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Potential Role of the Circadian Clock in the Regulation of Cancer Stem Cells and Cancer Therapy. Int J Mol Sci 2022; 23:ijms232214181. [PMID: 36430659 PMCID: PMC9698777 DOI: 10.3390/ijms232214181] [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: 08/26/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Circadian rhythms, including sleep/wake cycles as well as hormonal, immune, metabolic, and cell proliferation rhythms, are fundamental biological processes driven by a cellular time-keeping system called the circadian clock. Disruptions in these rhythms due to genetic alterations or irregular lifestyles cause fundamental changes in physiology, from metabolism to cellular proliferation and differentiation, resulting in pathological consequences including cancer. Cancer cells are not uniform and static but exist as different subtypes with phenotypic and functional differences in the tumor microenvironment. At the top of the heterogeneous tumor cell hierarchy, cancer stem cells (CSCs), a self-renewing and multi-potent cancer cell type, are most responsible for tumor recurrence and metastasis, chemoresistance, and mortality. Phenotypically, CSCs are associated with the epithelial-mesenchymal transition (EMT), which confers cancer cells with increased motility and invasion ability that is characteristic of malignant and drug-resistant stem cells. Recently, emerging studies of different cancer types, such as glioblastoma, leukemia, prostate cancer, and breast cancer, suggest that the circadian clock plays an important role in the maintenance of CSC/EMT characteristics. In this review, we describe recent discoveries regarding how tumor intrinsic and extrinsic circadian clock-regulating factors affect CSC evolution, highlighting the possibility of developing novel chronotherapeutic strategies that could be used against CSCs to fight cancer.
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Cheng J, Chen F, Cheng Y. Construction and Evaluation of a Risk Score Model for Lymph Node Metastasis-Associated Circadian Clock Genes in Esophageal Squamous Carcinoma. Cells 2022; 11:cells11213432. [PMID: 36359828 PMCID: PMC9655457 DOI: 10.3390/cells11213432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Background: Studies suggested that circadian clock genes (CCGs) in human esophageal squamous carcinoma (ESCC) samples are dysregulated. However, the relevance of CCGs to lymph node metastasis (LNM) and prognosis of ESCC remains unclear. Methods: The differentially expressed genes (DEGs) between normal and ESCC samples in The Cancer Genome Atlas database (TCGA) database were intersected with the genes associated with LNM (LNMGs) in ESCC samples and 300 CCGs to obtain the differentially expressed LNM-associated CCGs (DE-LNM-CCGs). The risk model was constructed by Cox regression analysis in the TCGA-ESCC training set, and the accuracy of the risk model was verified by risk profile and overall survival profile. Furthermore, differences of 23 immune cells, 13 immune functions, and immune checkpoint molecules between the high- and low-risk groups were assessed using the single-sample gene set enrichment analysis (ssGSEA) algorithm. Gene set enrichment analysis (GSEA) was conducted to investigate the functional differences between low- and high-risk groups. Finally, we validated the mRNA expression levels of prognostic model genes by quantitative real-time polymerase chain reaction (qRT-PCR). Results: A total of six DE-LNM-CCGs were identified in TCGA-ESCC. TP53 and NAGLU were selected by Cox regression analysis to construct the risk model. Risk profile plots, overall survival plots, and validation results of the risk model in the validation set indicated that the constructed risk model was reliable. The result of ssGSEA showed that the percentages of activated B cells, activated dendritic cells, effector memory CD8 T cells, immune function in neutrophils, plasmacytoid dendritic cells, T cell co-inhibition, and Type 17 T helper cells were different between the high- and low-risk groups. In addition, the expression of CD274, PDCD1, TNFRSF18, and TNFRSF9 was dysregulated between the high- and low-risk groups. GSEA revealed that the high-risk group was associated with cell differentiation, oxidative phosphorylation, and steroid biosynthesis pathways, while the low-risk group was associated with chromosome, ECM–receptor interaction, and other pathways. Finally, qRT-PCR results showed that the mRNA expression levels of two prognostic genes were consistent with TCGA. Conclusion: In conclusion, the risk model constructed based on TP53 and NAGLU could accurately predict the prognosis.
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Affiliation(s)
- Jian Cheng
- Department of Cancer Center, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan 250033, China
| | - Fang Chen
- Department of Pharmacy, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan 250033, China
| | - Yufeng Cheng
- Department of Radiation Oncology, Qilu Hospital of Shandong University, No. 107 West Wenhua Road, Jinan 250012, China
- Correspondence:
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Suraritdechachai S, Lakkanasirorat B, Uttamapinant C. Molecular probes for cellular imaging of post-translational proteoforms. RSC Chem Biol 2022; 3:201-219. [PMID: 35360891 PMCID: PMC8826509 DOI: 10.1039/d1cb00190f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022] Open
Abstract
Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However, it is not trivial to visualize post-translational modifications in a protein- and site-specific manner, especially in a living-cell context. Herein, we review recent advances in the development of molecular imaging tools to detect diverse classes of post-translational proteoforms in individual cells, and their applications in studying precise roles of PTMs in regulating the function of cellular proteins.
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Affiliation(s)
- Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Benya Lakkanasirorat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
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Multi-Modal Regulation of Circadian Physiology by Interactive Features of Biological Clocks. BIOLOGY 2021; 11:biology11010021. [PMID: 35053019 PMCID: PMC8772734 DOI: 10.3390/biology11010021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 12/26/2022]
Abstract
The circadian clock is a fundamental biological timing mechanism that generates nearly 24 h rhythms of physiology and behaviors, including sleep/wake cycles, hormone secretion, and metabolism. Evolutionarily, the endogenous clock is thought to confer living organisms, including humans, with survival benefits by adapting internal rhythms to the day and night cycles of the local environment. Mirroring the evolutionary fitness bestowed by the circadian clock, daily mismatches between the internal body clock and environmental cycles, such as irregular work (e.g., night shift work) and life schedules (e.g., jet lag, mistimed eating), have been recognized to increase the risk of cardiac, metabolic, and neurological diseases. Moreover, increasing numbers of studies with cellular and animal models have detected the presence of functional circadian oscillators at multiple levels, ranging from individual neurons and fibroblasts to brain and peripheral organs. These oscillators are tightly coupled to timely modulate cellular and bodily responses to physiological and metabolic cues. In this review, we will discuss the roles of central and peripheral clocks in physiology and diseases, highlighting the dynamic regulatory interactions between circadian timing systems and multiple metabolic factors.
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Sharma R, Parikh M, Mishra V, Soni A, Rubi S, Sahota P, Thakkar M. Antisense-induced downregulation of major circadian genes modulates the expression of histone deacetylase-2 (HDAC-2) and CREB-binding protein (CBP) in the medial shell region of nucleus accumbens of mice exposed to chronic excessive alcohol consumption. J Neurochem 2021; 161:8-19. [PMID: 34837399 DOI: 10.1111/jnc.15547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022]
Abstract
Circadian genes in the medial accumbal shell (mNAcSh) region regulate binge alcohol consumption. Here, we investigated if antisense-induced knockdown of major circadian genes (Per1, Per2, and NPAS2) in the mNAcSh of mice exposed to intermittent access two-bottle choice (IA2BC) paradigm modulates the expression of histone deacetylase-2 (HDAC-2) and CREB-binding protein (CBP), key epigenetic modifiers associated with withdrawal-associated behaviors such as anxiety. Adult male C57BL/6J mice (N = 28), surgically implanted with bilateral guide cannulas above the mNAcSh, were chronically (4 weeks) exposed to alcohol (20% v/v) or saccharin (0.03%) via IA2BC paradigm. In the fourth week, a mixture of antisense (AS-ODNs; N = 14/group) or nonsense (NS-ODNs; N = 14/group) oligodeoxynucleotides against circadian genes were bilaterally infused into the mNAcSh. Subsequently, alcohol/saccharin consumption and preference were measured followed by euthanization of animals and verification of microinjection sites by visual inspection and the expression of HDAC-2 and CBP by using RT-PCR along with the verification of antisense-induced downregulation of circadian genes in the mNAcSh. As compared with NS-ODNs, AS-ODNs infusion significantly attenuated the alcohol-induced increase in HDAC-2 and reduction in CBP expression in the mNAcSh along with a significant reduction in alcohol consumption and preference. No significant effect was observed on either saccharin consumption or preference. Our results suggest that circadian genes in the mNAcSh may have a causal to play in mediating epigenetic changes observed after chronic alcohol consumption.
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Affiliation(s)
- Rishi Sharma
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology, University of Missouri-School of Medicine, Columbia, Missouri, USA
| | - Meet Parikh
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology, University of Missouri-School of Medicine, Columbia, Missouri, USA
| | - Vaibhav Mishra
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology, University of Missouri-School of Medicine, Columbia, Missouri, USA
| | - Anshul Soni
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology, University of Missouri-School of Medicine, Columbia, Missouri, USA
| | - Sofia Rubi
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology, University of Missouri-School of Medicine, Columbia, Missouri, USA
| | - Pradeep Sahota
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology, University of Missouri-School of Medicine, Columbia, Missouri, USA
| | - Mahesh Thakkar
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology, University of Missouri-School of Medicine, Columbia, Missouri, USA
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Sharma R, Mishra V, Parikh M, Soni A, Sahota P, Thakkar M. Antisense-induced knockdown of cAMP response element-binding protein downregulates Per1 gene expression in the shell region of nucleus accumbens resulting in reduced alcohol consumption in mice. Alcohol Clin Exp Res 2021; 45:1940-1949. [PMID: 34424532 PMCID: PMC8602740 DOI: 10.1111/acer.14687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/29/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION We recently showed that circadian genes expressed in the shell region of nucleus accumbens (NAcSh) play a key role in alcohol consumption, though, the molecular mechanism of those effects is unclear. Because CREB-binding protein (CBP) promotes Per1 gene expression, we hypothesized that alcohol consumption would increase CBP expression in the NAcSh and antisense-induced knockdown of CBP would reduce Per1 expression and result in a reduction in alcohol consumption. METHODS To test our hypothesis, we performed two experiments. The Drinking-in-the-dark (DID) paradigm was used to evaluate alcohol consumption in male C57BL/6J mice. In Experiment 1 we examined the effects of alcohol consumption on CBP gene expression in the NAcSh. Control animals were exposed to, sucrose [10% (w/v) taste and calorie] and water (consummatory behavior). In Experiment 2 examined the effects of CBP gene silencing on the expression of the Per1 gene in the NAcSh and alcohol consumption in mice exposed to alcohol using the DID paradigm. CBP gene silencing was achieved by local infusion of two doses of either CBP antisense oligodeoxynucleotides (AS-ODNs; Antisense group) or nonsense ODNs (NS-ODNs; Nonsense group) bilaterally microinjected into the NAcSh within 24 h before alcohol consumption on Day 4 of the DID paradigm. The microinfusion sites were verified by cresyl violet staining. RESULTS Compared to sucrose, alcohol consumption, under the DID paradigm, significantly increased the expression of CBP in the NAcSh. Compared to Controls, bilateral infusion of CBP AS-ODNs significantly reduced the expression of Per1 in the NAcSh and alcohol consumption without affecting the amount of sucrose consumed. CONCLUSIONS Our results suggest that CBP is an upstream regulator of Per1 expression in the NAcSh and may act via Per1 to modulate alcohol consumption.
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Affiliation(s)
- Rishi Sharma
- Department of Neurology, Harry S. Truman Memorial Veterans Hospital, University of Missouri, Columbia, Missouri, USA
| | - Vaibhav Mishra
- Department of Neurology, Harry S. Truman Memorial Veterans Hospital, University of Missouri, Columbia, Missouri, USA
| | - Meet Parikh
- Department of Neurology, Harry S. Truman Memorial Veterans Hospital, University of Missouri, Columbia, Missouri, USA
| | - Anshul Soni
- Department of Neurology, Harry S. Truman Memorial Veterans Hospital, University of Missouri, Columbia, Missouri, USA
| | - Pradeep Sahota
- Department of Neurology, Harry S. Truman Memorial Veterans Hospital, University of Missouri, Columbia, Missouri, USA
| | - Mahesh Thakkar
- Department of Neurology, Harry S. Truman Memorial Veterans Hospital, University of Missouri, Columbia, Missouri, USA
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Abstract
Circadian clocks are biological timing mechanisms that generate 24-h rhythms of physiology and behavior, exemplified by cycles of sleep/wake, hormone release, and metabolism. The adaptive value of clocks is evident when internal body clocks and daily environmental cycles are mismatched, such as in the case of shift work and jet lag or even mistimed eating, all of which are associated with physiological disruption and disease. Studies with animal and human models have also unraveled an important role of functional circadian clocks in modulating cellular and organismal responses to physiological cues (ex., food intake, exercise), pathological insults (e.g. virus and parasite infections), and medical interventions (e.g. medication). With growing knowledge of the molecular and cellular mechanisms underlying circadian physiology and pathophysiology, it is becoming possible to target circadian rhythms for disease prevention and treatment. In this review, we discuss recent advances in circadian research and the potential for therapeutic applications that take patient circadian rhythms into account in treating disease.
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Affiliation(s)
- Yool Lee
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington
| | - Jeffrey M Field
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amita Sehgal
- Howard Hughes Medical Institute, Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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8
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Parnell AA, De Nobrega AK, Lyons LC. Translating around the clock: Multi-level regulation of post-transcriptional processes by the circadian clock. Cell Signal 2021; 80:109904. [PMID: 33370580 PMCID: PMC8054296 DOI: 10.1016/j.cellsig.2020.109904] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022]
Abstract
The endogenous circadian clock functions to maintain optimal physiological health through the tissue specific coordination of gene expression and synchronization between tissues of metabolic processes throughout the 24 hour day. Individuals face numerous challenges to circadian function on a daily basis resulting in significant incidences of circadian disorders in the United States and worldwide. Dysfunction of the circadian clock has been implicated in numerous diseases including cancer, diabetes, obesity, cardiovascular and hepatic abnormalities, mood disorders and neurodegenerative diseases. The circadian clock regulates molecular, metabolic and physiological processes through rhythmic gene expression via transcriptional and post-transcriptional processes. Mounting evidence indicates that post-transcriptional regulation by the circadian clock plays a crucial role in maintaining tissue specific biological rhythms. Circadian regulation affecting RNA stability and localization through RNA processing, mRNA degradation, and RNA availability for translation can result in rhythmic protein synthesis, even when the mRNA transcripts themselves do not exhibit rhythms in abundance. The circadian clock also targets the initiation and elongation steps of translation through multiple pathways. In this review, the influence of the circadian clock across the levels of post-transcriptional, translation, and post-translational modifications are examined using examples from humans to cyanobacteria demonstrating the phylogenetic conservation of circadian regulation. Lastly, we briefly discuss chronotherapies and pharmacological treatments that target circadian function. Understanding the complexity and levels through which the circadian clock regulates molecular and physiological processes is important for future advancement of therapeutic outcomes.
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Affiliation(s)
- Amber A Parnell
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Aliza K De Nobrega
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Lisa C Lyons
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA.
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Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G. SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies. Molecules 2021; 26:molecules26040828. [PMID: 33562565 PMCID: PMC7915335 DOI: 10.3390/molecules26040828] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
One major role of the eukaryotic peptidic post-translational modifier SUMO in the cell is transcriptional control. This occurs via modification of virtually all classes of transcriptional actors, which include transcription factors, transcriptional coregulators, diverse chromatin components, as well as Pol I-, Pol II- and Pol III transcriptional machineries and their regulators. For many years, the role of SUMOylation has essentially been studied on individual proteins, or small groups of proteins, principally dealing with Pol II-mediated transcription. This provided only a fragmentary view of how SUMOylation controls transcription. The recent advent of large-scale proteomic, modifomic and genomic studies has however considerably refined our perception of the part played by SUMO in gene expression control. We review here these developments and the new concepts they are at the origin of, together with the limitations of our knowledge. How they illuminate the SUMO-dependent transcriptional mechanisms that have been characterized thus far and how they impact our view of SUMO-dependent chromatin organization are also considered.
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Affiliation(s)
- Mathias Boulanger
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mehuli Chakraborty
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Denis Tempé
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Marc Piechaczyk
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
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Duffield GE, Han S, Hou TY, de la Iglesia HO, McDonald KA, Mecklenburg KL, Robles-Murguia M. Inhibitor of DNA binding 2 (Id2) Regulates Photic Entrainment Responses in Mice: Differential Responses of the Id2-/- Mouse Circadian System Are Dependent on Circadian Phase and on Duration and Intensity of Light. J Biol Rhythms 2020; 35:555-575. [PMID: 32981454 DOI: 10.1177/0748730420957504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
ID2 is a rhythmically expressed helix-loop-helix transcriptional repressor, and its deletion results in abnormal properties of photoentrainment. By examining parametric and nonparametric models of entrainment, we have started to explore the mechanism underlying this circadian phenotype. Id2-/- mice were exposed to differing photoperiods, and the phase angle of entrainment under short days was delayed 2 h as compared with controls. When exposed to long durations of continuous light, enhanced entrainment responses were observed after a delay of the clock but not with phase advances. However, the magnitude of phase shifts was not different in Id2-/- mice tested in constant darkness using a discrete pulse of saturating light. No differences were observed in the speed of clock resetting when challenged by a series of discrete pulses interspaced by varying time intervals. A photic phase-response curve was constructed, although no genotypic differences were observed. Although phase shifts produced by discrete saturating light pulses at CT16 were similar, treatment with a subsaturating pulse revealed a ~2-fold increase in the magnitude of the Id2-/- shift. A corresponding elevation of light-induced per1 expression was observed in the Id2-/- suprachiasmatic nucleus (SCN). To test whether the phenotype is based on a sensitivity change at the level of the retina, pupil constriction responses were measured. No differences were observed in responses or in retinal histology, suggesting that the phenotype occurs downstream of the retina and retinal hypothalamic tract. To test whether the phenotype is due to a reduced amplitude of state variables of the clock, the expression of clock genes per1 and per2 was assessed in vivo and in SCN tissue explants. Amplitude, phase, and period length were normal in Id2-/- mice. These findings suggest that ID2 contributes to a photoregulatory mechanism at the level of the SCN central pacemaker through control of the photic induction of negative elements of the clock.
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Affiliation(s)
- Giles E Duffield
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana
| | - Sung Han
- Department of Biology and Graduate Program in Neuroscience, University of Washington, Seattle, Washington
| | - Tim Y Hou
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, Indiana
| | - Horacio O de la Iglesia
- Department of Biology and Graduate Program in Neuroscience, University of Washington, Seattle, Washington
| | - Kathleen A McDonald
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, Indiana
| | - Kirk L Mecklenburg
- Department of Biology, Indiana University South Bend, South Bend, Indiana
| | - Maricela Robles-Murguia
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana
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11
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Srikanta SB, Cermakian N. To Ub or not to Ub: Regulation of circadian clocks by ubiquitination and deubiquitination. J Neurochem 2020; 157:11-30. [PMID: 32717140 DOI: 10.1111/jnc.15132] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 12/28/2022]
Abstract
Circadian clocks are internal timing systems that enable organisms to adjust their behavioral and physiological rhythms to the daily changes of their environment. These clocks generate self-sustained oscillations at the cellular, tissue, and behavioral level. The rhythm-generating mechanism is based on a gene expression network with a delayed negative feedback loop that causes the transcripts to oscillate with a period of approximately 24 hr. This oscillatory nature of the proteins involved in this network necessitates that they are intrinsically unstable, with a short half-life. Hence, post-translational modifications (PTMs) are important to precisely time the presence, absence, and interactions of these proteins at appropriate times of the day. Ubiquitination and deubiquitination are counter-balancing PTMs which play a key role in this regulatory process. In this review, we take a comprehensive look at the roles played by the processes of ubiquitination and deubiquitination in the clock machinery of the most commonly studied eukaryotic models of the circadian clock: plants, fungi, fruit flies, and mammals. We present the effects exerted by ubiquitinating and deubiquitinating enzymes on the stability, but also the activity, localization, and interactions of clock proteins. Overall, these PTMs have key roles in regulating not only the pace of the circadian clocks but also their response to external cues and their control of cellular functions.
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Affiliation(s)
- Shashank Bangalore Srikanta
- Integrated Program in Neuroscience, McGill University, Montréal, QC, Canada.,Laboratory of Molecular Chronobiology, Douglas Research Centre, Montréal, QC, Canada
| | - Nicolas Cermakian
- Laboratory of Molecular Chronobiology, Douglas Research Centre, Montréal, QC, Canada.,Department of Psychiatry, McGill University, Montréal, QC, Canada
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12
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Simak M, Lu HHS, Yang JM. Boolean function network analysis of time course liver transcriptome data to reveal novel circadian transcriptional regulators in mammals. J Chin Med Assoc 2019; 82:872-880. [PMID: 31469689 DOI: 10.1097/jcma.0000000000000180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Many biological processes in mammals are subject to circadian control at the molecular level. Disruption of circadian rhythms has been demonstrated to be associated with a wide range of diseases, such as diabetes mellitus, mental disorders, and cancer. Although the core circadian genes are well established, there are multiple reports of novel peripheral circadian regulators. The goal of this study was to provide a comprehensive computational analysis to identify novel potential circadian transcriptional regulators. METHODS To fulfill the aforementioned goal, we applied a Boolean function network method to analyze the microarray time course mouse and rat liver datasets available in the literature. The inferred direct pairwise relations were further investigated using the functional annotation tool. This approach generated a list of transcription factors (TFs) and cofactors, which were associated with significantly enriched circadian gene ontology (GO) categories. RESULTS As a result, we identified 93 transcriptional circadian regulators in mouse and 95 transcriptional circadian regulators in rat. Of these, 19 regulators in mouse and 21 regulators in rat were known, whereas the rest were novel. Furthermore, we validated novel circadian TFs with bioinformatics databases, previous large-scale circadian studies, and related small-scale studies. Moreover, according to predictions inferred from ChIP-Seq experiments reported in the database, 40 of our candidate circadian regulators were confirmed to have circadian genes as direct regulatory targets. In addition, we annotated candidate circadian regulators with disorders that were often associated with disruptions of circadian rhythm in the literature. CONCLUSION In summary, our computational analysis, which was followed by an extensive verification by means of a literature review, can contribute to translational study from endocrinology to cancer research and provide insights for future investigation.
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Affiliation(s)
- Maria Simak
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan, ROC
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, ROC
| | | | - Jinn-Moon Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, ROC
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13
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Khoder-Agha F, Sosicka P, Escriva Conde M, Hassinen A, Glumoff T, Olczak M, Kellokumpu S. N-acetylglucosaminyltransferases and nucleotide sugar transporters form multi-enzyme-multi-transporter assemblies in golgi membranes in vivo. Cell Mol Life Sci 2019; 76:1821-1832. [PMID: 30737517 PMCID: PMC6453868 DOI: 10.1007/s00018-019-03032-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/07/2019] [Accepted: 01/28/2019] [Indexed: 01/05/2023]
Abstract
Branching and processing of N-glycans in the medial-Golgi rely both on the transport of the donor UDP-N-acetylglucosamine (UDP-GlcNAc) to the Golgi lumen by the SLC35A3 nucleotide sugar transporter (NST) as well as on the addition of the GlcNAc residue to terminal mannoses in nascent N-glycans by several linkage-specific N-acetyl-glucosaminyltransferases (MGAT1-MGAT5). Previous data indicate that the MGATs and NSTs both form higher order assemblies in the Golgi membranes. Here, we investigate their specific and mutual interactions using high-throughput FRET- and BiFC-based interaction screens. We show that MGAT1, MGAT2, MGAT3, MGAT4B (but not MGAT5) and Golgi alpha-mannosidase IIX (MAN2A2) form several distinct molecular assemblies with each other and that the MAN2A2 acts as a central hub for the interactions. Similar assemblies were also detected between the NSTs SLC35A2, SLC35A3, and SLC35A4. Using in vivo BiFC-based FRET interaction screens, we also identified novel ternary complexes between the MGATs themselves or between the MGATs and the NSTs. These findings suggest that the MGATs and the NSTs self-assemble into multi-enzyme/multi-transporter complexes in the Golgi membranes in vivo to facilitate efficient synthesis of complex N-glycans.
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Affiliation(s)
- Fawzi Khoder-Agha
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, 90220, Oulu, Finland
| | - Paulina Sosicka
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wrocław, Poland
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Maria Escriva Conde
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, 90220, Oulu, Finland
- Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, 90220, Oulu, Finland
- Institute of Molecular Medicine, Helsinki, Finland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, 90220, Oulu, Finland
| | - Mariusz Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wrocław, Poland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, 90220, Oulu, Finland.
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14
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Ma TJ, Zhang ZW, Lu YL, Zhang YY, Tao DC, Liu YQ, Ma YX. CLOCK and BMAL1 stabilize and activate RHOA to promote F-actin formation in cancer cells. Exp Mol Med 2018; 50:1-15. [PMID: 30287810 PMCID: PMC6172197 DOI: 10.1038/s12276-018-0156-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 06/20/2018] [Accepted: 06/22/2018] [Indexed: 02/05/2023] Open
Abstract
Circadian genes control most of the physiological functions in cancer cells, including cell proliferation, migration, and invasion. The CLOCK and BMAL1 complex plays a central role in circadian rhythms. Previous studies have shown that circadian genes may act as oncogenes or tumor-suppressor genes. In addition, F-actin, regulated by RHOA, has been shown to participate in tumor progression. However, the roles of the CLOCK and BMAL1 genes in the regulation of tumor progression via the RHOA-ROCK-CFL pathway remain largely unclear. Here we first indicate that the rearrangement of F-actin is regulated by CLOCK and BMAL1. We found that CLOCK and BMAL1 can upregulate RHOA expression by inhibiting CUL3-mediated ubiquitination and activate RHOA by reducing the interaction between RHOA and RhoGDI. Consequently, CLOCK and BMAL1 control the expression of the components of the RHOA-ROCK-CFL pathway, which alters the dynamics of F-actin/G-actin turnover and promotes cancer cell proliferation, migration, and invasion. In conclusion, our research proposes a novel insight into the role of CLOCK and BMAL1 in tumor cells.
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Affiliation(s)
- Teng-Jiao Ma
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital and Collaborative Innovation Center, Sichuan University, 610041, Chengdu, China
| | - Zhi-Wei Zhang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital and Collaborative Innovation Center, Sichuan University, 610041, Chengdu, China
| | - Yi-Lu Lu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital and Collaborative Innovation Center, Sichuan University, 610041, Chengdu, China
| | - Ying-Ying Zhang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital and Collaborative Innovation Center, Sichuan University, 610041, Chengdu, China
| | - Da-Chang Tao
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital and Collaborative Innovation Center, Sichuan University, 610041, Chengdu, China
| | - Yun-Qiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital and Collaborative Innovation Center, Sichuan University, 610041, Chengdu, China
| | - Yong-Xin Ma
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital and Collaborative Innovation Center, Sichuan University, 610041, Chengdu, China.
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15
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Chen S, Yang J, Zhang Y, Duan C, Liu Q, Huang Z, Xu Y, Zhou L, Xu G. Ubiquitin-conjugating enzyme UBE2O regulates cellular clock function by promoting the degradation of the transcription factor BMAL1. J Biol Chem 2018; 293:11296-11309. [PMID: 29871923 DOI: 10.1074/jbc.ra117.001432] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/16/2018] [Indexed: 12/25/2022] Open
Abstract
Dysregulation of the circadian rhythm is associated with many diseases, including diabetes, obesity, and cancer. Aryl hydrocarbon receptor nuclear translocator-like protein 1 (Arntl or Bmal1) is the only clock gene whose loss disrupts circadian locomotor behavior in constant darkness. BMAL1 levels are affected by proteasomal inhibition and by several enzymes in the ubiquitin-proteasome system, but the exact molecular mechanism remains unclear. Here, using immunoprecipitation and MS analyses, we discovered an interaction between BMAL1 and ubiquitin-conjugating enzyme E2 O (UBE2O), an E3-independent E2 ubiquitin-conjugating enzyme (i.e. hybrid E2/E3 enzyme). Biochemical experiments with cell lines and animal tissues validated this specific interaction and uncovered that UBE2O expression reduces BMAL1 levels by promoting its ubiquitination and degradation. Moreover, UBE2O expression/knockdown diminished/increased, respectively, BMAL1-mediated transcriptional activity but did not affect BMAL1 gene expression. Bioluminescence experiments disclosed that UBE2O knockdown elevates the amplitude of the circadian clock in human osteosarcoma U2OS cells. Furthermore, mapping of the BMAL1-interacting domain in UBE2O and analyses of BMAL1 stability and ubiquitination revealed that the conserved region 2 (CR2) in UBE2O significantly enhances BMAL1 ubiquitination and decreases BMAL1 protein levels. A Cys-to-Ser substitution experiment identified the critical Cys residue in the CR2 domain responsible for BMAL1 ubiquitination. This work identifies UBE2O as a critical regulator in the ubiquitin-proteasome system, which modulates BMAL1 transcriptional activity and circadian function by promoting BMAL1 ubiquitination and degradation under normal physiological conditions.
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Affiliation(s)
- Suping Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Jing Yang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Yang Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Chunyan Duan
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Qing Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Zhengyun Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Liang Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China.
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16
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Dyar KA, Eckel-Mahan KL. Circadian Metabolomics in Time and Space. Front Neurosci 2017; 11:369. [PMID: 28744188 PMCID: PMC5504240 DOI: 10.3389/fnins.2017.00369] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/13/2017] [Indexed: 12/11/2022] Open
Abstract
Circadian rhythms are widely known to govern human health and disease, but specific pathogenic mechanisms linking circadian disruption to metabolic diseases are just beginning to come to light. This is thanks in part to the development and application of various "omics"-based tools in biology and medicine. Current high-throughput technologies allow for the simultaneous monitoring of multiple dynamic cellular events over time, ranging from gene expression to metabolite abundance and sub-cellular localization. These fundamental temporal and spatial perspectives have allowed for a more comprehensive understanding of how various dynamic cellular events and biochemical processes are related in health and disease. With advances in technology, metabolomics has become a more routine "omics" approach for studying metabolism, and "circadian metabolomics" (i.e., studying the 24-h metabolome) has recently been undertaken by several groups. To date, circadian metabolomes have been reported for human serum, saliva, breath, and urine, as well as tissues from several species under specific disease or mutagenesis conditions. Importantly, these studies have consistently revealed that 24-h rhythms are prevalent in almost every tissue and metabolic pathway. Furthermore, these circadian rhythms in tissue metabolism are ultimately linked to and directed by internal 24-h biological clocks. In this review, we will attempt to put these data-rich circadian metabolomics experiments into perspective to find out what they can tell us about metabolic health and disease, and what additional biomarker potential they may reveal.
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Affiliation(s)
- Kenneth A Dyar
- Molecular Endocrinology, Institute for Diabetes and Obesity, Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD)Munich, Germany
| | - Kristin L Eckel-Mahan
- Brown Foundation of Molecular Medicine for the Prevention of Human Diseases of McGovern Medical School, University of Texas Health Science Center at HoustonHouston, TX, United States
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17
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Rosonina E, Akhter A, Dou Y, Babu J, Sri Theivakadadcham VS. Regulation of transcription factors by sumoylation. Transcription 2017; 8:220-231. [PMID: 28379052 PMCID: PMC5574528 DOI: 10.1080/21541264.2017.1311829] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Transcription factors (TFs) are among the most frequently detected targets of sumoylation, and effects of the modification have been studied for about 200 individual TFs to date. TF sumoylation is most often associated with reduced target gene expression, which can be mediated by enhanced interactions with corepressors or by interference with protein modifications that promote transcription. However, recent studies show that sumoylation also regulates gene expression by controlling the levels of TFs that are associated with chromatin. SUMO can mediate this by modulating TF DNA-binding activity, promoting clearance of TFs from chromatin, or indirectly, by influencing TF abundance or localization.
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Affiliation(s)
- Emanuel Rosonina
- a Department of Biology , York University , Toronto , ON , Canada
| | - Akhi Akhter
- a Department of Biology , York University , Toronto , ON , Canada
| | - Yimo Dou
- a Department of Biology , York University , Toronto , ON , Canada
| | - John Babu
- a Department of Biology , York University , Toronto , ON , Canada
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18
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Mendoza-Viveros L, Cheng AH, Cheng HYM. GRK2: putting the brakes on the circadian clock. ACTA ACUST UNITED AC 2016; 3. [PMID: 27088110 DOI: 10.14800/rci.1175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
G protein-coupled receptor kinases (GRKs) are a family of serine/threonine protein kinases that terminate G protein-coupled receptor (GPCR) signaling by phosphorylating the receptor and inducing its internalization. In addition to their canonical function, some GRKs can phosphorylate non-GPCR substrates and regulate GPCR signaling in a kinase-independent manner. GPCRs are abundantly expressed in the suprachiasmatic nucleus (SCN), a structure in the mammalian brain that serves as the central circadian pacemaker. Various facets of circadian timekeeping are under the influence of GPCR signaling, and thus are potential targets for GRK regulation. Despite this, little attention has been given to the role of GRKs in circadian rhythms. In this research highlight, we discuss our latest findings on the functional involvement of GRK2 in mammalian circadian timekeeping in the SCN. Using grk2 knockout mice, we demonstrate that GRK2 is critical for maintaining proper clock speed and ensuring that the clock is appropriately synchronized to environmental light cycles. Although grk2 deficiency expectedly alters the expression of a key GPCR in the SCN, our study also reveals that GRK2 has a more direct function that touches the heart of the circadian clock.
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Affiliation(s)
- Lucia Mendoza-Viveros
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
| | - Arthur H Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
| | - Hai-Ying M Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
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