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Neumann E. Spatial Multiomics Toward Understanding Neurological Systems. JOURNAL OF MASS SPECTROMETRY : JMS 2025; 60:e5143. [PMID: 40360168 PMCID: PMC12074838 DOI: 10.1002/jms.5143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Revised: 04/15/2025] [Accepted: 04/29/2025] [Indexed: 05/15/2025]
Abstract
Dynamic biological processes in the brain involve complex interactions between various cell types, and these interactions span multiple biological scales. Each of these domains are crucial in maintaining brain health. Traditional methods, such as transcriptomics and protein labeling, provide valuable insights but fail to capture the full molecular landscape of neurological function. Multimodal imaging, combining multiple imaging techniques, offers a more comprehensive approach to studying biological systems by integrating different omics technologies. Spatial metabolomics involves using techniques like mass spectrometry imaging to enable detection of metabolites within their native tissue context and reveals functional roles that are crucial for understanding disease. Spatial transcriptomics and proteomics contribute information on gene expression and protein function but face challenges in resolution and integration with other omics approaches. Combining metabolomics, transcriptomics, and proteomics will enhance our understanding of cellular interactions, but challenges remain in optimizing sample preparation, maintaining molecular integrity, and integrating data across omics layers. Future advancements in spatial multiomics, incorporating epigenetics and extending to whole-body or nanoscale imaging, will significantly advance our understanding of neuroscience and complex diseases like Alzheimer's disease or autism spectrum disorder.
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2
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Kuo LT, Lu HY, Chen YH. Traumatic brain injury-induced disruption of the circadian clock. J Mol Med (Berl) 2024; 102:403-414. [PMID: 38285094 PMCID: PMC10879350 DOI: 10.1007/s00109-024-02416-w] [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: 02/22/2023] [Revised: 12/16/2023] [Accepted: 01/03/2024] [Indexed: 01/30/2024]
Abstract
Disturbances in the circadian rhythm have been reported in patients following traumatic brain injury (TBI). However, the rhythmic expression of circadian genes in peripheral blood leukocytes (PBL) following TBI has not yet been studied. The messenger ribonucleic acid (mRNA) expression of period 1 (Per1), Per2, Per3, cryptochrome 1 (Cry1), Cry2, brain and muscle aryl hydrocarbon receptor nuclear translocator-like 1 (Bmal1), and circadian locomotor output cycles kaput (Clock) was quantified in PBLs from sham-operated rats and rats with acute subdural hematoma (ASDH) over a 48-h period. The rectal temperature of the animals was measured every 4 h over 2 days. The mesor, rhythm, amplitude, and acrophase were estimated using cosinor analysis. Cosinor analysis revealed that Per2, Cry1, and Bmal1 mRNAs were rhythmically expressed in the PBLs of sham-operated rats. In contrast, fluctuations in rhythmic expression were not observed following ASDH. The rectal temperature of sham-operated rats also exhibited rhythmicity. ASDH rats had a disrupted rectal temperature rhythm, a diminished amplitude, and an acrophase shift. TBI with ASDH results in dysregulated expression of some circadian genes and changes in body temperature rhythm. Further research is required to understand the pathophysiology of altered circadian networks following TBI. KEY MESSAGES: First to investigate the mRNA expression of circadian genes in PBLs of ASDH rats. ASDH rats had disrupted rhythmicity of Per2, Cry1, and Bmal1 mRNA expression. Cosinor analysis showed that ASDH rats had a disrupted rectal temperature rhythm.
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Affiliation(s)
- Lu-Ting Kuo
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, 7 Chun-Shan South Road, Taipei, 100, Taiwan.
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Yun-Lin Branch, Douliu, Yunlin, 640, Taiwan.
| | - Hsueh-Yi Lu
- Department of Industrial Engineering and Management, National Yunlin University of Science and Technology, Douliu, Yunlin, 640, Taiwan
| | - Yi-Hsing Chen
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, 7 Chun-Shan South Road, Taipei, 100, Taiwan
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3
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Valachovic AC, Chaves JN, DeMoranville KJ, Garbenis T, Nguyen BMH, Hughes M, Huss JM, Schaeffer PJ. Manipulation of photoperiod induces fat storage, but not fat mobilization in the migratory songbird, Dumetella carolinensis (Gray Catbird). J Comp Physiol B 2023; 193:569-580. [PMID: 37728689 DOI: 10.1007/s00360-023-01508-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 07/27/2023] [Accepted: 08/05/2023] [Indexed: 09/21/2023]
Abstract
The annual cycle of migratory birds requires significant phenotypic remodeling. We sought to induce the migratory phenotype in Gray Catbirds by exposing them to a short-day light cycle. While adipose storage was stimulated, exceeding that typically seen in wild birds, other aspects of the migratory phenotype were unchanged. Of particular interest, the rate of lipid export from excised adipose tissue was nearly halved. This is in contrast to wild migratory birds in which lipid export rates are increased. These data suggest that exposure to an altered light cycle only activated the lipid storage program while inhibiting the lipid transport program. The factors governing lipid mobilization and transport remain to be elucidated.
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Affiliation(s)
- Abigail C Valachovic
- Department of Biology, Miami University, 700 E. High St., 212 Pearson Hall, Oxford, OH, 45056, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
| | - Jussara N Chaves
- Department of Biology, Miami University, 700 E. High St., 212 Pearson Hall, Oxford, OH, 45056, USA
- Rua Maria Do Bom Sucesso de Proença Moraes, No. 200 - Casa c34, São Paulo, 18214-570, Brazil
| | - Kristen J DeMoranville
- Department of Biology, Miami University, 700 E. High St., 212 Pearson Hall, Oxford, OH, 45056, USA
- Department of Natural Resources Science, University of Rhode Island, Kingston, RI, 02881, USA
| | - Taylor Garbenis
- Department of Statistics, Miami University, Oxford, OH, 45056, USA
- Nationwide Insurance, Columbus, OH, 43215, USA
| | - Boi Minh Ha Nguyen
- Department of Statistics, Miami University, Oxford, OH, 45056, USA
- Deloitte & Touche LLP, Chicago, IL, 60601, USA
| | - Michael Hughes
- Department of Statistics, Miami University, Oxford, OH, 45056, USA
| | - Janice M Huss
- Department of Molecular and Cellular Endocrinology, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
- Center for Cardiovascular Research, Cardiovascular Division, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Paul J Schaeffer
- Department of Biology, Miami University, 700 E. High St., 212 Pearson Hall, Oxford, OH, 45056, USA.
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Li G, Xiong H, Saeed K, Ma R, Xing Y, Bi Y, Li C, Huang J, Zhang Y. Comparative toxicity analysis of corannulene and benzo[a]pyrene in mice. Toxicol Lett 2020; 331:130-142. [PMID: 32417428 DOI: 10.1016/j.toxlet.2020.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/27/2020] [Accepted: 05/03/2020] [Indexed: 11/26/2022]
Abstract
Increasing production of corannulene (COR), a non-planar polycyclic aromatic hydrocarbon (PAH) with promising applications in many fields, has raised a concern about its potential toxic effects. However, no study has been undertaken to evaluate its metabolism and toxicity in mammals. In this study, the acute toxicities of COR in mice were compared with benzo[apyrene (BaP), a typical planar PAH with almost the same molecular weight. After 3-day exposures, the concentrations of COR in both plasma and tissues of mice were higher than that of BaP. However, blood chemistry and tissue weight monitoring showed no observable toxicities in COR-exposed mice. Compared to BaP, exposure to COR resulted in less activation of the aryl hydrocarbon receptor (AhR) and thus less induction of hepatic cytochrome P450 1A(CYP1A) enzymes, which play a critical role in metabolism of both COR and BaP. Additionally, COR also elicited less oxidative stress and microbiota alteration in the intestine than did BaP. RNA-seq analysis revealed that liver transcriptomes are responsive to COR and BaP, with less alterations observed in COR-exposed mice. Unlike BaP, exposure to COR had no effects on hepatic lipid and xenobiotic metabolism pathways. Nonetheless, COR appeared to alter the mRNA expressions of genes involved in carcinogenicity, oxidative stress, and immune-suppression. To conclude, this study for the first time unveils a comparative understanding of the acute toxic effects of COR to BaP in mice, and provides crucial insights into the future safety assessment of COR.
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Affiliation(s)
- Gentao Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Hui Xiong
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Khawar Saeed
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ruicong Ma
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Yufeng Xing
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Yajuan Bi
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Caiyu Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Jianhui Huang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Youcai Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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5
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Kovač U, Skubic C, Bohinc L, Rozman D, Režen T. Oxysterols and Gastrointestinal Cancers Around the Clock. Front Endocrinol (Lausanne) 2019; 10:483. [PMID: 31379749 PMCID: PMC6653998 DOI: 10.3389/fendo.2019.00483] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/03/2019] [Indexed: 12/24/2022] Open
Abstract
This review focuses on the role of oxidized sterols in three major gastrointestinal cancers (hepatocellular carcinoma, pancreatic, and colon cancer) and how the circadian clock affects the carcinogenesis by regulating the lipid metabolism and beyond. While each field of research (cancer, oxysterols, and circadian clock) is well-studied within their specialty, little is known about the intertwining mechanisms and how these influence the disease etiology in each cancer type. Oxysterols are involved in pathology of these cancers, but final conclusions about their protective or damaging effects are elusive, since the effect depends on the type of oxysterol, concentration, and the cell type. Oxysterol concentrations, the expression of key regulators liver X receptors (LXR), farnesoid X receptor (FXR), and oxysterol-binding proteins (OSBP) family are modulated in tumors and plasma of cancer patients, exposing these proteins and selected oxysterols as new potential biomarkers and drug targets. Evidence about how cholesterol/oxysterol pathways are intertwined with circadian clock is building. Identified key contact points are different forms of retinoic acid receptor related orphan receptors (ROR) and LXRs. RORs and LXRs are both regulated by sterols/oxysterols and the circadian clock and in return also regulate the same pathways, representing a complex interplay between sterol metabolism and the clock. With this in mind, in addition to classical therapies to modulate cholesterol in gastrointestinal cancers, such as the statin therapy, the time is ripe also for therapies where time and duration of the drug application is taken as an important factor for successful therapies. The final goal is the personalized approach with chronotherapy for disease management and treatment in order to increase the positive drug effects.
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Cheng A, Zhang Y, Mei H, Fang S, Ji P, Yang J, Yu L, Guo W. Construction of recombinant pEGFP-N1-hPer2 plasmid and its expression in osteosarcoma cells. Oncol Lett 2016; 11:2768-2772. [PMID: 27073550 PMCID: PMC4812405 DOI: 10.3892/ol.2016.4291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 11/10/2015] [Indexed: 01/26/2023] Open
Abstract
The aim of this study was to construct the eukaryotic expression vector pEGFP-N1-hPer2 and assess its expression in the human osteosarcoma cell line MG63. Total mRNA was extracted from human osteosarcoma MG63 cells, the human period 2 (hPer2) gene was obtained by reverse transcription-polymerase chain reaction (RT-PCR) and cloned into the pEGFP-N1 vector, then the recombinant pEGFP-N1-hPer2 plasmid was constructed and transfected into MG63 cells using Lipofectamine 2000. The expression of hPer2 in MG63 cells was measured by quantitative RT-PCR and western blot analysis. The accurate construction of pEGFP-N1-hPer2 was verified by double enzyme digestion and DNA sequencing. hPer2 gene expression in the transfected cells was assessed by RT-qPCR and western blot analysis. In conclusion, the recombinant pEGFP-N1-hPer2 plasmid was constructed successfully, and expressed effectively in MG63 cells.
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Affiliation(s)
- Anyuan Cheng
- Orthopedic Department, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Yan Zhang
- Department of Cardiology, The General Hospital of Fengfeng Group Co., Ltd., Handan, Hebei 056200, P.R. China
| | - Hongjun Mei
- Orthopedic Department, Wuhan No. 5 Hospital, Wuhan, Hubei 430050, P.R. China
| | - Shuo Fang
- Orthopedic Department, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Peng Ji
- Orthopedic Department, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Jian Yang
- Orthopedic Department, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Ling Yu
- Orthopedic Department, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Weichun Guo
- Orthopedic Department, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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Han X, Ding X, Xu LX, Liu MH, Feng X. [Expression profiles of miRNA-182 and Clock mRNA in the pineal gland of neonatal rats with hypoxic-ischemic brain damage]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016; 18:270-276. [PMID: 26975828 PMCID: PMC7389990 DOI: 10.7499/j.issn.1008-8830.2016.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/26/2016] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To study the changes of miRNA expression in the pineal gland of neonatal rats with hypoxic-ischemic brain damage (HIBD) and the possible roles of miRNA in the pathogenesis of circadian rhythm disturbance after HIBD. METHODS Seven-day-old Sprague-Dawley (SD) rats were randomly divided into 2 groups: HIBD and sham-operated. HIBD was induced according to the Rice-Vannucci method. The pineal glands were obtained 24 hours after the HIBD event. The expression profiles of miRNAs were determined using GeneChip technigue and quantitative real-time PCR (RT-PCR). Then the miRNA which was highly expressed was selected. The expression levels of the chosen miRNA were detected in different tissues (lungs, intestines, stomach, kidneys, cerebral cortex, pineal gland). RT-PCR analysis was performed to measure the expression profiles of the chosen miRNA and the targeted gene Clock mRNA in the pineal gland at 0, 24, 48 and 72 hours after HIBD. RESULTS miRNA-182 that met the criteria was selected by GeneChip and RT-PCR. miRNA-182 was highly expressed in the pineal gland. Compared with the sham-operated group, the expression of miRNA-182 was significantly up-regulated in the pineal gland at 24 and 48 hours after HIBD (P<0.05). Compared with the sham-operated group, Clock mRNA expression in the HIBD group increased at 0 hour after HIBD, decreased at 48 hours after HIBD and increased at 72 hours after HIBD (P<0.05). CONCLUSIONS miRNA-182 may be involved in the pathogenesis of circadian rhythm disturbance after HIBD.
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Affiliation(s)
- Xing Han
- Department of Neonatology, Children's Hospital of Soochow University, Suzhou, Jiangsu 215000, China.
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8
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Cheng AY, Zhang Y, Mei HJ, Fang S, Ji P, Yang J, Yu L, Guo WC. Construction of a plasmid for overexpression of human circadian gene period2 and its biological activity in osteosarcoma cells. Tumour Biol 2015; 36:3735-43. [DOI: 10.1007/s13277-014-3013-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 12/23/2014] [Indexed: 02/07/2023] Open
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9
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Kawasaki H, Doi R, Ito K, Shimoda M, Ishida N. The circadian binding of CLOCK protein to the promoter of C/ebpα gene in mouse cells. PLoS One 2013; 8:e58221. [PMID: 23505471 PMCID: PMC3594305 DOI: 10.1371/journal.pone.0058221] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 02/01/2013] [Indexed: 11/30/2022] Open
Abstract
C/EBPα plays important roles in metabolism as well as in the maintenance of energy homeostasis. Here we describe loss of the circadian oscillation of C/ebpα expression in liver of Clock mutant mice. Reporter assays indicate Clock and Bmal significantly induced C/ebpα gene expression whereas Cry suppressed. Real time reporter assays showed that two mutated E-boxes disrupted C/ebpα promoter dependent-oscillation. Chromatin immunoprecipitation suggests Clock can bind to two E-boxes in the C/ebpα promoter with a circadian manner in vivo. Thus, C/ebpα gene transcription is under circadian control of a core clock component, Clock. The data suggests that circadian disturbances may affect metabolic abnormalities through the C/ebpα pathway in liver.
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Affiliation(s)
- Haruhisa Kawasaki
- Ishida Group of Clock Gene, Biomedical Research Institute, National Institute of Advanced Science and Technology (AIST) 6-5 Central, Tsukuba, Ibaraki, Japan
| | - Ryosuke Doi
- Ishida Group of Clock Gene, Biomedical Research Institute, National Institute of Advanced Science and Technology (AIST) 6-5 Central, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, Tsukuba University, Tsukuba, Ibaraki, Japan
- Division of Cell Physiology, Department of Physiology and Cell Biology, Graduate School of Medicine, Kobe University, Kobe, Hyogo, Japan
| | - Kumpei Ito
- Ishida Group of Clock Gene, Biomedical Research Institute, National Institute of Advanced Science and Technology (AIST) 6-5 Central, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, Tsukuba University, Tsukuba, Ibaraki, Japan
| | - Masami Shimoda
- Division of Insect Sciences, National Institute of Agrobiological Science, Tsukuba, Ibaraki, Japan
| | - Norio Ishida
- Ishida Group of Clock Gene, Biomedical Research Institute, National Institute of Advanced Science and Technology (AIST) 6-5 Central, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, Tsukuba University, Tsukuba, Ibaraki, Japan
- * E-mail:
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Xie X, Yang S, Zou Y, Cheng S, Wang Y, Jiang Z, Xiao J, Wang Z, Liu Y. Influence of the core circadian gene "Clock" on obesity and leptin resistance in mice. Brain Res 2012; 1491:147-55. [PMID: 23159716 DOI: 10.1016/j.brainres.2012.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 10/25/2012] [Accepted: 11/07/2012] [Indexed: 11/28/2022]
Abstract
Alterations in metabolism could be due to cell-autonomous effects associated with altered expression of Clock in central nervous system feeding centers and/or peripheral tissues involved in metabolism. Clock mutant mice are hyperphagic and obese, which indicates that Clock is related to obesity. In the present study, we used intracerebroventricular injection of recombinant adenoviral vector harboring Clock genes to explore the role of Clock on diet induced obesity and the mechanisms involved in leptin resistance and leptin signaling in mice. The results demonstrated that expression of Clock in the arcuate nucleus of diet induced obesity mice was down-regulated. The recombinant adenoviral vector harboring Clock genes could reduce obesity indexes of diet induced obesity mice including body weight, BMI and total fat mass, attenuate hyperleptinemia, increase leptin sensitivity and decrease accumulated suppressor of cytokine signaling-3 in the arcuate nucleus. These results indicate that Clock plays an important role on obesity, which may be involved in leptin resistance and regulation of suppressor of cytokine signaling-3 in arcuate nucleus.
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Affiliation(s)
- Xiaoping Xie
- The Medical Center of Dujiangyan, Dujiangyan, Chengdu, Sichuan, PR China
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Sohur US, Arlotta P, Macklis JD. Developmental Controls are Re-Expressed during Induction of Neurogenesis in the Neocortex of Young Adult Mice. Front Neurosci 2012; 6:12. [PMID: 22347158 PMCID: PMC3272649 DOI: 10.3389/fnins.2012.00012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 01/18/2012] [Indexed: 11/13/2022] Open
Abstract
Whether induction of low-level neurogenesis in normally non-neurogenic regions of the adult brain mimics aspects of developmental neurogenesis is currently unknown. Previously, we and others identified that biophysically induced, neuron subtype-specific apoptosis in mouse neocortex results in induction of neurogenesis of limited numbers of subtype-appropriate projection neurons with axonal projections to either thalamus or spinal cord, depending on the neuron subtype activated to undergo targeted apoptosis. Here, we test the hypothesis that developmental genes from embryonic corticogenesis are re-activated, and that some of these genes might underlie induction of low-level adult neocortical neurogenesis. We directly investigated this hypothesis via microarray analysis of microdissected regions of young adult mouse neocortex undergoing biophysically activated targeted apoptosis of neocortical callosal projection neurons. We compared the microarray results identifying differentially expressed genes with public databases of embryonic developmental genes. We find that, following activation of subtype-specific neuronal apoptosis, three distinct sets of normal developmental genes are selectively re-expressed in neocortical regions of induced neurogenesis in young adult mice: (1) genes expressed by subsets of progenitors and immature neurons in the developing ventricular and/or subventricular zones; (2) genes normally expressed by developmental radial glial progenitors; and (3) genes involved in synaptogenesis. Together with previous results, the data indicate that at least some developmental molecular controls over embryonic neurogenesis can be re-activated in the setting of induction of neurogenesis in the young adult neocortex, and suggest that some of these activate and initiate adult neuronal differentiation from endogenous progenitor populations. Understanding molecular mechanisms contributing to induced adult neurogenesis might enable directed CNS repair.
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Affiliation(s)
- U Shivraj Sohur
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University Cambridge, MA, USA
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12
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Hemmeryckx B, Himmelreich U, Hoylaerts MF, Lijnen HR. Impact of clock gene Bmal1 deficiency on nutritionally induced obesity in mice. Obesity (Silver Spring) 2011; 19:659-61. [PMID: 21030946 DOI: 10.1038/oby.2010.266] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To evaluate the hypothesis that the clock gene Bmal1 (brain and muscle arnt like protein-1) plays a role in the development of obesity, 5-week-old male Bmal1-deficient (Bmal1(-/-)) mice and wild-type littermates (Bmal1(+/+)) were kept on a high-fat diet (HFD) for 15 weeks. Despite an initial accelerated weight gain of Bmal1(-/-) mice, body weight and subcutaneous (SC) and gonadal (GON) adipose tissue mass were comparable to Bmal1(+/+) mice at the end of the diet period. Noninvasive magnetic resonance imaging scanning revealed a modest increase in fat content in Bmal1(-/-) mice after 10 weeks of HFD, whereas at the start and the end of the HFD feeding no differences were observed between both genotypes. After 15 weeks of HFD, adipocyte and blood vessel size and density were similar for Bmal1(+/+) and Bmal1(-/-) mice. However, the weight of major organs was significantly reduced in Bmal1(-/-) mice, confirming the premature ageing phenotype. Thus, we hypothesize that an initial accelerated increase in body weight and fat mass of Bmal1(-/-) mice on HFD may have been offset by the effect of premature ageing on organ weight, resulting in comparable weights after 15 weeks of HFD.
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Affiliation(s)
- Bianca Hemmeryckx
- Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
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13
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Kosir R, Acimovic J, Golicnik M, Perse M, Majdic G, Fink M, Rozman D. Determination of reference genes for circadian studies in different tissues and mouse strains. BMC Mol Biol 2010; 11:60. [PMID: 20712867 PMCID: PMC2928770 DOI: 10.1186/1471-2199-11-60] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 08/16/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circadian rhythms have a profound effect on human health. Their disruption can lead to serious pathologies, such as cancer and obesity. Gene expression studies in these pathologies are often studied in different mouse strains by quantitative real time polymerase chain reaction (qPCR). Selection of reference genes is a crucial step of qPCR experiments. Recent studies show that reference gene stability can vary between species and tissues, but none has taken circadian experiments into consideration. RESULTS In the present study the expression of ten candidate reference genes (Actb, Eif2a, Gapdh, Hmbs, Hprt1, Ppib, Rn18s, Rplp0, Tbcc and Utp6c) was measured in 131 liver and 97 adrenal gland samples taken from three mouse strains (C57BL/6JOlaHsd, 129Pas plus C57BL/6J and Crem KO on 129Pas plus C57BL/6J background) every 4 h in a 24 h period. Expression stability was evaluated by geNorm and NormFinder programs. Differences in ranking of the most stable reference genes were observed both between individual mouse strains as well as between tissues within each mouse strain. We show that selection of reference gene (Actb) that is often used for analyses in individual mouse strains leads to errors if used for normalization when different mouse strains are compared. We identified alternative reference genes that are stable in these comparisons. CONCLUSIONS Genetic background and circadian time influence the expression stability of reference genes. Differences between mouse strains and tissues should be taken into consideration to avoid false interpretations. We show that the use of a single reference gene can lead to false biological conclusions. This manuscript provides a useful reference point for researchers that search for stable reference genes in the field of circadian biology.
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Affiliation(s)
- Rok Kosir
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloska 4, SI-1000 Ljubljana, Slovenia
| | - Jure Acimovic
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Marko Golicnik
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Martina Perse
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Zaloska 4, SI-1000 Ljubljana, Slovenia
| | - Gregor Majdic
- Center for Animal Genomics, Veterinary Faculty; University of Ljubljana, Gerbiceva 60, SI-1000 Ljubljana, Slovenia
| | - Martina Fink
- University Medical Center Ljubljana, Department of Haematology, Zaloska cesta 7, SI-1000 Ljubljana, Slovenia
| | - Damjana Rozman
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloska 4, SI-1000 Ljubljana, Slovenia
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14
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Miyazaki K, Wakabayashi M, Hara Y, Ishida N. Tumor growth suppression in vivo by overexpression of the circadian component, PER2. Genes Cells 2010; 15:351-8. [PMID: 20236181 DOI: 10.1111/j.1365-2443.2010.01384.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Some reports have indicated that the core clock gene, Per2 regulates the cell cycle, immune system and neural functions. To understand the effects of PER2 on tumor growth in vivo, stable transformants of murine sarcoma 180 (S-180) cell lines expressing different levels of PER2 were established. The growth of stable PER2 transformants in vivo was significantly and dose-dependently suppressed according to the amount of PER2 expressed, indicating that PER2 plays a role in the growth suppression of sarcoma cells. The anchorage-dependent and -independent growth in vitro and expression of the clock controlled cell-cycle related genes, wee1, myc, and VEGF were not altered in stable PER2 transformants. In contrast, susceptibility to murine natural killer (NK) cell cytolytic activity was enhanced in PER2 transformants. Furthermore, PER2 transformants suppressed cell motility and reduced fibronectin expression, but the expression of integrin receptors was not affected. These results suggest that sarcoma cells overexpressing PER2 suppress tumors in vivo by changing the nature of tumor cell adhesion.
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Affiliation(s)
- Koyomi Miyazaki
- Clock Cell Biology Group, Institute for Biological Resource and Function, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
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ISHIDA NK, UCHIDA D, DOI R, OISHI K, CHIKAHISA S, SEI H, HAMASAKA Y, SUZUKI T, HANAI S. Role of PPARα in control of torpor through FGF21-NPY pathway: From circadian clock genes to seasonal change and cardiovascular disease. Sleep Biol Rhythms 2010. [DOI: 10.1111/j.1479-8425.2009.00413.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hou TY, Ward SM, Murad JM, Watson NP, Israel MA, Duffield GE. ID2 (inhibitor of DNA binding 2) is a rhythmically expressed transcriptional repressor required for circadian clock output in mouse liver. J Biol Chem 2009; 284:31735-45. [PMID: 19740747 DOI: 10.1074/jbc.m109.013961] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Id2 is a helix-loop-helix transcription factor gene expressed in a circadian manner in multiple tissues with a phase-locked relationship with canonical clock genes. Our previous studies have identified circadian phenotypes in Id2 null mice, including enhanced photo-entrainment and disruption of activity rhythms, and have demonstrated a potent inhibitory effect of ID proteins upon CLOCK-BMAL1 transactivation of clock gene and clock-controlled gene activity. We have now begun to explore the potential role that ID2 may play in specifically regulating clock output. Here we show that ID2 protein is rhythmically expressed in mouse liver. Time-of-day-specific liver gene expression in Id2(+/+) and Id2(-/-) mice under circadian conditions was studied using DNA microarray analysis, identifying 651 differentially expressed genes, including a subset of 318 genes deemed rhythmically expressed in other studies. Examination of individual time courses reveals that these genes are dysregulated in a highly time-specific manner. A cohort of different functional groups were identified, including genes associated with glucose and lipid metabolism, e.g. serum protein Igfbp1 and lipoprotein lipase. We also reveal that the Id2(-/-) mice show a reduction in lipid storage in the liver and white adipose tissue, suggesting that disruption of normal circadian activity of components of lipid metabolism can result in overt physiological alterations. These data reveal a role for the transcriptional repressor ID2 as a circadian output regulator in the periphery.
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Affiliation(s)
- Tim Y Hou
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Kid-1 participates in regulating ERK phosphorylation as a part of the circadian clock output in rat kidney. J Recept Signal Transduct Res 2009; 29:94-9. [PMID: 19519174 DOI: 10.1080/10799890902830783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Circadian clock genes play a role for the regulation of cell cycle, but the factors connecting clock to cell cycle are not fully understood. We found that mRNA of Kid-1--a zinc-finger-type transcriptional repressor was localized to cortical and juxtamedullary segments of tubules but not to glomeruli in the rat kidney. Kid-1 mRNA showed robust circadian oscillation with a peak at ZT16. Under temporal restricted feeding, the phase of the oscillation shifted along with mRNAs of the clock genes--Per1 and Per2. The rhythm of S-phase in cell cycle disappeared in the kidney under the restricted feeding. The level of phosphorylation of extracellular signal-regulated kinase (ERK) 1/2 was rhythmic with a peak at ZT16 in the kidney. We found that knockdown and overexpression of Kid-1 in NRK52E (normal rat kidney epithelial) cells induced and reduced the phosphorylation of ERK1/2, respectively. The data suggest that clock-controlled Kid-1 regulates the cell cycle of proliferating renal tubular epithelial cells through ERK phosphorylation.
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Role of PPARα in the control of torpor through FGF21-NPY pathway: From circadian clock to seasonal change in mammals. PPAR Res 2009; 2009:412949. [PMID: 19536348 PMCID: PMC2695967 DOI: 10.1155/2009/412949] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 03/03/2009] [Accepted: 04/02/2009] [Indexed: 12/17/2022] Open
Abstract
In nature, hibernating animals encounter fasting, cold temperature and short day seasonally. Torpor is a state of decreased physiological activity in an animal, usually characterized by a reduced body temperature and rate of metabolism to adapt such a severe environment. Ablation of the central clock synchronizer, the suprachiasmatic nucleus in brain, abolishes torpor, a hibernation-like state, implicating the circadian clock involved in this seasonal change. Biologists knows well the energy source of daily heterotherms/hibernators changed from glucose to lipids in winter. Here we review several lines of evidence of a master transcriptional regulator in lipid catabolism, PPARα, in the control of torpor through FGF21-NPY pathway. This indicate the importance of circadian—and photoperiod—regulation of PPARα to tell seasons in our body.
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Jetten AM. Retinoid-related orphan receptors (RORs): critical roles in development, immunity, circadian rhythm, and cellular metabolism. NUCLEAR RECEPTOR SIGNALING 2009; 7:e003. [PMID: 19381306 PMCID: PMC2670432 DOI: 10.1621/nrs.07003] [Citation(s) in RCA: 530] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 03/18/2009] [Indexed: 12/11/2022]
Abstract
The last few years have witnessed a rapid increase in our knowledge of the retinoid-related orphan receptors RORalpha, -beta, and -gamma (NR1F1-3), their mechanism of action, physiological functions, and their potential role in several pathologies. The characterization of ROR-deficient mice and gene expression profiling in particular have provided great insights into the critical functions of RORs in the regulation of a variety of physiological processes. These studies revealed that RORalpha plays a critical role in the development of the cerebellum, that both RORalpha and RORbeta are required for the maturation of photoreceptors in the retina, and that RORgamma is essential for the development of several secondary lymphoid tissues, including lymph nodes. RORs have been further implicated in the regulation of various metabolic pathways, energy homeostasis, and thymopoiesis. Recent studies identified a critical role for RORgamma in lineage specification of uncommitted CD4+ T helper cells into Th17 cells. In addition, RORs regulate the expression of several components of the circadian clock and may play a role in integrating the circadian clock and the rhythmic pattern of expression of downstream (metabolic) genes. Study of ROR target genes has provided insights into the mechanisms by which RORs control these processes. Moreover, several reports have presented evidence for a potential role of RORs in several pathologies, including osteoporosis, several autoimmune diseases, asthma, cancer, and obesity, and raised the possibility that RORs may serve as potential targets for chemotherapeutic intervention. This prospect was strengthened by recent evidence showing that RORs can function as ligand-dependent transcription factors.
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MESH Headings
- Animals
- Circadian Rhythm/genetics
- Circadian Rhythm/physiology
- Growth/physiology
- Humans
- Immune System/physiology
- Nuclear Receptor Subfamily 1, Group F, Member 1
- Nuclear Receptor Subfamily 1, Group F, Member 2
- Nuclear Receptor Subfamily 1, Group F, Member 3
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/physiology
- Receptors, Retinoic Acid/genetics
- Receptors, Retinoic Acid/physiology
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/physiology
- Trans-Activators/genetics
- Trans-Activators/physiology
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Affiliation(s)
- Anton M Jetten
- Cell Biology Section, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
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Hara Y, Onishi Y, Oishi K, Miyazaki K, Fukamizu A, Ishida N. Molecular characterization of Mybbp1a as a co-repressor on the Period2 promoter. Nucleic Acids Res 2009; 37:1115-26. [PMID: 19129230 PMCID: PMC2651808 DOI: 10.1093/nar/gkn1013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The circadian clock comprises transcriptional feedback loops of clock genes. Cryptochromes are essential components of the negative feedback loop in mammals as they inhibit CLOCK-BMAL1-mediated transcription. We purified mouse CRY1 (mCRY1) protein complexes from Sarcoma 180 cells to determine their roles in circadian gene expression and discovered that Myb-binding protein 1a (Mybbp1a) interacts with mCRY1. Mybbp1a regulates various transcription factors, but its role in circadian gene expression is unknown. We found that Mybbp1a functions as a co-repressor of Per2 expression and repressed Per2 promoter activity in reporter assays. Chromatin immunoprecipitation (ChIP) assays revealed endogenous Mybbp1a binding to the Per2 promoter that temporally matched that of mCRY1. Furthermore, Mybbp1a binding to the Per2 promoter correlated with the start of the down-regulation of Per2 expression and with the dimethylation of histone H3 Lys9, to which it could also bind. These findings suggest that Mybbp1a and mCRY1 can form complexes on the Per2 promoter that function as negative regulators of Per2 expression.
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Affiliation(s)
- Yasuhiro Hara
- Clock Cell Biology, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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Ohsaki K, Oishi K, Kozono Y, Nakayama K, Nakayama KI, Ishida N. The Role of β-TrCP1 and β-TrCP2 in Circadian Rhythm Generation by Mediating Degradation of Clock Protein PER2. ACTA ACUST UNITED AC 2008; 144:609-18. [DOI: 10.1093/jb/mvn112] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Abstract
Although Bmal1 is a key component of the mammalian clock system, little is understood about the actual mechanism of circadian Bmal1 gene transcription, particularly at the chromatin level. Here we discovered a unique chromatin structure within the Bmal1 promoter. The RORE region, which is a critical cis element for the circadian regulation of the Bmal1 gene, is comprised of GC-rich open chromatin. The 3'-flanking region of the promoter inhibited rhythmic transcription in the reporter gene assay in vitro even in the presence of RORalpha and REV-ERBalpha. We also found that the nuclear matrix protein SAF-A binds to the 3'-flanking region with circadian timing, which was correlated with Bmal1 expression by footprinting in vivo. These results suggest that the unique chromatin structure containing SAF-A is required for the circadian transcriptional regulation of the Bmal1 gene in cells.
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Kotaka M, Onishi Y, Ohno T, Akaike T, Ishida N. Identification of negative transcriptional factor E4BP4-binding site in the mouse circadian-regulated gene Mdr2. Neurosci Res 2008; 60:307-13. [PMID: 18242748 DOI: 10.1016/j.neures.2007.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 11/02/2007] [Accepted: 11/27/2007] [Indexed: 02/07/2023]
Abstract
The hepatic transporter Mdr2 is an ATP-binding cassette transporter which excretes phosphatidylcholine into the bile. We showed that the level of Mdr2 mRNA oscillated in circadian fashion in mouse liver whereas such oscillation was dampened in the liver of Clock mutants. To examine transcriptional regulation of the Mdr2 gene we performed luciferase reporter assays using plasmid constructs containing the 5'-flanking region of the Mdr2 gene. Reporter assays using deletion constructs demonstrated that E4BP4 represses the transcriptional activity of the promoter including the D1 and D2 sites within four putative E4BP4-binding sites. Chromatin immunoprecipitation and gel shift assays showed that E4BP4 binds to the D2 site, but not to the D1 site. These data suggested that E4BP4 is a negative transcription factor for circadian Mdr2 mRNA expression.
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Affiliation(s)
- Maki Kotaka
- Clock Cell Biology Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
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Kusanagi H, Hida A, Satoh K, Echizenya M, Shimizu T, Pendergast JS, Yamazaki S, Mishima K. Expression profiles of 10 circadian clock genes in human peripheral blood mononuclear cells. Neurosci Res 2008; 61:136-42. [PMID: 18336944 DOI: 10.1016/j.neures.2008.01.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/03/2008] [Accepted: 01/25/2008] [Indexed: 11/19/2022]
Abstract
The circadian clock system regulates daily rhythms of physiology and behavior. The mammalian master clock in the suprachiasmatic nuclei orchestrates these biological rhythms in peripheral tissues. Since blood is the most accessible tissue source, we sought to dissect the human circadian clock system by characterizing clock gene expression in human peripheral blood mononuclear cells (PBMCs) isolated from eight young, healthy subjects. By evaluating the temporal expression profiles of 10 circadian clock genes, we found that Period 1 (Per1), Per2, and Per3 are rhythmically expressed in human blood samples. Our results suggest that evaluating the rhythmic expression of human Per genes could reveal an individual's circadian phenotype.
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Affiliation(s)
- Hiroaki Kusanagi
- Division of Neuropsychiatry, Department of Neuro and Locomotor Science, Akita University School of Medicine, Akita, Japan
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Gery S, Virk RK, Chumakov K, Yu A, Koeffler HP. The clock gene Per2 links the circadian system to the estrogen receptor. Oncogene 2007; 26:7916-20. [PMID: 17599055 DOI: 10.1038/sj.onc.1210585] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Circadian rhythms regulate diverse physiological processes including homeostatic functions of steroid hormones and their receptors. Estrogen receptor-alpha (ERalpha) is essential for normal mammary gland physiology and is a prognostic marker for the treatment of breast cancer. We report that Per2, a core clock gene, links the circadian cycle to the ERalpha signaling network. Binding of enhances ERalpha degradation, while suppression of Per2 levels leads to ERalpha stabilization. In turn, Per2 itself is estrogen inducible in these cells, suggesting a feedback mechanism to attenuate stimulation by estrogen. In addition, overexpression of Per2 in breast cancer cells leads to significant growth inhibition, loss of clonogenic ability and apoptosis. Taken together, these results further support a critical role for peripheral circadian regulation in tissue homeostasis and suggest a novel role for clock genes in estrogen receptor-positive breast cancer.
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Affiliation(s)
- S Gery
- Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, University of California, Los Angeles, CA 90048, USA.
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