell-derived cardiomyocytes. EMBO Rep 2017; 18:1199-1212. [PMID: 28536247 PMCID: PMC5494509 DOI: 10.15252/embr.201743897] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/29/2017] [Accepted: 04/10/2017] [Indexed: 11/09/2022] Open
Abstract
Cell-autonomous circadian oscillations strongly influence tissue physiology and pathophysiology of peripheral organs including the heart, in which the circadian clock is known to determine cardiac metabolism and the outcome of for instance ischemic stress. Human pluripotent stem cells represent a powerful tool to study developmental processes in vitro, but the extent to which human embryonic stem (ES) cell-derived cardiomyocytes establish circadian rhythmicity in the absence of a systemic context is unknown. Here we demonstrate that while undifferentiated human ES cells do not possess an intrinsic functional clock, oscillatory expression of known core clock genes emerges spontaneously during directed cardiac differentiation. We identify a set of clock-controlled output genes that contain an oscillatory network of stress-related transcripts. Furthermore, we demonstrate that this network results in a time-dependent functional response to doxorubicin, a frequently used anti-cancer drug with known cardiotoxic side effects. Taken together, our data provide a framework from which the effect of oscillatory gene expression on cardiomyocyte physiology can be modeled in vitro, and demonstrate the influence of a functional clock on experimental outcome.
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Affiliation(s)
- Pieterjan Dierickx
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands .,Division of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marit W Vermunt
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mauro J Muraro
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Menno P Creyghton
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Pieter A Doevendans
- Division of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Netherlands Heart Institute, Utrecht, The Netherlands
| | | | - Niels Geijsen
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Linda W Van Laake
- Division of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands .,Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht, The Netherlands
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Stokes K, Cooke A, Chang H, Weaver DR, Breault DT, Karpowicz P. The Circadian Clock Gene BMAL1 Coordinates Intestinal Regeneration. Cell Mol Gastroenterol Hepatol 2017; 4:95-114. [PMID: 28593182 PMCID: PMC5453906 DOI: 10.1016/j.jcmgh.2017.03.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/24/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The gastrointestinal syndrome is an illness of the intestine caused by high levels of radiation. It is characterized by extensive loss of epithelial tissue integrity, which initiates a regenerative response by intestinal stem and precursor cells. The intestine has 24-hour rhythms in many physiological functions that are believed to be outputs of the circadian clock: a molecular system that produces 24-hour rhythms in transcription/translation. Certain gastrointestinal illnesses are worsened when the circadian rhythms are disrupted, but the role of the circadian clock in gastrointestinal regeneration has not been studied. METHODS We tested the timing of regeneration in the mouse intestine during the gastrointestinal syndrome. The role of the circadian clock was tested genetically using the BMAL1 loss of function mouse mutant in vivo, and in vitro using intestinal organoid culture. RESULTS The proliferation of the intestinal epithelium follows a 24-hour rhythm during the gastrointestinal syndrome. The circadian clock runs in the intestinal epithelium during this pathologic state, and the loss of the core clock gene, BMAL1, disrupts both the circadian clock and rhythmic proliferation. Circadian activity in the intestine involves a rhythmic production of inflammatory cytokines and subsequent rhythmic activation of the JNK stress response pathway. CONCLUSIONS Our results show that a circadian rhythm in inflammation and regeneration occurs during the gastrointestinal syndrome. The study and treatment of radiation-induced illnesses, and other gastrointestinal illnesses, should consider 24-hour timing in physiology and pathology.
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Affiliation(s)
- Kyle Stokes
- Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada
| | - Abrial Cooke
- Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada
| | - Hanna Chang
- Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada
| | - David R. Weaver
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - David T. Breault
- Harvard Stem Cell Institute, Cambridge, Massachusetts,Division of Endocrinology, Boston Children’s Hospital, Boston, Massachusetts,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Phillip Karpowicz
- Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada,Correspondence Address correspondence to: Phillip Karpowicz, PhD, Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada N9B 3P4.Department of Biological SciencesUniversity of WindsorWindsorOntarioCanada N9B 3P4
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Polidarová L, Houdek P, Sládek M, Novosadová Z, Pácha J, Sumová A. Mechanisms of hormonal regulation of the peripheral circadian clock in the colon. Chronobiol Int 2016; 34:1-16. [PMID: 27661138 DOI: 10.1080/07420528.2016.1231198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Colonic function is controlled by an endogenous clock that allows the colon to optimize its function on the daytime basis. For the first time, this study provided evidence that the clock is synchronized by rhythmic hormonal signals. In rat colon, adrenalectomy decreased and repeated applications of dexamethasone selectively rescued circadian rhythm in the expression of the clock gene Per1. Dexamethasone entrained the colonic clock in explants from mPer2Luc mice in vitro. In contrast, pinealectomy had no effect on the rat colonic clock, and repeated melatonin injections were not able to rescue the clock in animals maintained in constant light. Additionally, melatonin did not entrain the clock in colonic explants from mPer2Luc mice in vitro. However, melatonin affected rhythmic regulation of Nr1d1 gene expression in vivo. The findings provide novel insight into possible beneficial effects of glucocorticoids in the treatment of digestive tract-related diseases, greatly exceeding their anti-inflammatory action.
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Affiliation(s)
| | | | | | | | - Jiří Pácha
- b Department of Epithelial Function, Institute of Physiology , The Czech Academy of Sciences , Videnska , Prague , Czech Republic
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Abstract
Circadian clocks are fundamental properties of all eukaryotic organisms and at least some prokaryotic organisms. Recent studies in our laboratory have shown that the gastrointestinal system contains a circadian clock that controls many, if not all, aspects of gastrointestinal function. We now report that at least one species of intestinal bacteria, Enterobacter aerogenes, responds to the pineal and gastrointestinal hormone melatonin by an increase in swarming activity. This swarming behavior is expressed rhythmically, with a period of approximately 24 hrs. Transformation of E. aerogenes to express luciferase with a MotA promoter reveals circadian patterns of bioluminescence that are synchronized by melatonin and whose periods are temperature compensated from 26°C to 40°C. Bioinformatics suggest similarities between the E. aerogenes and cyanobacterial clocks, suggesting the circadian clock may have evolved very early in the evolution of life. They also point to a coordination of host circadian clocks with those residing in the microbiota themselves.
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36
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Heath-Heckman EAC. The Metronome of Symbiosis: Interactions Between Microbes and the Host Circadian Clock. Integr Comp Biol 2016; 56:776-783. [PMID: 27371387 DOI: 10.1093/icb/icw067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The entrainment of circadian rhythms, physiological cycles with a period of about 24 h, is regulated by a variety of mechanisms, including nonvisual photoreception. While circadian rhythms have been shown to be integral to many processes in multicellular organisms, including immune regulation, the effect of circadian rhythms on symbiosis, or host-microbe interactions, has only recently begun to be studied. This review summarizes recent work in the interactions of both pathogenic and mutualistic associations with host and symbiont circadian rhythms, focusing specifically on three mutualistic systems in which this phenomenon has been best studied. One important theme taken from these studies is the fact that mutualisms are profoundly affected by the circadian rhythms of the host, but that the microbial symbionts in these associations can, in turn, manipulate host rhythms. The interplay between circadian rhythms and symbiosis is a promising new field with effects that should be kept in mind when designing future studies across biology.
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37
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Palmieri O, Mazzoccoli G, Bossa F, Maglietta R, Palumbo O, Ancona N, Corritore G, Latiano T, Martino G, Rubino R, Biscaglia G, Scimeca D, Carella M, Annese V, Andriulli A, Latiano A. Systematic analysis of circadian genes using genome-wide cDNA microarrays in the inflammatory bowel disease transcriptome. Chronobiol Int 2016; 32:903-16. [PMID: 26172092 DOI: 10.3109/07420528.2015.1050726] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Simultaneous analysis of the transcripts of thousands of genes by cDNA microarrays allows the identification of genetic regulatory mechanisms involved in disease pathophysiology. The circadian clock circuitry controls essential cell processes and the functioning of organ systems, which are characterized by rhythmic variations with 24-hour periodicity. The derangement of these processes is involved in the basic mechanisms of inflammatory, metabolic, degenerative and neoplastic diseases. We evaluated by genome-wide cDNA microarray analysis the transcriptome of endoscopic mucosal biopsies of patients with inflammatory bowel diseases (IBD) focusing on the expression of circadian genes in Crohn's disease (CD) and ulcerative colitis (UC). Twenty-nine IBD patients (15 with CD and 14 with UC) were enrolled and mucosal biopsies were sampled at either inflamed or adjacent non-inflamed areas of the colon. A total of 150 circadian genes involved in pathways controlling crucial cell processes and tissue functions were investigated. In CD specimens 50 genes were differentially expressed, and 21 genes resulted up-regulated when compared to healthy colonic mucosa. In UC specimens 50 genes were differentially expressed, and 27 genes resulted up-regulated when compared to healthy colonic mucosa. Among the core clock genes ARNTL2 and RORA were up-regulated, while CSNK2B, NPAS2, PER1 and PER3 were down-regulated in CD specimens. Conversely, ARNTL2, CRY1, CSNK1E, RORA and TIPIN were up-regulated, while NR1D2 and PER3 were down-regulated in UC. In conclusion, in CD and UC patients there are differences in the expression of circadian genes between normal and diseased intestinal mucosa. The deregulated genes evidenced by transcriptome analysis in the major IBDs may play a crucial role in the pathophysiological mechanisms and may suggest novel therapeutic approaches.
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Affiliation(s)
- Orazio Palmieri
- a Department of Medical Sciences , Division of Gastroenterology and
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PFKFB3 Control of Cancer Growth by Responding to Circadian Clock Outputs. Sci Rep 2016; 6:24324. [PMID: 27079271 PMCID: PMC4832144 DOI: 10.1038/srep24324] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/24/2016] [Indexed: 01/18/2023] Open
Abstract
Circadian clock dysregulation promotes cancer growth. Here we show that PFKFB3, the gene that encodes for inducible 6-phosphofructo-2-kinase as an essential supporting enzyme of cancer cell survival through stimulating glycolysis, mediates circadian control of carcinogenesis. In patients with tongue cancers, PFKFB3 expression in both cancers and its surrounding tissues was increased significantly compared with that in the control, and was accompanied with dys-regulated expression of core circadian genes. In the in vitro systems, SCC9 tongue cancer cells displayed rhythmic expression of PFKFB3 and CLOCK that was distinct from control KC cells. Furthermore, PFKFB3 expression in SCC9 cells was stimulated by CLOCK through binding and enhancing the transcription activity of PFKFB3 promoter. Inhibition of PFKFB3 at zeitgeber time 7 (ZT7), but not at ZT19 caused significant decreases in lactate production and in cell proliferation. Consistently, PFKFB3 inhibition in mice at circadian time (CT) 7, but not CT19 significantly reduced the growth of implanted neoplasms. Taken together, these findings demonstrate PFKFB3 as a mediator of circadian control of cancer growth, thereby highlighting the importance of time-based PFKFB3 inhibition in cancer treatment.
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Lück S, Westermark PO. Circadian mRNA expression: insights from modeling and transcriptomics. Cell Mol Life Sci 2016; 73:497-521. [PMID: 26496725 PMCID: PMC11108398 DOI: 10.1007/s00018-015-2072-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
Abstract
Circadian clocks synchronize organisms to the 24 h rhythms of the environment. These clocks persist under constant conditions, have their origin at the cellular level, and produce an output of rhythmic mRNA expression affecting thousands of transcripts in many mammalian cell types. Here, we review the charting of circadian output rhythms in mRNA expression, focusing on mammals. We emphasize the challenges in statistics, interpretation, and quantitative descriptions that such investigations have faced and continue to face, and outline remaining outstanding questions.
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Affiliation(s)
- Sarah Lück
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany
| | - Pål O Westermark
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany.
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Hughey JJ, Hastie T, Butte AJ. ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system. Nucleic Acids Res 2016; 44:e80. [PMID: 26819407 PMCID: PMC4856978 DOI: 10.1093/nar/gkw030] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/11/2016] [Indexed: 12/13/2022] Open
Abstract
Numerous biological systems oscillate over time or space. Despite these oscillators' importance, data from an oscillatory system is problematic for existing methods of regularized supervised learning. We present ZeitZeiger, a method to predict a periodic variable (e.g. time of day) from a high-dimensional observation. ZeitZeiger learns a sparse representation of the variation associated with the periodic variable in the training observations, then uses maximum-likelihood to make a prediction for a test observation. We applied ZeitZeiger to a comprehensive dataset of genome-wide gene expression from the mammalian circadian oscillator. Using the expression of 13 genes, ZeitZeiger predicted circadian time (internal time of day) in each of 12 mouse organs to within ∼1 h, resulting in a multi-organ predictor of circadian time. Compared to the state-of-the-art approach, ZeitZeiger was faster, more accurate and used fewer genes. We then validated the multi-organ predictor on 20 additional datasets comprising nearly 800 samples. Our results suggest that ZeitZeiger not only makes accurate predictions, but also gives insight into the behavior and structure of the oscillator from which the data originated. As our ability to collect high-dimensional data from various biological oscillators increases, ZeitZeiger should enhance efforts to convert these data to knowledge.
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Affiliation(s)
- Jacob J Hughey
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Trevor Hastie
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Atul J Butte
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
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Mazzoccoli G, Colangelo T, Panza A, Rubino R, De Cata A, Tiberio C, Valvano MR, Pazienza V, Merla G, Augello B, Trombetta D, Storlazzi CT, Macchia G, Gentile A, Tavano F, Vinciguerra M, Bisceglia G, Rosato V, Colantuoni V, Sabatino L, Piepoli A. Deregulated expression of cryptochrome genes in human colorectal cancer. Mol Cancer 2016; 15:6. [PMID: 26768731 PMCID: PMC4714521 DOI: 10.1186/s12943-016-0492-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 01/09/2016] [Indexed: 02/08/2023] Open
Abstract
Background Circadian disruption and deranged molecular clockworks are involved in carcinogenesis. The cryptochrome genes (CRY1 and CRY2) encode circadian proteins important for the functioning of biological oscillators. Their expression in human colorectal cancer (CRC) and in colon cancer cell lines has not been evaluated so far. Methods We investigated CRY1 and CRY2 expression in fifty CRCs and in the CaCo2, HCT116, HT29, SW480 cell lines. Results CRY1 (p = 0.01) and CRY2 (p < 0.0001) expression was significantly changed in tumour tissue, as confirmed in a large independent CRC dataset. In addition, lower CRY1 mRNA levels were observed in patients in the age range of 62-74 years (p = 0.018), in female patients (p = 0.003) and in cancers located at the transverse colon (p = 0.008). Lower CRY2 levels were also associated with cancer location at the transverse colon (p = 0.007). CRC patients displaying CRY1 (p = 0.042) and CRY2 (p = 0.043) expression levels over the median were hallmarked by a poorer survival rate. Survey of selected colon cancer cell lines evidenced variable levels of cryptochrome genes expression and time-dependent changes in their mRNA levels. Moreover, they showed reduced apoptosis, increased proliferation and different response to 5-fluorouracil and oxaliplatin upon CRY1 and CRY2 ectopic expression. The relationship with p53 status came out as an additional layer of regulation: higher CRY1 and CRY2 protein levels coincided with a wild type p53 as in HCT116 cells and this condition only marginally affected the apoptotic and cell proliferation characteristics of the cells upon CRY ectopic expression. Conversely, lower CRY and CRY2 levels as in HT29 and SW480 cells coincided with a mutated p53 and a more robust apoptosis and proliferation upon CRY transfection. Besides, an heterogeneous pattern of ARNTL, WEE and c-MYC expression hallmarked the chosen colon cancer cell lines and likely influenced their phenotypic changes. Conclusion Cryptochrome gene expression is altered in CRC, particularly in elderly subjects, female patients and cancers located at the transverse colon, affecting overall survival. Altered CRY1 and CRY2 expression patterns and the interplay with the genetic landscape in colon cancer cells may underlie phenotypic divergence that could influence disease behavior as well as CRC patients survival and response to chemotherapy. Electronic supplementary material The online version of this article (doi:10.1186/s12943-016-0492-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gianluigi Mazzoccoli
- Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy. .,Department of Medical Sciences, Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, 71013, Italy.
| | - Tommaso Colangelo
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Anna Panza
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Rosa Rubino
- Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Angelo De Cata
- Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Cristiana Tiberio
- Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Maria Rosa Valvano
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Valerio Pazienza
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Giuseppe Merla
- Medical Genetics, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Bartolomeo Augello
- Medical Genetics, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Domenico Trombetta
- Oncology-Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | | | - Gemma Macchia
- Department of Biology, University of Bari, Bari, Italy
| | - Annamaria Gentile
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Manlio Vinciguerra
- Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy.,Euro-Mediterranean Institute of Sciences and Technology (IEMEST), Palermo, Italy.,School of Science and Technology, Nottingham Trent University, Nottingham, UK.,Division of Medicine, University College London, Institute for Liver and Digestive Health, Royal Free Campus, London, UK
| | - Giovanni Bisceglia
- Division of Abdominal Surgery, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Valeria Rosato
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Vittorio Colantuoni
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Lina Sabatino
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Ada Piepoli
- Division of Epidemiology and Health Statistics, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
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Paulose JK, Wright JM, Patel AG, Cassone VM. Human Gut Bacteria Are Sensitive to Melatonin and Express Endogenous Circadian Rhythmicity. PLoS One 2016; 11:e0146643. [PMID: 26751389 PMCID: PMC4709092 DOI: 10.1371/journal.pone.0146643] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/21/2015] [Indexed: 12/29/2022] Open
Abstract
Circadian rhythms are fundamental properties of most eukaryotes, but evidence of biological clocks that drive these rhythms in prokaryotes has been restricted to Cyanobacteria. In vertebrates, the gastrointestinal system expresses circadian patterns of gene expression, motility and secretion in vivo and in vitro, and recent studies suggest that the enteric microbiome is regulated by the host's circadian clock. However, it is not clear how the host's clock regulates the microbiome. Here, we demonstrate at least one species of commensal bacterium from the human gastrointestinal system, Enterobacter aerogenes, is sensitive to the neurohormone melatonin, which is secreted into the gastrointestinal lumen, and expresses circadian patterns of swarming and motility. Melatonin specifically increases the magnitude of swarming in cultures of E. aerogenes, but not in Escherichia coli or Klebsiella pneumoniae. The swarming appears to occur daily, and transformation of E. aerogenes with a flagellar motor-protein driven lux plasmid confirms a temperature-compensated circadian rhythm of luciferase activity, which is synchronized in the presence of melatonin. Altogether, these data demonstrate a circadian clock in a non-cyanobacterial prokaryote and suggest the human circadian system may regulate its microbiome through the entrainment of bacterial clocks.
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Affiliation(s)
- Jiffin K. Paulose
- Department of Biology, University of Kentucky, Lexington, KY, 40506, United States of America
| | - John M. Wright
- Department of Biology, University of Kentucky, Lexington, KY, 40506, United States of America
| | - Akruti G Patel
- Department of Biology, University of Kentucky, Lexington, KY, 40506, United States of America
| | - Vincent M. Cassone
- Department of Biology, University of Kentucky, Lexington, KY, 40506, United States of America
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Zhang L, Prosdocimo DA, Bai X, Fu C, Zhang R, Campbell F, Liao X, Coller J, Jain MK. KLF15 Establishes the Landscape of Diurnal Expression in the Heart. Cell Rep 2015; 13:2368-2375. [PMID: 26686628 DOI: 10.1016/j.celrep.2015.11.038] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 10/05/2015] [Accepted: 11/12/2015] [Indexed: 01/17/2023] Open
Abstract
Circadian rhythms offer temporal control of anticipatory physiologic adaptations in animals. In the mammalian cardiovascular system, the importance of these rhythms is underscored by increased cardiovascular disease in shift workers, findings recapitulated in experimental animal models. However, a nodal regulator that allows integration of central and peripheral information and coordinates cardiac rhythmic output has been elusive. Here, we show that kruppel-like factor 15 (KLF15) governs a biphasic transcriptomic oscillation in the heart with a maximum ATP production phase and a remodeling and repair phase corresponding to the active and resting phase of a rodent. Depletion of KLF15 in cardiomyocytes leads to a disorganized oscillatory behavior without phasic partition despite an intact core clock. Thus, KLF15 is a nodal connection between the clock and meaningful rhythmicity in the heart.
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Affiliation(s)
- Lilei Zhang
- Case Cardiovascular Research Institute, Department of Medicine, Harrington Heart and Vascular Institute, University Hospitals Case Medical Center, Cleveland, OH 44106, USA; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Domenick A Prosdocimo
- Case Cardiovascular Research Institute, Department of Medicine, Harrington Heart and Vascular Institute, University Hospitals Case Medical Center, Cleveland, OH 44106, USA
| | - Xiaodong Bai
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Chen Fu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rongli Zhang
- Case Cardiovascular Research Institute, Department of Medicine, Harrington Heart and Vascular Institute, University Hospitals Case Medical Center, Cleveland, OH 44106, USA
| | - Frank Campbell
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Xudong Liao
- Case Cardiovascular Research Institute, Department of Medicine, Harrington Heart and Vascular Institute, University Hospitals Case Medical Center, Cleveland, OH 44106, USA
| | - Jeff Coller
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mukesh K Jain
- Case Cardiovascular Research Institute, Department of Medicine, Harrington Heart and Vascular Institute, University Hospitals Case Medical Center, Cleveland, OH 44106, USA.
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Yoshida D, Aoki N, Tanaka M, Aoyama S, Shibata S. The circadian clock controls fluctuations of colonic cell proliferation during the light/dark cycle via feeding behavior in mice. Chronobiol Int 2015; 32:1145-55. [PMID: 26376208 DOI: 10.3109/07420528.2015.1065415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The mammalian circadian system is controlled not only by the suprachiasmatic nucleus (SCN), but also by the peripheral clocks located in tissues such as liver, kidney, small intestine, and colon, mediated through signals such as hormones. Peripheral clocks, but not the SCN, can be entrained by food intake schedules. While it is known that cell proliferation exhibits a circadian rhythm in the colon epithelium, it is unclear how this rhythm is influenced by food intake schedules. Here, we aimed to determine the relationships between feeding schedules and cell proliferation in the colon epithelium by means of immunochemical analysis, using 5-bromo-2'-deoxyuridine (BrdU), as well as to elucidate how feeding schedules influence the colonic expression of clock and cell cycle genes, using real-time reverse-transcription PCR (qRT-PCR). Cell proliferation in the colonic epithelium of normal mice exhibited a daily fluctuation, which was abrogated in Clock mutant mice. The day/night pattern of cellular proliferation and clock gene expression under daytime and nighttime restricted feeding (RF) schedules showed opposite tendencies. While daytime RF for every 4 h attenuated the day/night pattern of cell proliferation, this was restored to normal in the Clock mutant mice under the nighttime RF schedule. These results suggest that feeding schedules contribute to the establishment of a daily fluctuation of cell proliferation and RF can recover it in Clock mutant mice. Thus, this study demonstrates that the daily fluctuation of cell proliferation in the murine colon is controlled by a circadian feeding rhythm, suggesting that feeding schedules are important for rhythmicity in the proliferation of colon cells.
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Affiliation(s)
- Daisuke Yoshida
- a Laboratory of Physiology and Pharmacology , School of Advanced Sciences and Engineering, Waseda University , Tokyo , Japan
| | - Natsumi Aoki
- a Laboratory of Physiology and Pharmacology , School of Advanced Sciences and Engineering, Waseda University , Tokyo , Japan
| | - Mizuho Tanaka
- a Laboratory of Physiology and Pharmacology , School of Advanced Sciences and Engineering, Waseda University , Tokyo , Japan
| | - Shinya Aoyama
- a Laboratory of Physiology and Pharmacology , School of Advanced Sciences and Engineering, Waseda University , Tokyo , Japan
| | - Shigenobu Shibata
- a Laboratory of Physiology and Pharmacology , School of Advanced Sciences and Engineering, Waseda University , Tokyo , Japan
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45
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Forsyth CB, Voigt RM, Burgess HJ, Swanson GR, Keshavarzian A. Circadian rhythms, alcohol and gut interactions. Alcohol 2015; 49:389-98. [PMID: 25499101 DOI: 10.1016/j.alcohol.2014.07.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/09/2014] [Accepted: 07/17/2014] [Indexed: 12/14/2022]
Abstract
The circadian clock establishes rhythms throughout the body with an approximately 24 hour period that affect expression of hundreds of genes. Epidemiological data reveal chronic circadian misalignment, common in our society, significantly increases the risk for a myriad of diseases, including cardiovascular disease, diabetes, cancer, infertility and gastrointestinal disease. Disruption of intestinal barrier function, also known as gut leakiness, is especially important in alcoholic liver disease (ALD). Several studies have shown that alcohol causes ALD in only a 20-30% subset of alcoholics. Thus, a better understanding is needed of why only a subset of alcoholics develops ALD. Compelling evidence shows that increased gut leakiness to microbial products and especially LPS play a critical role in the pathogenesis of ALD. Clock and other circadian clock genes have been shown to regulate lipid transport, motility and other gut functions. We hypothesized that one possible mechanism for alcohol-induced intestinal hyperpermeability is through disruption of central or peripheral (intestinal) circadian regulation. In support of this hypothesis, our recent data shows that disruption of circadian rhythms makes the gut more susceptible to injury. Our in vitro data show that alcohol stimulates increased Clock and Per2 circadian clock proteins and that siRNA knockdown of these proteins prevents alcohol-induced permeability. We also show that intestinal Cyp2e1-mediated oxidative stress is required for alcohol-induced upregulation of Clock and Per2 and intestinal hyperpermeability. Our mouse model of chronic alcohol feeding shows that circadian disruption through genetics (in Clock(▵19) mice) or environmental disruption by weekly 12h phase shifting results in gut leakiness alone and exacerbates alcohol-induced gut leakiness and liver pathology. Our data in human alcoholics show they exhibit abnormal melatonin profiles characteristic of circadian disruption. Taken together our data support circadian mechanisms for alcohol-induced gut leakiness that could provide new therapeutic targets for ALD.
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Affiliation(s)
- Christopher B Forsyth
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, USA; Department of Biochemistry, Rush University Medical Center, Chicago, IL, USA.
| | - Robin M Voigt
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, USA
| | - Helen J Burgess
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL USA
| | - Garth R Swanson
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, USA
| | - Ali Keshavarzian
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, USA; Department of Pharmacology, Rush University Medical Center, Chicago, IL, USA; Department of Molecular Biophysics & Physiology, Rush University Medical Center, Chicago, IL, USA; Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
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Kojima S, Green CB. Circadian genomics reveal a role for post-transcriptional regulation in mammals. Biochemistry 2015; 54:124-33. [PMID: 25303020 PMCID: PMC4302021 DOI: 10.1021/bi500707c] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/21/2014] [Indexed: 12/28/2022]
Abstract
To maintain daily cycles, the circadian clock must tightly regulate the rhythms of thousands of mRNAs and proteins with the correct period, phase, and amplitude to ultimately drive the wide range of rhythmic biological processes. Recent genomic approaches have revolutionized our view of circadian gene expression and highlighted the importance of post-transcriptional regulation in driving mRNA rhythmicity. Even after transcripts are made from DNA, subsequent processing and regulatory steps determine when, where, and how much protein will be generated. These post-transcriptional regulatory mechanisms can add flexibility to overall gene expression and alter protein levels rapidly without requiring transcript synthesis and are therefore beneficial for cells; however, the extent to which circadian post-transcriptional mechanisms contribute to rhythmic profiles throughout the genome and the mechanisms involved have not been fully elucidated. In this review, we will summarize how circadian genomics have revealed new insights into rhythmic post-transcriptional regulation in mammals and discuss potential implications of such regulation in controlling many circadian-driven physiologies.
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Affiliation(s)
- Shihoko Kojima
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9111, United States
| | - Carla B. Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9111, United States
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Nueda MJ, Tarazona S, Conesa A. Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. Bioinformatics 2014; 30:2598-602. [PMID: 24894503 PMCID: PMC4155246 DOI: 10.1093/bioinformatics/btu333] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Motivation: The widespread adoption of RNA-seq to quantitatively measure gene expression has increased the scope of sequencing experimental designs to include time-course experiments. maSigPro is an R package specifically suited for the analysis of time-course gene expression data, which was developed originally for microarrays and hence was limited in its application to count data. Results: We have updated maSigPro to support RNA-seq time series analysis by introducing generalized linear models in the algorithm to support the modeling of count data while maintaining the traditional functionalities of the package. We show a good performance of the maSigPro-GLM method in several simulated time-course scenarios and in a real experimental dataset. Availability and implementation: The package is freely available under the LGPL license from the Bioconductor Web site (http://bioconductor.org). Contact:mj.nueda@ua.es or aconesa@cipf.es
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Affiliation(s)
- María José Nueda
- Statistics and Operational Research Department, University of Alicante, 03690, Alicante, Spain, Genomics of Gene Expression Laboratory, Prince Felipe Research Centre, 46012 Valencia, Spain and Applied Statistics, Operational Research and Quality Department, Polytechnic University of Valencia, 46020 Valencia, Spain
| | - Sonia Tarazona
- Statistics and Operational Research Department, University of Alicante, 03690, Alicante, Spain, Genomics of Gene Expression Laboratory, Prince Felipe Research Centre, 46012 Valencia, Spain and Applied Statistics, Operational Research and Quality Department, Polytechnic University of Valencia, 46020 Valencia, Spain Statistics and Operational Research Department, University of Alicante, 03690, Alicante, Spain, Genomics of Gene Expression Laboratory, Prince Felipe Research Centre, 46012 Valencia, Spain and Applied Statistics, Operational Research and Quality Department, Polytechnic University of Valencia, 46020 Valencia, Spain
| | - Ana Conesa
- Statistics and Operational Research Department, University of Alicante, 03690, Alicante, Spain, Genomics of Gene Expression Laboratory, Prince Felipe Research Centre, 46012 Valencia, Spain and Applied Statistics, Operational Research and Quality Department, Polytechnic University of Valencia, 46020 Valencia, Spain
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Hale AN, Ledbetter DJ, Gawriluk TR, Rucker EB. Autophagy: regulation and role in development. Autophagy 2014; 9:951-72. [PMID: 24121596 DOI: 10.4161/auto.24273] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Autophagy is an evolutionarily conserved cellular process through which long-lived proteins and damaged organelles are recycled to maintain energy homeostasis. These proteins and organelles are sequestered into a double-membrane structure, or autophagosome, which subsequently fuses with a lysosome in order to degrade the cargo. Although originally classified as a type of programmed cell death, autophagy is more widely viewed as a basic cell survival mechanism to combat environmental stressors. Autophagy genes were initially identified in yeast and were found to be necessary to circumvent nutrient stress and starvation. Subsequent elucidation of mammalian gene counterparts has highlighted the importance of this process to normal development. This review provides an overview of autophagy, the types of autophagy, its regulation and its known impact on development gleaned primarily from murine models.
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Affiliation(s)
- Amber N Hale
- Department of Biology; University of Kentucky; Lexington, KY USA
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Tahara Y, Shibata S. Chrono-biology, chrono-pharmacology, and chrono-nutrition. J Pharmacol Sci 2014; 124:320-35. [PMID: 24572815 DOI: 10.1254/jphs.13r06cr] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The circadian clock system in mammals drives many physiological processes including the daily rhythms of sleep-wake behavior, hormonal secretion, and metabolism. This system responds to daily environmental changes, such as the light-dark cycle, food intake, and drug administration. In this review, we focus on the central and peripheral circadian clock systems in response to drugs, food, and nutrition. We also discuss the adaptation and anticipation mechanisms of our body with regard to clock system regulation of various kinetic and dynamic pathways, including absorption, distribution, metabolism, and excretion of drugs and nutrients. "Chrono-pharmacology" and "chrono-nutrition" are likely to become important research fields in chrono-biological studies.
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Affiliation(s)
- Yu Tahara
- Laboratory of Physiology and Pharmacology, School of Advanced Science and Engineering, Waseda University, Japan
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Siffroi-Fernandez S, Dulong S, Li XM, Filipski E, Gréchez-Cassiau A, Peteri-Brünback B, Meijer L, Lévi F, Teboul M, Delaunay F. Functional genomics identify Birc5/survivin as a candidate gene involved in the chronotoxicity of cyclin-dependent kinase inhibitors. Cell Cycle 2014; 13:984-91. [PMID: 24552823 DOI: 10.4161/cc.27868] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The circadian timing system orchestrates most of mammalian physiology and behavior in synchrony with the external light/dark cycle. This regulation is achieved through endogenous clocks present in virtually all body cells, where they control key cellular processes, including metabolism, transport, and the cell cycle. Consistently, it has been observed in preclinical cancer models that both the efficacy and toxicity of most chemotherapeutic drugs depend on their time of administration. To further explore the molecular basis underlying the link between the circadian timing system and the cellular response to anticancer drugs, we investigated the circadian transcriptome and CDK inhibitor toxicity in colon mucosa cells. We first show here that among 181 circadian transcripts, approximately 30% of them drive the cell cycle in the healthy mouse colon mucosa, with a majority peaking during the early resting phase. The identification of 26 mitotic genes within this cluster further indicated that the transcriptional coordination of mitosis by the circadian clock participates in the gating of cell division in this tissue. Subsequent selective siRNA-mediated silencing of these 26 targets revealed that low expression levels of the mitotic and anti-apoptotic gene Birc5/survivin significantly and specifically increased the sensitivity of colon epithelial cells to CDK inhibitors. By identifying Birc5/survivin as a potential determinant for the circadian modulation of CDK inhibitor toxicity, these data provide a mechanistic basis for the preclinical development of future CDK inhibitor-based chronotherapeutic strategies.
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Affiliation(s)
- Sandrine Siffroi-Fernandez
- Institut de Biologie Valrose; Université Nice Sophia Antipolis; CNRS UMR7277; INSERM U1091; Nice, France
| | - Sandrine Dulong
- INSERM U776 Rythmes biologiques et cancers; Villejuif, France; University Paris-Sud, Orsay; France
| | - Xiao-Mei Li
- INSERM U776 Rythmes biologiques et cancers; Villejuif, France; University Paris-Sud, Orsay; France
| | - Elisabeth Filipski
- INSERM U776 Rythmes biologiques et cancers; Villejuif, France; University Paris-Sud, Orsay; France
| | - Aline Gréchez-Cassiau
- Institut de Biologie Valrose; Université Nice Sophia Antipolis; CNRS UMR7277; INSERM U1091; Nice, France
| | - Brigitta Peteri-Brünback
- Institut de Biologie Valrose; Université Nice Sophia Antipolis; CNRS UMR7277; INSERM U1091; Nice, France
| | | | - Francis Lévi
- INSERM U776 Rythmes biologiques et cancers; Villejuif, France; University Paris-Sud, Orsay; France; Assistance Publique-Hôpitaux de Paris; Unité de Chronothérapie; Département d'Oncologie Médicale; Hôpital Paul Brousse; Villejuif, France
| | - Michèle Teboul
- Institut de Biologie Valrose; Université Nice Sophia Antipolis; CNRS UMR7277; INSERM U1091; Nice, France
| | - Franck Delaunay
- Institut de Biologie Valrose; Université Nice Sophia Antipolis; CNRS UMR7277; INSERM U1091; Nice, France
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