1
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Sasaki H, Mizuta K. Diurnal Variation in Asthma Symptoms: Exploring the Role of Melatonin. J Oral Biosci 2024:S1349-0079(24)00145-2. [PMID: 38925352 DOI: 10.1016/j.job.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Asthma is a common chronic inflammatory disease affecting more than 260 million people worldwide. Nocturnal exacerbations of asthma symptoms significantly affect sleep quality and contribute to the most serious asthma exacerbations, which can lead to respiratory failure or death. Although β2-adrenoceptor agonists are the standard of care for asthma, their bronchodilatory effect for nocturnal asthma is limited, and medications that specifically target symptoms of nocturnal asthma are lacking. HIGHLIGHT Melatonin, which is secreted by the pineal gland, plays a crucial role in regulating circadian rhythms. Peak serum melatonin concentrations, which are inversely correlated with diurnal changes in pulmonary function, are higher in patients with nocturnal asthma than in healthy individuals. Melatonin potentiates bronchoconstriction through the melatonin MT2 receptor expressed in the smooth muscles of the airway and attenuates the bronchodilatory effects of β2-adrenoceptor agonists, thereby exacerbating asthma symptoms. Melatonin inhibits mucus secretion and airway inflammation, potentially ameliorating asthma symptoms. CONCLUSION Melatonin may exacerbate or ameliorate various pathophysiological conditions associated with asthma. As a potential therapeutic agent for asthma, the balance between its detrimental effects on airway smooth muscles and its beneficial effects on mucus production and inflammation remains unclear. Further studies are needed to elucidate whether melatonin worsens or improves asthma symptoms.
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Affiliation(s)
- Haruka Sasaki
- Division of Dento-oral Anesthesiology, Tohoku University Graduate School of Dentistry, 4-1 Seiryo-machi, Aoba, Sendai, Miyagi 9808575 Japan.
| | - Kentaro Mizuta
- Division of Dento-oral Anesthesiology, Tohoku University Graduate School of Dentistry, 4-1 Seiryo-machi, Aoba, Sendai, Miyagi 9808575 Japan.
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2
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He J, Hu J, Liu H. A three-gene random forest model for diagnosing idiopathic pulmonary fibrosis based on circadian rhythm-related genes in lung tissue. Expert Rev Respir Med 2023; 17:1307-1320. [PMID: 38285622 DOI: 10.1080/17476348.2024.2311262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND The disorder of circadian rhythm could be a key factor mediating fibrotic lung disease Therefore, our study aims to determine the diagnostic value of circadian rhythm-related genes (CRRGs) in IPF. METHODS We retrieved the data on CRRGs from previous studies and the GSE150910 dataset. The participants from the GSE150910 dataset were divided into training and internal validation sets. Next, we used several various bioinformatics methods and machine learning algorithms to screen genes. Next, we identified SEMA5A, COL7A1, and TUBB3, which were included in the random forest (RF) diagnostic model. Finally, external validation was conducted on data retrieved from the GSE184316 datasets. RESULTS The results revealed that the RF diagnostic model could diagnose patients with IPF in the internal validation set with the area under the ROC curve (AUC) value of 0.905 and in the external validation with the AUC value of 0.767. Furthermore, real-time quantitative PCR and western blotting results revealed a significant decrease in SEMA5A (p < 0.05) expression level and an increase in COL7A1 and TUBB3 expression levels in TGF-β1-treated normal human lung fibroblasts. CONCLUSION We constructed an RF diagnostic model based on SEMA5A, COL7A1, and TUBB3 expression in lung tissue for diagnosing patients with IPF.
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Affiliation(s)
- Jie He
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Hu
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Otolaryngology - Head and Neck Surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Hairong Liu
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Geriatric Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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3
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Naik A, Forrest KM, Paul O, Issah Y, Valekunja UK, Tang SY, Reddy AB, Hennessy EJ, Brooks TG, Chaudhry F, Babu A, Morley M, Zepp JA, Grant GR, FitzGerald GA, Sehgal A, Worthen GS, Frank DB, Morrisey EE, Sengupta S. Circadian regulation of lung repair and regeneration. JCI Insight 2023; 8:e164720. [PMID: 37463053 PMCID: PMC10543710 DOI: 10.1172/jci.insight.164720] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
Optimal lung repair and regeneration are essential for recovery from viral infections, including influenza A virus (IAV). We have previously demonstrated that acute inflammation and mortality induced by IAV is under circadian control. However, it is not known whether the influence of the circadian clock persists beyond the acute outcomes. Here, we utilize the UK Biobank to demonstrate an association between poor circadian rhythms and morbidity from lower respiratory tract infections, including the need for hospitalization and mortality after discharge; this persists even after adjusting for common confounding factors. Furthermore, we use a combination of lung organoid assays, single-cell RNA sequencing, and IAV infection in different models of clock disruption to investigate the role of the circadian clock in lung repair and regeneration. We show that lung organoids have a functional circadian clock and the disruption of this clock impairs regenerative capacity. Finally, we find that the circadian clock acts through distinct pathways in mediating lung regeneration - in tracheal cells via the Wnt/β-catenin pathway and through IL-1β in alveolar epithelial cells. We speculate that adding a circadian dimension to the critical process of lung repair and regeneration will lead to novel therapies and improve outcomes.
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Affiliation(s)
- Amruta Naik
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Oindrila Paul
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Yasmine Issah
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Utham K. Valekunja
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Soon Y. Tang
- Institute of Translational Medicine and Therapeutics (ITMAT), and
| | - Akhilesh B. Reddy
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Thomas G. Brooks
- Institute of Translational Medicine and Therapeutics (ITMAT), and
| | - Fatima Chaudhry
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Gregory R. Grant
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Department of Genetics
| | - Garret A. FitzGerald
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amita Sehgal
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neuroscience, and
| | - G. Scott Worthen
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - David B. Frank
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Edward E. Morrisey
- Penn-CHOP Lung Biology Institute
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shaon Sengupta
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Penn-CHOP Lung Biology Institute
- Department of Pediatrics
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4
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Richardson R, Feigin CY, Bano-Otalora B, Johnson MR, Allen AE, Park J, McDowell RJ, Mereby SA, Lin IH, Lucas RJ, Mallarino R. The genomic basis of temporal niche evolution in a diurnal rodent. Curr Biol 2023; 33:3289-3298.e6. [PMID: 37480852 PMCID: PMC10529858 DOI: 10.1016/j.cub.2023.06.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 05/05/2023] [Accepted: 06/26/2023] [Indexed: 07/24/2023]
Abstract
Patterns of diel activity-how animals allocate their activity throughout the 24-h daily cycle-play key roles in shaping the internal physiology of an animal and its relationship with the external environment.1,2,3,4,5 Although shifts in diel activity patterns have occurred numerous times over the course of vertebrate evolution,6 the genomic correlates of such transitions remain unknown. Here, we use the African striped mouse (Rhabdomys pumilio), a species that transitioned from the ancestrally nocturnal diel niche of its close relatives to a diurnal one,7,8,9,10,11 to define patterns of naturally occurring molecular variation in diel niche traits. First, to facilitate genomic analyses, we generate a chromosome-level genome assembly of the striped mouse. Next, using transcriptomics, we show that the switch to daytime activity in this species is associated with a realignment of daily rhythms in peripheral tissues with respect to the light:dark cycle and the central circadian clock. To uncover selection pressures associated with this temporal niche shift, we perform comparative genomic analyses with closely related rodent species and find evidence of relaxation of purifying selection on striped mouse genes in the rod phototransduction pathway. In agreement with this, electroretinogram measurements demonstrate that striped mice have functional differences in dim-light visual responses compared with nocturnal rodents. Taken together, our results show that striped mice have undergone a drastic change in circadian organization and provide evidence that the visual system has been a major target of selection as this species transitioned to a novel temporal niche.
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Affiliation(s)
- Rose Richardson
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Charles Y Feigin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Beatriz Bano-Otalora
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Diabetes, Endocrinology, & Gastroenterology, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Matthew R Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Annette E Allen
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jongbeom Park
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Richard J McDowell
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Sarah A Mereby
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - I-Hsuan Lin
- Bioinformatics Core Facility, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Robert J Lucas
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA.
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5
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Tang L, Zhang X, Xu Y, Liu L, Sun X, Wang B, Yu K, Zhang H, Zhao X, Wang X. BMAL1 regulates MUC1 overexpression in ovalbumin-induced asthma. Mol Immunol 2023; 156:77-84. [PMID: 36906987 DOI: 10.1016/j.molimm.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 03/12/2023]
Abstract
Asthma often presents with a daily rhythm; however, the underlying mechanisms remain unclear. Circadian rhythm genes have been proposed to regulate inflammation and mucin expression. Here, ovalbumin (OVA)-induced mice and serum shock human bronchial epidermal cells (16HBE) were used in in vivo and in vitro models, respectively. We constructed a brain and muscle ARNT-like 1 (BMAL1) knockdown 16HBE cell line to analyze the effects of rhythmic fluctuations on mucin expression. Serum immunoglobulin E (IgE) and circadian rhythm genes in asthmatic mice showed rhythmic fluctuation amplitude. Mucin (MUC) 1 and MUC5AC expression was increased in the lung tissue of the asthmatic mice. MUC1 expression was negatively correlated with that of the circadian rhythm genes, particularly BMAL1 (r = -0.546, P = 0.006). There was also a negative correlation between BMAL1 and MUC1 expression (r = -0.507, P = 0.002) in the serum shock 16HBE cells. BMAL1 knockdown negated the rhythmic fluctuation amplitude of MUC1 expression and upregulated MUC1 expression in the 16HBE cells. These results indicate that the key circadian rhythm gene, BMAL1, causes periodic changes in airway MUC1 expression in OVA-induced asthmatic mice. Targeting BMAL1 to regulate periodic changes in MUC1 expression may, therefore, improve asthma treatments.
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Affiliation(s)
- Lingling Tang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210004, China
| | - Xiaona Zhang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210004, China
| | - Yanqiu Xu
- Nanjing Jiangning Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu 211100, China
| | - Li Liu
- Department of Central Lab, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210029, China
| | - Xianhong Sun
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210004, China
| | - Bohan Wang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210004, China
| | - Keyao Yu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210004, China
| | - Hui Zhang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China
| | - Xia Zhao
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Xiongbiao Wang
- Department of Respiratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China.
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6
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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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7
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Guo D, Zhang J, Han Y, Cui L, Wang H, Wang K, Li P, Deng R, Kang J, Duan Z. Transcriptomic Study on the Lungs of Broilers with Ascites Syndrome. Animals (Basel) 2023; 13:ani13010175. [PMID: 36611783 PMCID: PMC9817706 DOI: 10.3390/ani13010175] [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: 12/05/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Although broiler ascites syndrome (AS) has been extensively studied, its pathogenesis remains unclear. The lack of cardiopulmonary function in broilers causes relative hypoxia in the body; hence, the lung is the main target organ of AS. However, the transcriptome of AS lung tissue in broilers has not been studied. In this study, an AS model was successfully constructed, and lung tissues of three AS broilers and three healthy broilers were obtained for RNA sequencing (RNA-seq) and pathological observation. The results showed that 614 genes were up-regulated and 828 genes were down-regulated in the AS group compared with the normal group. Gene Ontology (GO) functional annotation revealed the following up-regulated genes: FABP4, APLN, EIF2AK4, HMOX1, MMP9, THBS1, TLR4, BCL2; and down-regulated genes: APELA, FGF7, WNT5A, CDK6, IL7, IL7R, APLNR. These genes have attracted much attention in cardiovascular diseases such as pulmonary hypertension. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that multiple metabolic processes were enriched, indicating abnormal lung metabolism of AS in broilers. These findings elucidate the potential genes and signal pathways in the lungs of broilers with AS and provide a potential target for studying the pathogenesis and preventing AS.
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8
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Li L, Zhang M, Zhao C, Cheng Y, Liu C, Shi M. Circadian clock gene Clock-Bmal1 regulates cellular senescence in Chronic obstructive pulmonary disease. BMC Pulm Med 2022; 22:435. [PMID: 36419003 PMCID: PMC9682805 DOI: 10.1186/s12890-022-02237-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a progressive respiratory disease. COPD is associated with accelerated lung aging. Circadian clock is believed to play important roles in COPD. Although the circadian molecular clock regulates cellular senescence, there is no information available regarding the impact of COPD. The aim of this study is to investigate the role of the circadian clock protein BMAL1 and CLOCK in cellular senescence in order to understand the cellular mechanisms of accelerated aging of COPD. Bmal1 and Clock levels were assessed in the plasma samples of non-smokers, smokers, and patients with COPD. The regulation of ciracadian clock expression and cell senescence by cigarette smoke extract (CSE) was studied in vitro, and small interfering RNA (siRNA) and overexpression of Bmal1 or Clock were employed to investigate the role of circadian clock on cell senescence. Herein, patients with COPD showed lower Bmal1 and Clock expression in the plasma. Interestingly, CSE exposure contributed to the increased cell senescence, decreased Clock and Bmal1 in human bronchial epithelial cells (Beas-2B cells). We found that knockdown of Clock or Bmal1 lead to upregulation of cell senescence in Beas-2B cells, while overexpression of Clock or Bmal1 inhibited cell senescence in Beas-2B cells, which is through the MAPK pathways. Therefore, our findings indicated that Bmal1 or Clock deficiency may be a significant factor to increase cellular senescence of the lung to develop COPD.
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Affiliation(s)
- Lingling Li
- grid.452666.50000 0004 1762 8363Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China ,grid.452929.10000 0004 8513 0241Department of Pulmonary and Critical Care Medicine, Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Min Zhang
- grid.443626.10000 0004 1798 4069Department of Emergency, Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Chunyang Zhao
- grid.452929.10000 0004 8513 0241Department of Pulmonary and Critical Care Medicine, Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Yusheng Cheng
- grid.452929.10000 0004 8513 0241Department of Pulmonary and Critical Care Medicine, Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Chuanmei Liu
- grid.452929.10000 0004 8513 0241Department of Pulmonary and Critical Care Medicine, Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Minhua Shi
- grid.452666.50000 0004 1762 8363Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
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9
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Tiwari D, Ahuja N, Kumar S, Kalra R, Nanduri R, Gupta S, Khare AK, Bhagyaraj E, Arora R, Gupta P. Nuclear receptor Nr1d1 alleviates asthma by abating GATA3 gene expression and Th2 cell differentiation. Cell Mol Life Sci 2022; 79:308. [PMID: 35596832 PMCID: PMC11073070 DOI: 10.1007/s00018-022-04323-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/30/2022] [Accepted: 04/21/2022] [Indexed: 11/03/2022]
Abstract
Nuclear receptors are a unique family of transcription factors that play cardinal roles in physiology and plethora of human diseases. The adopted orphan nuclear receptor Nr1d1 is a constitutive transcriptional repressor known to modulate several biological processes. In this study, we found that Nr1d1 plays a decisive role in T helper (Th)-cell polarization and transcriptionally impedes the formation of Th2 cells by directly binding to the promoter region of GATA binding protein 3 (GATA3) gene. Nr1d1 interacts with its cellular companion, the nuclear receptor corepressor and histone deacetylase 3 to form a stable repression complex on the GATA3 promoter. The presence of Nr1d1 also imparts protection against associated inflammatory responses in murine model of asthma and its ligand SR9011 eased disease severity by suppressing Th2 responses. Moreover, Chip-seq profiling uncovered Nr1d1 interactions with other gene subsets that impedes Th2-linked pathways and regulates metabolism, immunity and brain functions, therefore, providing empirical evidence regarding the genetic link between asthma and other comorbid conditions. Thus, Nr1d1 emerges as a molecular switch that could be targeted to subdue asthma.
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Affiliation(s)
- Drishti Tiwari
- Department of Molecular Immunology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India.
| | - Nancy Ahuja
- Department of Molecular Immunology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Sumit Kumar
- Department of Molecular Immunology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Rashi Kalra
- Department of Molecular Immunology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ravikanth Nanduri
- Department of Molecular Immunology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Shalini Gupta
- Department of Molecular Immunology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Asheesh Kumar Khare
- Department of Molecular Immunology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Ella Bhagyaraj
- Department of Molecular Immunology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
- Department of Infectious Disease and Immunology, University of Florida, Gainesville, FL, USA
| | - Rashmi Arora
- Department of Molecular Immunology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Pawan Gupta
- Department of Molecular Immunology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India.
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10
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Giri A, Wang Q, Rahman I, Sundar IK. Circadian molecular clock disruption in chronic pulmonary diseases. Trends Mol Med 2022; 28:513-527. [DOI: 10.1016/j.molmed.2022.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/25/2022] [Accepted: 04/01/2022] [Indexed: 12/31/2022]
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11
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Urban C, Kiefer A, Conradt R, Kabesch M, Lex C, Zacharasiewicz A, Kerzel S. Validation of the LEOSound® monitor for standardized detection of wheezing and cough in children. Pediatr Pulmonol 2022; 57:551-559. [PMID: 34800333 DOI: 10.1002/ppul.25768] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/29/2021] [Accepted: 11/18/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND A hallmark of many respiratory conditions is the presence of nocturnal symptoms. Nevertheless, especially in children there is currently still a huge diagnostic gap in detecting nighttime symptoms, which leads to an underestimation of the frequency in clinical practise. METHODS We evaluated the clinical applicability and determined the formal test characteristics of the LEOSound ® system, a device for digital long-time recording and automated detection of acoustic airway events. Airway sounds were recorded overnight in 115 children and adolescents (1-17 years) with and without respiratory conditions. The automated classification for "cough" and "wheezing" was subsequently validated against the manual acoustic reassessment by an expert physician. RESULTS The general acceptance was good across all age groups and a technically successful recording was obtained in 98 children, corresponding to 92,976 sound epochs (à 30 s) or a total of 774 h of lung sounds. We found a sensitivity of 89% and a specificity of 99% for the automated detection of cough. For detection of wheezing, sensitivity and specificity were both 98%. The cough index and the wheeze index (events per hour) of individual patients showed a strong positive correlation (cough: rS = 0.85, wheeze: rS = 0.95) and a sufficient agreement of the two assessment methods in the Bland-Altman analysis. CONCLUSION Our data show that the LEOSound® is a suitable device for standardized detection of cough and wheezing and hence a promising diagnostic tool to detect nocturnal respiratory symptoms, especially in children. However, a validation process to reduce false positive classifications is essential in clinical routine use.
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Affiliation(s)
- Christof Urban
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, Regensburg, Germany.,Alpenklinik Santa Maria, Bad Hindelang, Germany
| | - Alexander Kiefer
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, Regensburg, Germany
| | - Regina Conradt
- Division of Pneumology, Department of Internal Medicine, Intensive Care and Sleep Medicine, Philipps-University Marburg, Marburg, Germany
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, Regensburg, Germany
| | - Christiane Lex
- Department of Pediatric Cardiology and Intensive Care Medicine, University Hospital Goettingen, Goettingen, Germany
| | - Angela Zacharasiewicz
- Department of Pediatrics and Adolescent Medicine, Wilhelminenspital, Teaching Hospital of the University of Vienna, Vienna, Austria
| | - Sebastian Kerzel
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, Regensburg, Germany
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12
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Crislip GR, Johnston JG, Douma LG, Costello HM, Juffre A, Boyd K, Li W, Maugans CC, Gutierrez-Monreal M, Esser KA, Bryant AJ, Liu AC, Gumz ML. Circadian Rhythm Effects on the Molecular Regulation of Physiological Systems. Compr Physiol 2021; 12:2769-2798. [PMID: 34964116 DOI: 10.1002/cphy.c210011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Nearly every system within the body contains an intrinsic cellular circadian clock. The circadian clock contributes to the regulation of a variety of homeostatic processes in mammals through the regulation of gene expression. Circadian disruption of physiological systems is associated with pathophysiological disorders. Here, we review the current understanding of the molecular mechanisms contributing to the known circadian rhythms in physiological function. This article focuses on what is known in humans, along with discoveries made with cell and rodent models. In particular, the impact of circadian clock components in metabolic, cardiovascular, endocrine, musculoskeletal, immune, and central nervous systems are discussed. © 2021 American Physiological Society. Compr Physiol 11:1-30, 2021.
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Affiliation(s)
- G Ryan Crislip
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA
| | - Jermaine G Johnston
- Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, University of Florida, Gainesville, Florida, USA
| | - Lauren G Douma
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Hannah M Costello
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA
| | - Alexandria Juffre
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Kyla Boyd
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Wendy Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Cheoting C Maugans
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Miguel Gutierrez-Monreal
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA
| | - Karyn A Esser
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA.,Myology Institute, University of Florida, Gainesville, Florida, USA
| | - Andrew J Bryant
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| | - Andrew C Liu
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA.,Myology Institute, University of Florida, Gainesville, Florida, USA
| | - Michelle L Gumz
- Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, University of Florida, Gainesville, Florida, USA.,Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA.,Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA.,Center for Integrative Cardiovascular and Metabolic Disease, University of Florida, Gainesville, Florida, USA
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13
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Gao L, Wang K, Cheng M, Zeng Z, Wang T, Wen F, Chen J. Circadian clock dysfunction of epithelial cells in pulmonary diseases. Int J Biochem Cell Biol 2021; 141:106110. [PMID: 34699979 DOI: 10.1016/j.biocel.2021.106110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/17/2021] [Accepted: 10/21/2021] [Indexed: 02/05/2023]
Abstract
Highly-differentiated pulmonary epithelial cells are essential for maintaining lung homeostasis by exerting various physiological functions, which are regulated by circadian clock consisted of an autoregulatory feedback loop of clock genes, including Brain-Muscle Aryl-hydrocarbon Receptor Nuclear Translocator-Like 1 (BMAL1) and Nuclear Heme Receptor Reverse Erythroblastosis Virus α (REV-ERB-α). The circadian clock dysfunction of epithelial cells has been increasingly associated with the pulmonary diseases: BMAL1 and REV-ERB-α regulates inflammatory response of club cells induced by lipopolysaccharide and cigarette smoke (CS) respectively; the clock disfunction in alveolar epithelial type2 cells (AEC-II) has been implicated in CS-induced airway inflammation and early-life hyperoxia-related susceptibility to influenza infection; the ciliary beat frequency of ciliated cells also shows circadian rhythms. Here, we review the current knowledge on the circadian regulation of different epithelial-cell subtypes, attempting to provide insights into how clock dysfunction contributes to pulmonary diseases, and explore possible pharmacological therapies and future directions for fundamental studies.
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Affiliation(s)
- Lijuan Gao
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, and Department of Respiratory and Critical Care Medicine, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ke Wang
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, and Department of Respiratory and Critical Care Medicine, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Mengxin Cheng
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, and Department of Respiratory and Critical Care Medicine, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zijian Zeng
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, and Department of Respiratory and Critical Care Medicine, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Tao Wang
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, and Department of Respiratory and Critical Care Medicine, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Fuqiang Wen
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, and Department of Respiratory and Critical Care Medicine, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Jun Chen
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, and Department of Respiratory and Critical Care Medicine, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
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14
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Wang R, Murray CS, Fowler SJ, Simpson A, Durrington HJ. Asthma diagnosis: into the fourth dimension. Thorax 2021; 76:624-631. [PMID: 33504564 PMCID: PMC8223645 DOI: 10.1136/thoraxjnl-2020-216421] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/18/2020] [Accepted: 12/31/2020] [Indexed: 02/06/2023]
Abstract
Asthma is the most common chronic respiratory disease in the UK; however, the misdiagnosis rate is substantial. The lack of consistency in national guidelines and the paucity of data on the performance of diagnostic algorithms compound the challenges in asthma diagnosis. Asthma is a highly rhythmic disease, characterised by diurnal variability in clinical symptoms and pathogenesis. Asthma also varies day to day, seasonally and from year to year. As much as it is a hallmark for asthma, this variability also poses significant challenges to asthma diagnosis. Almost all established asthma diagnostic tools demonstrate diurnal variation, yet few are performed with standardised timing of measurements. The dichotomous interpretation of diagnostic outcomes using fixed cut-off values may further limit the accuracy of the tests, particularly when diurnal variability straddles cut-off values within a day, and careful interpretation beyond the 'positive' and 'negative' outcome is needed. The day-to-day and more long-term variations are less predictable and it is unclear whether performing asthma diagnostic tests during asymptomatic periods may influence diagnostic sensitivities. With the evolution of asthma diagnostic tools, home monitoring and digital apps, novel strategies are needed to bridge these gaps in knowledge, and circadian variability should be considered during the standardisation process. This review summarises the biological mechanisms of circadian rhythms in asthma and highlights novel data on the significance of time (the fourth dimension) in asthma diagnosis.
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Affiliation(s)
- Ran Wang
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK,Manchester Academic Health Science Centre and NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Clare S Murray
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK,Manchester Academic Health Science Centre and NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Stephen J Fowler
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK,Manchester Academic Health Science Centre and NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK,Manchester Academic Health Science Centre and NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Hannah Jane Durrington
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK .,Manchester Academic Health Science Centre and NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
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15
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Pathway-level analysis of genome-wide circadian dynamics in diverse tissues in rat and mouse. J Pharmacokinet Pharmacodyn 2021; 48:361-374. [PMID: 33768484 DOI: 10.1007/s10928-021-09750-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
A computational framework is developed to enable the characterization of genome-wide, multi-tissue circadian dynamics at the level of "functional groupings of genes" defined in the context of signaling, cellular/genetic processing and metabolic pathways in rat and mouse. Our aim is to identify how individual genes come together to generate orchestrated rhythmic patterns and how these may vary within and across tissues. We focus our analysis on four tissues (adipose, liver, lung, and muscle). A genome-wide pathway-centric analysis enables us to develop a comprehensive picture on how the observed circadian variation at the individual gene level, orchestrates functional responses at the pathway level. Such pathway-based "meta-data" analysis enables the rational integration and comparison across platforms and/or experimental designs evaluating emergent dynamics, as opposed to comparisons of individual elements. One of our key findings is that when considering the dynamics at the pathway level, a complex behavior emerges. Our work proposes that tissues tend to coordinate gene's circadian expression in a way that optimizes tissue-specific pathway activity, depending of each tissue's broader role in homeostasis.
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16
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Abo SMC, Layton AT. Modeling the circadian regulation of the immune system: Sexually dimorphic effects of shift work. PLoS Comput Biol 2021; 17:e1008514. [PMID: 33788832 PMCID: PMC8041207 DOI: 10.1371/journal.pcbi.1008514] [Citation(s) in RCA: 13] [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: 10/26/2020] [Revised: 04/12/2021] [Accepted: 03/06/2021] [Indexed: 12/31/2022] Open
Abstract
The circadian clock exerts significance influence on the immune system and disruption of circadian rhythms has been linked to inflammatory pathologies. Shift workers often experience circadian misalignment as their irregular work schedules disrupt the natural light-dark cycle, which in turn can cause serious health problems associated with alterations in genetic expressions of clock genes. In particular, shift work is associated with impairment in immune function, and those alterations are sex-specific. The goal of this study is to better understand the mechanisms that explain the weakened immune system in shift workers. To achieve that goal, we have constructed a mathematical model of the mammalian pulmonary circadian clock coupled to an acute inflammation model in the male and female rats. Shift work was simulated by an 8h-phase advance of the circadian system with sex-specific modulation of clock genes. The model reproduces the clock gene expression in the lung and the immune response to various doses of lipopolysaccharide (LPS). Under normal conditions, our model predicts that a host is more sensitive to LPS at circadian time (CT) CT12 versus CT0 due to a dynamic change of Interleukin 10 (IL-10), an anti-inflammatory cytokine. We identify REV-ERB as a key modulator of IL-10 activity throughout the circadian day. The model also predicts a reversal of the times of lowest and highest sensitivity to LPS, with males and females exhibiting an exaggerated response to LPS at CT0, which is countered by a blunted immune response at CT12. Overall, females produce fewer pro-inflammatory cytokines than males, but the extent of sequelae experienced by males and females varies across the circadian day. This model can serve as an essential component in an integrative model that will yield mechanistic understanding of how shift work-mediated circadian disruptions affect the inflammatory and other physiological responses.
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Affiliation(s)
- Stéphanie M. C. Abo
- Department of Applied Mathematics, University of Waterloo, Waterloo, Ontario, Canada
| | - Anita T. Layton
- Department of Applied Mathematics, University of Waterloo, Waterloo, Ontario, Canada
- Department of Biology, Cheriton School of Computer Science, and School of Pharmacology, University of Waterloo, Waterloo, Ontario, Canada
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17
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Jacob H, Curtis AM, Kearney CJ. Therapeutics on the clock: Circadian medicine in the treatment of chronic inflammatory diseases. Biochem Pharmacol 2020; 182:114254. [PMID: 33010213 DOI: 10.1016/j.bcp.2020.114254] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
The circadian clock is a collection of endogenous oscillators with a periodicity of ~ 24 h. Recently, our understanding of circadian rhythms and their regulation at genomic and physiologic scales has grown significantly. Knowledge of the circadian influence on biological processes has provided new possibilities for novel pharmacological strategies. Directly targeting the biological clock or its downstream targets, and/or using timing as a variable in drug therapy are now important pharmacological considerations. The circadian machinery mediates many aspects of the inflammatory response and, reciprocally, an inflammatory environment can disrupt circadian rhythms. Therefore, intense interest exists in leveraging circadian biology as a means to treat chronic inflammatory diseases such as sepsis, asthma, rheumatoid arthritis, osteoarthritis, and cardiovascular disease, which all display some type of circadian signature. The purpose of this review is to evaluate the crosstalk between circadian rhythms, inflammatory diseases, and their pharmacological treatment. Evidence suggests that carefully rationalized application of chronotherapy strategies - alone or in combination with small molecule modulators of circadian clock components - can improve efficacy and reduce toxicity, thus warranting further investigation and use.
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Affiliation(s)
- Haritha Jacob
- Tissue Engineering Research Group, Department of Anatomy and Regenerative Medicine, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), RCSI and Trinity College Dublin, Dublin, Ireland
| | - Annie M Curtis
- Tissue Engineering Research Group, Department of Anatomy and Regenerative Medicine, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), RCSI and Trinity College Dublin, Dublin, Ireland; School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland.
| | - Cathal J Kearney
- Tissue Engineering Research Group, Department of Anatomy and Regenerative Medicine, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), RCSI and Trinity College Dublin, Dublin, Ireland; Department of Biomedical Engineering, University of Massachusetts Amherst, MA, USA.
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18
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Ayyar VS, Jusko WJ. Transitioning from Basic toward Systems Pharmacodynamic Models: Lessons from Corticosteroids. Pharmacol Rev 2020; 72:414-438. [PMID: 32123034 DOI: 10.1124/pr.119.018101] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Technology in bioanalysis, -omics, and computation have evolved over the past half century to allow for comprehensive assessments of the molecular to whole body pharmacology of diverse corticosteroids. Such studies have advanced pharmacokinetic and pharmacodynamic (PK/PD) concepts and models that often generalize across various classes of drugs. These models encompass the "pillars" of pharmacology, namely PK and target drug exposure, the mass-law interactions of drugs with receptors/targets, and the consequent turnover and homeostatic control of genes, biomarkers, physiologic responses, and disease symptoms. Pharmacokinetic methodology utilizes noncompartmental, compartmental, reversible, physiologic [full physiologically based pharmacokinetic (PBPK) and minimal PBPK], and target-mediated drug disposition models using a growing array of pharmacometric considerations and software. Basic PK/PD models have emerged (simple direct, biophase, slow receptor binding, indirect response, irreversible, turnover with inactivation, and transduction models) that place emphasis on parsimony, are mechanistic in nature, and serve as highly useful "top-down" methods of quantitating the actions of diverse drugs. These are often components of more complex quantitative systems pharmacology (QSP) models that explain the array of responses to various drugs, including corticosteroids. Progressively deeper mechanistic appreciation of PBPK, drug-target interactions, and systems physiology from the molecular (genomic, proteomic, metabolomic) to cellular to whole body levels provides the foundation for enhanced PK/PD to comprehensive QSP models. Our research based on cell, animal, clinical, and theoretical studies with corticosteroids have provided ideas and quantitative methods that have broadly advanced the fields of PK/PD and QSP modeling and illustrates the transition toward a global, systems understanding of actions of diverse drugs. SIGNIFICANCE STATEMENT: Over the past half century, pharmacokinetics (PK) and pharmacokinetics/pharmacodynamics (PK/PD) have evolved to provide an array of mechanism-based models that help quantitate the disposition and actions of most drugs. We describe how many basic PK and PK/PD model components were identified and often applied to the diverse properties of corticosteroids (CS). The CS have complications in disposition and a wide array of simple receptor-to complex gene-mediated actions in multiple organs. Continued assessments of such complexities have offered opportunities to develop models ranging from simple PK to enhanced PK/PD to quantitative systems pharmacology (QSP) that help explain therapeutic and adverse CS effects. Concurrent development of state-of-the-art PK, PK/PD, and QSP models are described alongside experimental studies that revealed diverse CS actions.
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Affiliation(s)
- Vivaswath S Ayyar
- Department of Pharmaceutical Sciences University at Buffalo, School of Pharmacy and Pharmaceutical Sciences, Buffalo, New York
| | - William J Jusko
- Department of Pharmaceutical Sciences University at Buffalo, School of Pharmacy and Pharmaceutical Sciences, Buffalo, New York
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19
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Bartman CM, Matveyenko A, Prakash YS. It's about time: clocks in the developing lung. J Clin Invest 2020; 130:39-50. [PMID: 31895049 DOI: 10.1172/jci130143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The discovery of peripheral intracellular clocks revealed circadian oscillations of clock genes and their targets in all cell types, including those in the lung, sparking exploration of clocks in lung disease pathophysiology. While the focus has been on the role of these clocks in adult airway diseases, clock biology is also likely to be important in perinatal lung development, where it has received far less attention. Historically, fetal circadian rhythms have been considered irrelevant owing to lack of external light exposure, but more recent insights into peripheral clock biology raise questions of clock emergence, its concordance with tissue-specific structure/function, the interdependence of clock synchrony and functionality in perinatal lung development, and the possibility of lung clocks in priming the fetus for postnatal life. Understanding the perinatal molecular clock may unravel mechanistic targets for chronic airway disease across the lifespan. With current research providing more questions than answers, it is about time to investigate clocks in the developing lung.
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Affiliation(s)
| | - Aleksey Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Y S Prakash
- Department of Anesthesiology and Perioperative Medicine and.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
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20
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Bartman CM, Prakash YS. Bringing the cellular clock into understanding lung disease: it's time, period! Am J Physiol Lung Cell Mol Physiol 2020; 319:L273-L276. [PMID: 32639868 DOI: 10.1152/ajplung.00320.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
| | - Y S Prakash
- Department of Anesthesiology, Mayo Clinic, Rochester, Minnesota.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
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21
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Hadadi E, Taylor W, Li XM, Aslan Y, Villote M, Rivière J, Duvallet G, Auriau C, Dulong S, Raymond-Letron I, Provot S, Bennaceur-Griscelli A, Acloque H. Chronic circadian disruption modulates breast cancer stemness and immune microenvironment to drive metastasis in mice. Nat Commun 2020; 11:3193. [PMID: 32581213 PMCID: PMC7314789 DOI: 10.1038/s41467-020-16890-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 05/29/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common type of cancer worldwide and one of the major causes of cancer death in women. Epidemiological studies have established a link between night-shift work and increased cancer risk, suggesting that circadian disruption may play a role in carcinogenesis. Here, we aim to shed light on the effect of chronic jetlag (JL) on mammary tumour development. To do this, we use a mouse model of spontaneous mammary tumourigenesis and subject it to chronic circadian disruption. We observe that circadian disruption significantly increases cancer-cell dissemination and lung metastasis. It also enhances the stemness and tumour-initiating potential of tumour cells and creates an immunosuppressive shift in the tumour microenvironment. Finally, our results suggest that the use of a CXCR2 inhibitor could correct the effect of JL on cancer-cell dissemination and metastasis. Altogether, our data provide a conceptual framework to better understand and manage the effects of chronic circadian disruption on breast cancer progression. Circadian disruption is implicated in the development of different human cancers. Here the authors show that chronic circadian disruption, through continuous jet lag, only moderately affects primary tumour growth but promotes cancer-cell dissemination and metastasis in a mouse model of spontaneous mammary tumorigenesis.
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Affiliation(s)
- Eva Hadadi
- Inserm, U935, Université Paris Sud, Villejuif, France.
| | | | - Xiao-Mei Li
- Inserm, U935, Université Paris Sud, Villejuif, France.,Université Paris Sud, Université Paris Saclay, UFR de Médecine Kremlin Bicêtre, Le Kremlin-Bicêtre, France
| | - Yetki Aslan
- Inserm, U1132, Université Paris Diderot, Hôpital Lariboisière - Centre Viggo Petersen, 75010, Paris, France
| | - Marthe Villote
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | - Julie Rivière
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | | | | | - Sandrine Dulong
- Inserm, U935, Université Paris Sud, Villejuif, France.,Université Paris Sud, Université Paris Saclay, UFR de Médecine Kremlin Bicêtre, Le Kremlin-Bicêtre, France
| | - Isabelle Raymond-Letron
- Département des Sciences Biologiques et Fonctionnelles, Laboratoire d'HistoPathologie Expérimentale et Comparée (LabHPEC), ENVT, Université de Toulouse, Toulouse, France.,STROMALab, CNRS ERL5311, EFS, ENVT, Inserm U1031, Université de Toulouse, Toulouse, France
| | - Sylvain Provot
- Inserm, U1132, Université Paris Diderot, Hôpital Lariboisière - Centre Viggo Petersen, 75010, Paris, France
| | - Annelise Bennaceur-Griscelli
- Inserm, U935, Université Paris Sud, Villejuif, France.,Université Paris Sud, Université Paris Saclay, UFR de Médecine Kremlin Bicêtre, Le Kremlin-Bicêtre, France.,Service d'hématologie, APHP, GHU Paris Sud, Paris, France
| | - Hervé Acloque
- Inserm, U935, Université Paris Sud, Villejuif, France. .,GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France.
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22
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Role of Non-Coding RNAs in Lung Circadian Clock Related Diseases. Int J Mol Sci 2020; 21:ijms21083013. [PMID: 32344623 PMCID: PMC7215637 DOI: 10.3390/ijms21083013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
Circadian oscillations are regulated at both central and peripheral levels to maintain physiological homeostasis. The central circadian clock consists of a central pacemaker in the suprachiasmatic nucleus that is entrained by light dark cycles and this, in turn, synchronizes the peripheral clock inherent in other organs. Circadian dysregulation has been attributed to dysregulation of peripheral clock and also associated with several diseases. Components of the molecular clock are disrupted in lung diseases like chronic obstructive pulmonary disease (COPD), asthma and IPF. Airway epithelial cells play an important role in temporally organizing magnitude of immune response, DNA damage response and acute airway inflammation. Non-coding RNAs play an important role in regulation of molecular clock and in turn are also regulated by clock components. Dysregulation of these non-coding RNAs have been shown to impact the expression of core clock genes as well as clock output genes in many organs. However, no studies have currently looked at the potential impact of these non-coding RNAs on lung molecular clock. This review focuses on the ways how these non-coding RNAs regulate and in turn are regulated by the lung molecular clock and its potential impact on lung diseases.
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23
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Zhang Z, Loudon A. Circadian Gene Profiling in Laser Capture Microdissected Mouse Club Cells. Bio Protoc 2020; 10:e3590. [PMID: 33659556 DOI: 10.21769/bioprotoc.3590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/27/2020] [Accepted: 03/22/2020] [Indexed: 11/02/2022] Open
Abstract
Cell heterogeneity is high in tissues like lung. Research conducted on pure population of cells usually offers more insights than bulk tissues, such as circadian clock work. In this protocol, we provide a detailed work flow on how to do circadian clock study by RNA seq in laser capture micro-dissected mouse lung club cells. The method uses frozen tissues and is highly reproduciable.
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Affiliation(s)
- Zhenguang Zhang
- School of Medical Science, Faculty of Biology, medicine and Health, University of Manchester, Manchester, UK
| | - Andrew Loudon
- School of Medical Science, Faculty of Biology, medicine and Health, University of Manchester, Manchester, UK
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24
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Laloum D, Robinson-Rechavi M. Methods detecting rhythmic gene expression are biologically relevant only for strong signal. PLoS Comput Biol 2020; 16:e1007666. [PMID: 32182235 PMCID: PMC7100990 DOI: 10.1371/journal.pcbi.1007666] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/27/2020] [Accepted: 01/18/2020] [Indexed: 12/03/2022] Open
Abstract
The nycthemeral transcriptome embodies all genes displaying a rhythmic variation of their mRNAs periodically every 24 hours, including but not restricted to circadian genes. In this study, we show that the nycthemeral rhythmicity at the gene expression level is biologically functional and that this functionality is more conserved between orthologous genes than between random genes. We used this conservation of the rhythmic expression to assess the ability of seven methods (ARSER, Lomb Scargle, RAIN, JTK, empirical-JTK, GeneCycle, and meta2d) to detect rhythmic signal in gene expression. We have contrasted them to a naive method, not based on rhythmic parameters. By taking into account the tissue-specificity of rhythmic gene expression and different species comparisons, we show that no method is strongly favored. The results show that these methods designed for rhythm detection, in addition to having quite similar performances, are consistent only among genes with a strong rhythm signal. Rhythmic genes defined with a standard p-value threshold of 0.01 for instance, could include genes whose rhythmicity is biologically irrelevant. Although these results were dependent on the datasets used and the evolutionary distance between the species compared, we call for caution about the results of studies reporting or using large sets of rhythmic genes. Furthermore, given the analysis of the behaviors of the methods on real and randomized data, we recommend using primarily ARS, empJTK, or GeneCycle, which verify expectations of a classical distribution of p-values. Experimental design should also take into account the circumstances under which the methods seem more efficient, such as giving priority to biological replicates over the number of time-points, or to the number of time-points over the quality of the technique (microarray vs RNAseq). GeneCycle, and to a lesser extent empirical-JTK, might be the most robust method when applied to weakly informative datasets. Finally, our analyzes suggest that rhythmic genes are mainly highly expressed genes. To be active, genes have to be transcribed to RNA. For some genes, the transcription rate follows a circadian rhythm with a periodicity of approximately 24 hours; we call these genes “rhythmic”. In this study, we compared methods designed to detect rhythmic genes in gene expression data. The data are measures of the number of RNA molecules for each gene, given at several time-points, usually spaced 2 to 4 hours, over one or several periods of 24 hours. There are many such methods, but it is not known which ones work best to detect genes whose rhythmic expression is biologically functional. We compared these methods using a reference group of evolutionarily conserved rhythmic genes. We compared data from baboon, mouse, rat, zebrafish, fly, and mosquitoes. Surprisingly, no method was particularly effective. Furthermore, we found that only very strong rhythmic signals were relevant with each method. More precisely, when we use a usual cut-off to define rhythmic genes, the group of genes considered as rhythmic contains many genes whose rhythmicity cannot be confirmed to be biologically relevant. We also show that rhythmic genes mainly contain highly expressed genes. Finally, based on our results, we provide recommendations on which methods to use and how, and suggestions for future experimental designs.
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Affiliation(s)
- David Laloum
- Department of Ecology and Evolution, Batiment Biophore, Quartier UNIL-Sorge, Université de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Batiment Génopode, Quartier UNIL-Sorge, Université de Lausanne, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, Batiment Biophore, Quartier UNIL-Sorge, Université de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Batiment Génopode, Quartier UNIL-Sorge, Université de Lausanne, Lausanne, Switzerland
- * E-mail:
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Xenobiotica-metabolizing enzymes in the lung of experimental animals, man and in human lung models. Arch Toxicol 2019; 93:3419-3489. [PMID: 31673725 DOI: 10.1007/s00204-019-02602-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/15/2019] [Indexed: 12/15/2022]
Abstract
The xenobiotic metabolism in the lung, an organ of first entry of xenobiotics into the organism, is crucial for inhaled compounds entering this organ intentionally (e.g. drugs) and unintentionally (e.g. work place and environmental compounds). Additionally, local metabolism by enzymes preferentially or exclusively occurring in the lung is important for favorable or toxic effects of xenobiotics entering the organism also by routes other than by inhalation. The data collected in this review show that generally activities of cytochromes P450 are low in the lung of all investigated species and in vitro models. Other oxidoreductases may turn out to be more important, but are largely not investigated. Phase II enzymes are generally much higher with the exception of UGT glucuronosyltransferases which are generally very low. Insofar as data are available the xenobiotic metabolism in the lung of monkeys comes closed to that in the human lung; however, very few data are available for this comparison. Second best rate the mouse and rat lung, followed by the rabbit. Of the human in vitro model primary cells in culture, such as alveolar macrophages and alveolar type II cells as well as the A549 cell line appear quite acceptable. However, (1) this generalization represents a temporary oversimplification born from the lack of more comparable data; (2) the relative suitability of individual species/models is different for different enzymes; (3) when more data become available, the conclusions derived from these comparisons quite possibly may change.
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Janjić K, Kurzmann C, Moritz A, Agis H. Core circadian clock gene expression in human dental pulp-derived cells in response to L-mimosine, hypoxia and echinomycin. Eur J Oral Sci 2019; 126:263-271. [PMID: 30006964 PMCID: PMC6585758 DOI: 10.1111/eos.12535] [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] [Indexed: 12/16/2022]
Abstract
Core circadian clock genes set the pace for a wide range of physiological functions, including regeneration. The role of these genes and their regulation in the dental pulp, in particular under hypoxic conditions, is unknown. Here we investigated if core clock genes are expressed in human dental pulp‐derived cells (DPC) and if their expression is modulated by the hypoxia mimetic agent, L‐mimosine (L‐MIM), hypoxia or echinomycin. Dental pulp‐derived cells in monolayers and spheroids were treated with L‐MIM, hypoxia or echinomycin. mRNA levels of the core circadian clock genes were analysed using quantitative PCR (qPCR) and their protein levels were analysed by western blot. All core clock genes and proteins were produced in DPC monolayer and spheroid cultures. The expression of cryptochrome circadian regulators and period circadian regulators was reduced by L‐MIM, hypoxia and echinomycin at mRNA, but not at protein levels. Time course experiments indicated that modulations were based on alterations in overall mRNA levels of core circadian clock genes. Our results suggest a potential role of the core circadian clock in the response of dental pulp to hypoxia. Future studies need to consider that regulation of the core circadian clock at mRNA levels might not be paralleled by modulation of protein levels.
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Affiliation(s)
- Klara Janjić
- Department of Conservative Dentistry and Periodontology, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Christoph Kurzmann
- Department of Conservative Dentistry and Periodontology, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Andreas Moritz
- Department of Conservative Dentistry and Periodontology, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Hermann Agis
- Department of Conservative Dentistry and Periodontology, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Vienna, Austria
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Zhang Z, Hunter L, Wu G, Maidstone R, Mizoro Y, Vonslow R, Fife M, Hopwood T, Begley N, Saer B, Wang P, Cunningham P, Baxter M, Durrington H, Blaikley JF, Hussell T, Rattray M, Hogenesch JB, Gibbs J, Ray DW, Loudon ASI. Genome-wide effect of pulmonary airway epithelial cell-specific Bmal1 deletion. FASEB J 2019; 33:6226-6238. [PMID: 30794439 PMCID: PMC6463917 DOI: 10.1096/fj.201801682r] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 01/22/2019] [Indexed: 12/16/2022]
Abstract
Pulmonary airway epithelial cells (AECs) form a critical interface between host and environment. We investigated the role of the circadian clock using mice bearing targeted deletion of the circadian gene brain and muscle ARNT-like 1 (Bmal1) in AECs. Pulmonary neutrophil infiltration, biomechanical function, and responses to influenza infection were all disrupted. A circadian time-series RNA sequencing study of laser-captured AECs revealed widespread disruption in genes of the core circadian clock and output pathways regulating cell metabolism (lipids and xenobiotics), extracellular matrix, and chemokine signaling, but strikingly also the gain of a novel rhythmic transcriptome in Bmal1-targeted cells. Many of the rhythmic components were replicated in primary AECs cultured in air-liquid interface, indicating significant cell autonomy for control of pulmonary circadian physiology. Finally, we found that metabolic cues dictate phasing of the pulmonary clock and circadian responses to immunologic challenges. Thus, the local circadian clock in AECs is vital in lung health by coordinating major cell processes such as metabolism and immunity.-Zhang, Z. Hunter, L., Wu, G., Maidstone, R., Mizoro, Y., Vonslow, R., Fife, M., Hopwood, T., Begley, N., Saer, B., Wang, P., Cunningham, P., Baxter, M., Durrington, H., Blaikley, J. F., Hussell, T., Rattray, M., Hogenesch, J. B., Gibbs, J., Ray, D. W., Loudon, A. S. I. Genome-wide effect of pulmonary airway epithelial cell-specific Bmal1 deletion.
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Affiliation(s)
- Zhenguang Zhang
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Louise Hunter
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Gang Wu
- Division of Human Genetics, Department of Pediatrics, Center for Chronobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Division of Immunobiology, Department of Pediatrics, Center for Chronobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Robert Maidstone
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom; and
| | - Yasutaka Mizoro
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Ryan Vonslow
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Mark Fife
- Manchester Center for Collaborative Inflammation Research, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, United Kingdom
| | - Thomas Hopwood
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Nicola Begley
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Ben Saer
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Ping Wang
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom; and
| | - Peter Cunningham
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Matthew Baxter
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Hannah Durrington
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - John F. Blaikley
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Tracy Hussell
- Manchester Center for Collaborative Inflammation Research, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, United Kingdom
| | - Magnus Rattray
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom; and
| | - John B. Hogenesch
- Division of Human Genetics, Department of Pediatrics, Center for Chronobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Julie Gibbs
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - David W. Ray
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
| | - Andrew S. I. Loudon
- Centre for Biological Timing, Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, United Kingdom
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Abstract
Cystic fibrosis (CF) is autosomal recessive disease that affects multiple body systems. CF patients often experience sleep disturbances, altered sleep patterns, and sleep apnea. Sleep in mammals is controlled in part by circadian clock genes, including Clock, Bmal1, Period1, Period2, Cryptochrome1, and Cryptochrome2. The purpose of this study was to gain a better understanding of the biological underpinnings of disordered sleep experienced in CF. To accomplish this, we evaluated circadian clock gene expression profiles in CF and wildtype mice, divided into two subgroups each based on sleep condition. One subgroup of each genotype was permitted to maintain their sleep-wake cycle while the other was deprived of sleep for six hours prior to sacrifice. Brain, skeletal muscle, jejunum, colon, lung and adipose tissues were collected from each mouse. Quantitative polymerase chain reaction (PCR) was used to quantify expression of Clock, Bmal1, Period1, Period2, Cryptochrome1 and Cryptochrome2, and expression levels were compared between study groups. Our comparisons showed distinct differences between the CF groups and the wildtype groups under both sleep conditions. Additionally, we found the CF mice that had been sleep deprived had severely dysregulated expression of all measured genes in the lung apart from Cry1. Our findings suggest that (1) disordered sleep in CF may be caused by circadian system dysregulation and (2) the loss of the cystic fibrosis transmembrane conductance regulator (CFTR) is a causative factor in the dysregulated circadian clock gene expression profiles of CF mice.
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Lung physiology and defense. CURRENT OPINION IN PHYSIOLOGY 2018. [DOI: 10.1016/j.cophys.2018.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Mavroudis PD, DuBois DC, Almon RR, Jusko WJ. Modeling circadian variability of core-clock and clock-controlled genes in four tissues of the rat. PLoS One 2018; 13:e0197534. [PMID: 29894471 PMCID: PMC5997360 DOI: 10.1371/journal.pone.0197534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/03/2018] [Indexed: 12/26/2022] Open
Abstract
Circadian clocks, present in almost all cells of the body, are entrained to rhythmic changes in the environment (e.g. light/dark cycles). Genes responsible for this timekeeping are named core-clock genes, which through transcriptional feedback interactions mediated by transcription factor binding to Ebox/RRE/Dbox elements can generate oscillatory activity of their expression. By regulating the transcription of other clock-controlled genes (CCGs) circadian information is transmitted to tissue and organ levels. Recent studies have indicated that there is a considerable variability of clock-controlled gene expression between tissues both with respect to the circadian genes that are regulated and to their phase lags. In this work, a mathematical model was adapted to explore the dynamics of core-clock and clock-controlled genes measured in four tissues of the rat namely liver, muscle, adipose, and lung. The model efficiently described the synchronous rhythmicity of core-clock genes and further predicted that their phases are mainly regulated by Per2 and Cry1 transcriptional delays and Rev-Erba and Cry1 degradation rates. Similarly, after mining databases for potential Ebox/RRE/Dbox elements in the promoter region of clock-controlled genes, the phase variabilities of the same genes between different tissues were described. The analysis suggests that inter-tissue circadian variability of the same clock-controlled genes is an inherent component of homeostatic function and may arise due to different transcription factor activities on Ebox/RRE/Dbox elements.
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Affiliation(s)
- Panteleimon D. Mavroudis
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, United States of America
| | - Debra C. DuBois
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, United States of America
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, United States of America
| | - Richard R. Almon
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, United States of America
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, United States of America
| | - William J. Jusko
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, United States of America
- * E-mail:
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Krakowiak K, Durrington HJ. The Role of the Body Clock in Asthma and COPD: Implication for Treatment. Pulm Ther 2018; 4:29-43. [PMID: 32026248 PMCID: PMC6967276 DOI: 10.1007/s41030-018-0058-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Indexed: 01/12/2023] Open
Abstract
Asthma exhibits a marked time of day variation in symptoms, airway physiology, and airway inflammation. This is also seen in chronic obstructive pulmonary disease (COPD), but to a lesser extent. Our understanding of how physiological daily rhythms are regulated by the circadian clock is increasing, and there is growing evidence that the molecular clock is important in the pathogenesis of these two airway diseases. If time of day is important, then it follows that treatment of asthma and COPD should also be tailored to the most efficacious time of the day, a concept known as 'chronotherapy'. There have been a number of studies to determine the optimal time of day at which to take medications for asthma and COPD. Some of these agents are already used 'chronotherapeutically' in practice (often at night-time). However, several studies investigating systemic and inhaled corticosteroids have consistently shown that the best time of day to take these medications for treating asthma is in the afternoon or early evening and not in the morning, when these medications are often prescribed. Future, large, randomized, placebo-controlled studies of systemic and inhaled corticosteroids in asthma and COPD are needed to inform clinical practice.
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Affiliation(s)
- Karolina Krakowiak
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Hannah J Durrington
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK.
- Wythenshawe Hospital, Manchester University NHS Foundation Trust, Southmoor Road, Wythenshawe, Manchester, M23 9LT, UK.
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Krakowiak K, Durrington HJ. The Role of the Body Clock in Asthma and COPD: Implication for Treatment. Pulm Ther 2018. [DOI: 10.1007/s41030-018-0058-6#x002a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
AbstractAsthma exhibits a marked time of day variation in symptoms, airway physiology, and airway inflammation. This is also seen in chronic obstructive pulmonary disease (COPD), but to a lesser extent. Our understanding of how physiological daily rhythms are regulated by the circadian clock is increasing, and there is growing evidence that the molecular clock is important in the pathogenesis of these two airway diseases. If time of day is important, then it follows that treatment of asthma and COPD should also be tailored to the most efficacious time of the day, a concept known as ‘chronotherapy’. There have been a number of studies to determine the optimal time of day at which to take medications for asthma and COPD. Some of these agents are already used ‘chronotherapeutically’ in practice (often at night-time). However, several studies investigating systemic and inhaled corticosteroids have consistently shown that the best time of day to take these medications for treating asthma is in the afternoon or early evening and not in the morning, when these medications are often prescribed. Future, large, randomized, placebo-controlled studies of systemic and inhaled corticosteroids in asthma and COPD are needed to inform clinical practice.
Digital Features
This article is published with a graphical abstract to facilitate understanding of the article. To view digital features for this article go to the Supplementary Information of the article.
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Mavroudis PD, DuBois DC, Almon RR, Jusko WJ. Daily variation of gene expression in diverse rat tissues. PLoS One 2018; 13:e0197258. [PMID: 29746605 PMCID: PMC5945012 DOI: 10.1371/journal.pone.0197258] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 04/30/2018] [Indexed: 11/30/2022] Open
Abstract
Circadian information is maintained in mammalian tissues by a cell-autonomous network of transcriptional feedback loops that have evolved to optimally regulate tissue-specific functions. An analysis of daily gene expression in different tissues, as well as an evaluation of inter-tissue circadian variability, is crucial for a systems-level understanding of this transcriptional circuitry. Affymetrix gene chip measurements of liver, muscle, adipose, and lung tissues were obtained from a rich time series light/dark experiment, involving 54 normal rats sacrificed at 18 time points within the 24-hr cycle. Our analysis revealed a high degree of circadian regulation with a variable distribution of phases among the four tissues. Interestingly, only a small number of common genes maintain circadian activity in all tissues, with many of them consisting of "core-clock" components with synchronous rhythms. Our results suggest that inter-tissue circadian variability is a critical component of homeostatic body function and is mediated by diverse signaling pathways that ultimately lead to highly tissue-specific transcription regulation.
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Affiliation(s)
- Panteleimon D. Mavroudis
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Debra C. DuBois
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Richard R. Almon
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - William J. Jusko
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
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The temporospatial pattern of energy metabolism coordinates the interactions between the bones and other organ systems. J Oral Biosci 2018. [DOI: 10.1016/j.job.2017.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Paganelli R, Petrarca C, Di Gioacchino M. Biological clocks: their relevance to immune-allergic diseases. Clin Mol Allergy 2018; 16:1. [PMID: 29344005 PMCID: PMC5763605 DOI: 10.1186/s12948-018-0080-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 01/02/2018] [Indexed: 01/24/2023] Open
Abstract
The 2017 Nobel Prize for Physiology or Medicine, awarded for the discoveries made in the past 15 years on the genetic and molecular mechanisms regulating many physiological functions, has renewed the attention to the importance of circadian rhythms. These originate from a central pacemaker in the suprachiasmatic nucleus in the brain, photoentrained via direct connection with melanopsin containing, intrinsically light-sensitive retinal ganglion cells, and it projects to periphery, thus creating an inner circadian rhythm. This regulates several activities, including sleep, feeding times, energy metabolism, endocrine and immune functions. Disturbances of these rhythms, mainly of wake/sleep, hormonal secretion and feeding, cause decrease in quality of life, as well as being involved in development of obesity, metabolic syndrome and neuropsychiatric disorders. Most immunological functions, from leukocyte numbers, activity and cytokine secretion undergo circadian variations, which might affect susceptibility to infections. The intensity of symptoms and disease severity show a 24 h pattern in many immunological and allergic diseases, including rheumatoid arthritis, bronchial asthma, atopic eczema and chronic urticaria. This is accompanied by altered sleep duration and quality, a major determinant of quality of life. Shift work and travel through time zones as well as artificial light pose new health threats by disrupting the circadian rhythms. Finally, the field of chronopharmacology uses these concepts for delivering drugs in synchrony with biological rhythms.
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Affiliation(s)
- Roberto Paganelli
- 1Dipartimento di Medicina e Scienze dell'invecchiamento, Università "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini, 5, 66013 Chieti, Italy.,Ce.S.I.-Me.T., Chieti, Italy
| | - Claudia Petrarca
- 1Dipartimento di Medicina e Scienze dell'invecchiamento, Università "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini, 5, 66013 Chieti, Italy.,Ce.S.I.-Me.T., Chieti, Italy
| | - Mario Di Gioacchino
- 1Dipartimento di Medicina e Scienze dell'invecchiamento, Università "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini, 5, 66013 Chieti, Italy.,Ce.S.I.-Me.T., Chieti, Italy
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Comas M, Gordon CJ, Oliver BG, Stow NW, King G, Sharma P, Ammit AJ, Grunstein RR, Phillips CL. A circadian based inflammatory response – implications for respiratory disease and treatment. SLEEP SCIENCE AND PRACTICE 2017. [DOI: 10.1186/s41606-017-0019-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Janjić K, Kurzmann C, Moritz A, Agis H. Expression of circadian core clock genes in fibroblasts of human gingiva and periodontal ligament is modulated by L-Mimosine and hypoxia in monolayer and spheroid cultures. Arch Oral Biol 2017; 79:95-99. [PMID: 28350992 DOI: 10.1016/j.archoralbio.2017.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/06/2017] [Accepted: 03/10/2017] [Indexed: 12/25/2022]
Abstract
OBJECTIVE The circadian clock is involved in a plethora of physiological processes including bone formation and tooth development. While expression of circadian core clock genes was observed in various tissues, their role in the periodontium is unclear. We hypothesized that periodontal cells express circadian core clock genes and that their levels are modulated by hypoxia mimetic agents and hypoxia. MATERIAL AND METHODS Fibroblasts of human gingiva (GF) and periodontal ligament (PDLF) in monolayer and spheroid cultures were treated with the hypoxia mimetic agent L-Mimosine (L-MIM) or hypoxia. Reverse transcription and quantitative PCR were performed to assess the impact on mRNA levels of the circadian core clock genes Clock, Bmal1, Cry1, Cry2, Per1, Per2, and Per3. RESULTS GF and PDLF expressed Clock, Bmal1, Cry1, Cry2, Per1, Per2, and Per3 in monolayer and spheroid cultures. In monolayer cultures, L-MIM significantly reduced Clock, Cry2, and Per3 mRNA expression in GF and Clock, Cry1, Cry2, Per1, and Per3 in PDLF. Hypoxia significantly reduced Clock, Cry2, and Per3 in GF and Cry1, Cry2, and Per3 in PDLF. In spheroid cultures, L-MIM significantly decreased Clock, Cry1, Cry2, and Per3 in GF and PDLF. Hypoxia significantly decreased Cry2 and Per3 in GF and Clock and Per3 in PDLF. CONCLUSIONS GF and PDLF express circadian core clock genes. The hypoxia mimetic agent L-MIM and hypoxic conditions can decrease the expression of Clock, Cry1-2 and Per1 and Per3. The specific response depends on cell type and culture model. Future studies will show how this effect contributes to periodontal health and disease.
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Affiliation(s)
- Klara Janjić
- Department of Conservative Dentistry and Periodontology, School of Dentistry, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Christoph Kurzmann
- Department of Conservative Dentistry and Periodontology, School of Dentistry, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Andreas Moritz
- Department of Conservative Dentistry and Periodontology, School of Dentistry, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Hermann Agis
- Department of Conservative Dentistry and Periodontology, School of Dentistry, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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Ayyar VS, Almon RR, DuBois DC, Sukumaran S, Qu J, Jusko WJ. Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism. J Proteomics 2017; 160:84-105. [PMID: 28315483 DOI: 10.1016/j.jprot.2017.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/15/2017] [Accepted: 03/10/2017] [Indexed: 02/07/2023]
Abstract
Corticosteroids (CS) are anti-inflammatory agents that cause extensive pharmacogenomic and proteomic changes in multiple tissues. An understanding of the proteome-wide effects of CS in liver and its relationships to altered hepatic and systemic physiology remains incomplete. Here, we report the application of a functional pharmacoproteomic approach to gain integrated insight into the complex nature of CS responses in liver in vivo. An in-depth functional analysis was performed using rich pharmacodynamic (temporal-based) proteomic data measured over 66h in rat liver following a single dose of methylprednisolone (MPL). Data mining identified 451 differentially regulated proteins. These proteins were analyzed on the basis of temporal regulation, cellular localization, and literature-mined functional information. Of the 451 proteins, 378 were clustered into six functional groups based on major clinically-relevant effects of CS in liver. MPL-responsive proteins were highly localized in the mitochondria (20%) and cytosol (24%). Interestingly, several proteins were related to hepatic stress and signaling processes, which appear to be involved in secondary signaling cascades and in protecting the liver from CS-induced oxidative damage. Consistent with known adverse metabolic effects of CS, several rate-controlling enzymes involved in amino acid metabolism, gluconeogenesis, and fatty-acid metabolism were altered by MPL. In addition, proteins involved in the metabolism of endogenous compounds, xenobiotics, and therapeutic drugs including cytochrome P450 and Phase-II enzymes were differentially regulated. Proteins related to the inflammatory acute-phase response were up-regulated in response to MPL. Functionally-similar proteins showed large diversity in their temporal profiles, indicating complex mechanisms of regulation by CS. SIGNIFICANCE Clinical use of corticosteroid (CS) therapy is frequent and chronic. However, current knowledge on the proteome-level effects of CS in liver and other tissues is sparse. While transcriptomic regulation following methylprednisolone (MPL) dosing has been temporally examined in rat liver, proteomic assessments are needed to better characterize the tissue-specific functional aspects of MPL actions. This study describes a functional pharmacoproteomic analysis of dynamic changes in MPL-regulated proteins in liver and provides biological insight into how steroid-induced perturbations on a molecular level may relate to both adverse and therapeutic responses presented clinically.
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Affiliation(s)
- Vivaswath S Ayyar
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, NY, United States
| | - Richard R Almon
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, NY, United States; Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Debra C DuBois
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, NY, United States; Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Siddharth Sukumaran
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, NY, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, NY, United States
| | - William J Jusko
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, NY, United States.
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Zhang R, Podtelezhnikov AA, Hogenesch JB, Anafi RC. Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA). J Biol Rhythms 2016; 31:244-57. [PMID: 26955841 DOI: 10.1177/0748730416631895] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Several tools use prior biological knowledge to interpret gene expression data. However, existing enrichment tools assume that variables are monotonic and incorrectly measure the distance between periodic phases. As a result, these tools are poorly suited for the analysis of the cell cycle, circadian clock, or other periodic systems. Here, we develop Phase Set Enrichment Analysis (PSEA) to incorporate prior knowledge into the analysis of periodic data. PSEA identifies biologically related gene sets showing temporally coordinated expression. Using synthetic gene sets of various sizes generated from von Mises (circular normal) distributions, we benchmarked PSEA alongside existing methods. PSEA offered enhanced sensitivity over a broad range of von Mises distributions and gene set sizes. Importantly, and unlike existing tools, the sensitivity of PSEA is independent of the mean expression phase of the set. We applied PSEA to 4 published datasets. Application of PSEA to the mouse circadian atlas revealed that several pathways, including those regulating immune and cell-cycle function, demonstrate temporal orchestration across multiple tissues. We then applied PSEA to the phase shifts following a restricted feeding paradigm. We found that this perturbation disrupts intraorgan metabolic synchrony in the liver, altering the timing between anabolic and catabolic pathways. Reanalysis of expression data using custom gene sets derived from recent ChIP-seq results revealed circadian transcriptional targets bound exclusively by CLOCK, independently of BMAL1, differ from other exclusive circadian output genes and have well-synchronized phases. Finally, we used PSEA to compare 2 cell-cycle datasets. PSEA increased the apparent biological overlap while also revealing evidence of cell-cycle dysregulation in these cancer cells. To encourage its use by the community, we have implemented PSEA as a Java application. In sum, PSEA offers a powerful new tool to investigate large-scale, periodic data for biological insight.
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Affiliation(s)
- Ray Zhang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Alexei A Podtelezhnikov
- Department of Genetics and Pharmacogenomics, Merck Research Laboratories, West Point, Pennsylvania
| | - John B Hogenesch
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, Ohio
| | - Ron C Anafi
- Department of Medicine and Center for Sleep and Circadian Neurobiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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42
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Numaguchi S, Esumi M, Sakamoto M, Endo M, Ebihara T, Soma H, Yoshida A, Tokuhashi Y. Passive cigarette smoking changes the circadian rhythm of clock genes in rat intervertebral discs. J Orthop Res 2016; 34:39-47. [PMID: 25939642 DOI: 10.1002/jor.22941] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 05/01/2015] [Indexed: 02/04/2023]
Abstract
We aimed to elucidate the molecular changes in intervertebral discs (IVDs) caused by passive smoking. Rats were subjected to 8 weeks of passive smoking; thereafter, their lumbar vertebrae were harvested. The annulus fibrosus and cartilage endplate (AF/CEP) were harvested together, and the nucleus pulposus (NP) was isolated separately. The expression of 27,342 rat genes was analyzed. In 3 "nonsmoking" rats, 96 of 112 genes whose expression varied ≥10-fold between the AF/CEP and NP were more highly expressed in the AF/CEP. With these differentially expressed genes, we uncovered novel AF/CEP and NP marker genes and indicated their possible novel functions. Although passive smoking induced less marked alteration in the gene expression profiles of both the AF/CEP and NP, multiple clock-related genes showed altered expression. These genes were expressed with a circadian rhythm in IVD cells, and most genes showed a phase shift of -6 to -9 h induced by passive smoking. Some clock-related genes showed abolished oscillation in the NP. Passive smoking also changed the expression levels of proteases and protease inhibitors and reduced the expression of NP marker genes. Thus, passive smoking induces changes in the circadian rhythm of a peripheral clock (IVD clock) that might be involved in molecular events related to IVD degeneration.
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Affiliation(s)
- Shumpei Numaguchi
- Department of Therapeutics for Aging Locomotive Disorders, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Pathology, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Orthopedic Surgery, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Mariko Esumi
- Department of Therapeutics for Aging Locomotive Disorders, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Pathology, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Mika Sakamoto
- Department of Therapeutics for Aging Locomotive Disorders, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Pathology, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Michiko Endo
- Department of Therapeutics for Aging Locomotive Disorders, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Pathology, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Takayuki Ebihara
- Department of Therapeutics for Aging Locomotive Disorders, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Pathology, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Orthopedic Surgery, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Hirotoki Soma
- Department of Therapeutics for Aging Locomotive Disorders, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Pathology, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Orthopedic Surgery, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Akio Yoshida
- Department of Therapeutics for Aging Locomotive Disorders, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Pathology, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Orthopedic Surgery, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Yasuaki Tokuhashi
- Department of Therapeutics for Aging Locomotive Disorders, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Orthopedic Surgery, Nihon University School of Medicine, Tokyo, 173-8610, Japan
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Sundar IK, Yao H, Sellix MT, Rahman I. Circadian clock-coupled lung cellular and molecular functions in chronic airway diseases. Am J Respir Cell Mol Biol 2015; 53:285-90. [PMID: 25938935 DOI: 10.1165/rcmb.2014-0476tr] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Airway diseases are associated with abnormal circadian rhythms of lung function, reflected in daily changes of airway caliber, airway resistance, respiratory symptoms, and abnormal immune-inflammatory responses. Circadian rhythms are generated at the cellular level by an autoregulatory feedback loop of interlocked transcription factors collectively referred to as clock genes. The molecular clock is altered by cigarette smoke, LPS, and bacterial and viral infections in mouse and human lungs and in patients with chronic airway diseases. Stress-mediated post-translational modification of molecular clock proteins, brain and muscle aryl hydrocarbon receptor nuclear translocator-like 1 (BMAL1) and PERIOD 2, is associated with a reduction in the activity/level of the deacetylase sirtuin 1 (SIRT1). Similarly, the levels of the nuclear receptor REV-ERBα and retinoic acid receptor-related orphan receptor α (ROR α), critical regulators of Bmal1 expression, are altered by environmental stresses. Molecular clock dysfunction is implicated in immune and inflammatory responses, DNA damage response, and cellular senescence. The molecular clock in the lung also regulates the timing of glucocorticoid sensitivity and phasic responsiveness to inflammation. Herein, we review our current understanding of clock-controlled cellular and molecular functions in the lungs, the impact of clock dysfunction in chronic airway disease, and the response of the pulmonary clock to different environmental perturbations. Furthermore, we discuss the evidence for candidate signaling pathways, such as the SIRT1-BMAL1-REV-ERBα axis, as novel targets for chronopharmacological management of chronic airway diseases.
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Affiliation(s)
- Isaac K Sundar
- Departments of 1 Environmental Medicine, Lung Biology and Disease Program, and
| | - Hongwei Yao
- Departments of 1 Environmental Medicine, Lung Biology and Disease Program, and
| | - Michael T Sellix
- 2 Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Rochester Medical Center, Rochester, New York
| | - Irfan Rahman
- Departments of 1 Environmental Medicine, Lung Biology and Disease Program, and
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Hirai T, Tanaka K, Togari A. α1B-Adrenergic receptor signaling controls circadian expression of Tnfrsf11b by regulating clock genes in osteoblasts. Biol Open 2015; 4:1400-9. [PMID: 26453621 PMCID: PMC4728343 DOI: 10.1242/bio.012617] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Circadian clocks are endogenous and biological oscillations that occur with a period of <24 h. In mammals, the central circadian pacemaker is localized in the suprachiasmatic nucleus (SCN) and is linked to peripheral tissues through neural and hormonal signals. In the present study, we investigated the physiological function of the molecular clock on bone remodeling. The results of loss-of-function and gain-of-function experiments both indicated that the rhythmic expression of Tnfrsf11b, which encodes osteoprotegerin (OPG), was regulated by Bmal1 in MC3T3-E1 cells. We also showed that REV-ERBα negatively regulated Tnfrsf11b as well as Bmal1 in MC3T3-E1 cells. We systematically investigated the relationship between the sympathetic nervous system and the circadian clock in osteoblasts. The administration of phenylephrine, a nonspecific α1-adrenergic receptor (AR) agonist, stimulated the expression of Tnfrsf11b, whereas the genetic ablation of α1B-AR signaling led to the alteration of Tnfrsf11b expression concomitant with Bmal1 and Per2 in bone. Thus, this study demonstrated that the circadian regulation of Tnfrsf11b was regulated by the clock genes encoding REV-ERBα (Nr1d1) and Bmal1 (Bmal1, also known as Arntl), which are components of the core loop of the circadian clock in osteoblasts. Summary: This study demonstrates that the circadian regulation of TNFRSF11B is regulated by the clock genes Nr1d1 and Arntl, which are components of the core loop of the circadian clock in osteoblasts, providing a molecular mechanism for the control of bone remodelling by circadian rhythms.
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Affiliation(s)
- Takao Hirai
- Department of Pharmacology, School of Dentistry, Aichi-Gakuin University, Nagoya 464-8650, Japan
| | - Kenjiro Tanaka
- Department of Pharmacology, School of Dentistry, Aichi-Gakuin University, Nagoya 464-8650, Japan
| | - Akifumi Togari
- Department of Pharmacology, School of Dentistry, Aichi-Gakuin University, Nagoya 464-8650, Japan
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Sundar IK, Yao H, Sellix MT, Rahman I. Circadian molecular clock in lung pathophysiology. Am J Physiol Lung Cell Mol Physiol 2015; 309:L1056-75. [PMID: 26361874 DOI: 10.1152/ajplung.00152.2015] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/08/2015] [Indexed: 02/06/2023] Open
Abstract
Disrupted daily or circadian rhythms of lung function and inflammatory responses are common features of chronic airway diseases. At the molecular level these circadian rhythms depend on the activity of an autoregulatory feedback loop oscillator of clock gene transcription factors, including the BMAL1:CLOCK activator complex and the repressors PERIOD and CRYPTOCHROME. The key nuclear receptors and transcription factors REV-ERBα and RORα regulate Bmal1 expression and provide stability to the oscillator. Circadian clock dysfunction is implicated in both immune and inflammatory responses to environmental, inflammatory, and infectious agents. Molecular clock function is altered by exposomes, tobacco smoke, lipopolysaccharide, hyperoxia, allergens, bleomycin, as well as bacterial and viral infections. The deacetylase Sirtuin 1 (SIRT1) regulates the timing of the clock through acetylation of BMAL1 and PER2 and controls the clock-dependent functions, which can also be affected by environmental stressors. Environmental agents and redox modulation may alter the levels of REV-ERBα and RORα in lung tissue in association with a heightened DNA damage response, cellular senescence, and inflammation. A reciprocal relationship exists between the molecular clock and immune/inflammatory responses in the lungs. Molecular clock function in lung cells may be used as a biomarker of disease severity and exacerbations or for assessing the efficacy of chronotherapy for disease management. Here, we provide a comprehensive overview of clock-controlled cellular and molecular functions in the lungs and highlight the repercussions of clock disruption on the pathophysiology of chronic airway diseases and their exacerbations. Furthermore, we highlight the potential for the molecular clock as a novel chronopharmacological target for the management of lung pathophysiology.
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Affiliation(s)
- Isaac K Sundar
- Department of Environmental Medicine, Lung Biology and Disease Program, University of Rochester Medical Center, Rochester, New York; and
| | - Hongwei Yao
- Department of Environmental Medicine, Lung Biology and Disease Program, University of Rochester Medical Center, Rochester, New York; and
| | - Michael T Sellix
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Rochester Medical Center, Rochester, New York
| | - Irfan Rahman
- Department of Environmental Medicine, Lung Biology and Disease Program, University of Rochester Medical Center, Rochester, New York; and
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46
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Sundar IK, Ahmad T, Yao H, Hwang JW, Gerloff J, Lawrence BP, Sellix MT, Rahman I. Influenza A virus-dependent remodeling of pulmonary clock function in a mouse model of COPD. Sci Rep 2015; 4:9927. [PMID: 25923474 PMCID: PMC4413879 DOI: 10.1038/srep09927] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/23/2015] [Indexed: 12/18/2022] Open
Abstract
Daily oscillations of pulmonary function depend on the rhythmic activity of the circadian timing system. Environmental tobacco/cigarette smoke (CS) disrupts circadian clock leading to enhanced inflammatory responses. Infection with influenza A virus (IAV) increases hospitalization rates and death in susceptible individuals, including patients with Chronic Obstructive Pulmonary Disease (COPD). We hypothesized that molecular clock disruption is enhanced by IAV infection, altering cellular and lung function, leading to severity in airway disease phenotypes. C57BL/6J mice exposed to chronic CS, BMAL1 knockout (KO) mice and wild-type littermates were infected with IAV. Following infection, we measured diurnal rhythms of clock gene expression in the lung, locomotor activity, pulmonary function, inflammatory, pro-fibrotic and emphysematous responses. Chronic CS exposure combined with IAV infection altered the timing of clock gene expression and reduced locomotor activity in parallel with increased lung inflammation, disrupted rhythms of pulmonary function, and emphysema. BMAL1 KO mice infected with IAV showed pronounced detriments in behavior and survival, and increased lung inflammatory and pro-fibrotic responses. This suggests that remodeling of lung clock function following IAV infection alters clock-dependent gene expression and normal rhythms of lung function, enhanced emphysematous and injurious responses. This may have implications for the pathobiology of respiratory virus-induced airway disease severity and exacerbations.
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Affiliation(s)
- Isaac K. Sundar
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - Tanveer Ahmad
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - Hongwei Yao
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - Jae-woong Hwang
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - Janice Gerloff
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - B. Paige Lawrence
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - Michael T. Sellix
- Department of Medicine, Division of Endocrinology, Diabetes and
Metabolism, University of Rochester Medical Center, Rochester,
NY, USA
| | - Irfan Rahman
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
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47
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Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch JB. Machine learning helps identify CHRONO as a circadian clock component. PLoS Biol 2014; 12:e1001840. [PMID: 24737000 PMCID: PMC3988006 DOI: 10.1371/journal.pbio.1001840] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 03/07/2014] [Indexed: 12/03/2022] Open
Abstract
Over the last decades, researchers have characterized a set of "clock genes" that drive daily rhythms in physiology and behavior. This arduous work has yielded results with far-reaching consequences in metabolic, psychiatric, and neoplastic disorders. Recent attempts to expand our understanding of circadian regulation have moved beyond the mutagenesis screens that identified the first clock components, employing higher throughput genomic and proteomic techniques. In order to further accelerate clock gene discovery, we utilized a computer-assisted approach to identify and prioritize candidate clock components. We used a simple form of probabilistic machine learning to integrate biologically relevant, genome-scale data and ranked genes on their similarity to known clock components. We then used a secondary experimental screen to characterize the top candidates. We found that several physically interact with known clock components in a mammalian two-hybrid screen and modulate in vitro cellular rhythms in an immortalized mouse fibroblast line (NIH 3T3). One candidate, Gene Model 129, interacts with BMAL1 and functionally represses the key driver of molecular rhythms, the BMAL1/CLOCK transcriptional complex. Given these results, we have renamed the gene CHRONO (computationally highlighted repressor of the network oscillator). Bi-molecular fluorescence complementation and co-immunoprecipitation demonstrate that CHRONO represses by abrogating the binding of BMAL1 to its transcriptional co-activator CBP. Most importantly, CHRONO knockout mice display a prolonged free-running circadian period similar to, or more drastic than, six other clock components. We conclude that CHRONO is a functional clock component providing a new layer of control on circadian molecular dynamics.
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Affiliation(s)
- Ron C. Anafi
- Division of Sleep Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yool Lee
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Trey K. Sato
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Anand Venkataraman
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Chidambaram Ramanathan
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, United States of America
| | - Ibrahim H. Kavakli
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Michael E. Hughes
- Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, United States of America
| | - Julie E. Baggs
- Department of Pharmacology, Morehouse School of Medicine, Atlanta, Georgia, United States of America
| | - Jacqueline Growe
- Division of Sleep Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Andrew C. Liu
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, United States of America
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - John B. Hogenesch
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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Li H, Wang C, Hu J, Tan J. A study on circadian rhythm disorder of rat lung tissue caused by mechanical ventilation induced lung injury. Int Immunopharmacol 2014; 18:249-54. [DOI: 10.1016/j.intimp.2013.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 12/05/2013] [Accepted: 12/05/2013] [Indexed: 10/25/2022]
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49
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Liu ZP, Zhang W, Horimoto K, Chen L. Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data. IET Syst Biol 2014; 7:143-52. [PMID: 24067414 DOI: 10.1049/iet-syb.2012.0062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
With rapid accumulation of functional relationships between biological molecules, knowledge-based networks have been constructed and stocked in many databases. These networks provide curated and comprehensive information for functional linkages among genes and proteins, whereas their activities are highly related with specific phenotypes and conditions. To evaluate a knowledge-based network in a specific condition, the consistency between its structure and conditionally specific gene expression profiling data are an important criterion. In this study, the authors propose a Gaussian graphical model to evaluate the documented regulatory networks by the consistency between network architectures and time course gene expression profiles. They derive a dynamic Bayesian network model to evaluate gene regulatory networks in both simulated and true time course microarray data. The regulatory networks are evaluated by matching network structure with gene expression to achieve consistency measurement. To demonstrate the effectiveness of the authors method, they identify significant regulatory networks in response to the time course of circadian rhythm. The knowledge-based networks are screened and ranked by their structural consistencies with dynamic gene expression profiling.
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Abstract
It is characteristic of asthma that symptoms worsen overnight, particularly in the early hours of the morning. Nocturnal symptoms in asthma are common and are an important indicator for escalation of treatment. An extensive body of research has demonstrated that nocturnal symptoms of cough and dyspnea are accompanied by circadian variations in airway inflammation and physiologic variables, including airflow limitation and airways hyper-responsiveness. The molecular apparatus that underpins circadian variations, controlled by so called 'clock' genes, has recently been characterised. Clock genes control circadian rhythms both centrally, in the suprachiasmatic nucleus of the brain and peripherally, within every organ of the body. Here, we will discuss how clock genes regulate circadian rhythms. We will focus particularly on the peripheral lung clock and the peripheral immune clock and discuss how these might relate to both the pathogenesis and treatment of asthma.
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Affiliation(s)
- Hannah J Durrington
- Faculty of Medical and Human Sciences, Institute of Human Development, , Manchester, UK
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