1
|
Panda K, Chinnapaiyan S, Rahman MS, Santiago MJ, Black SM, Unwalla HJ. Circadian-Coupled Genes Expression and Regulation in HIV-Associated Chronic Obstructive Pulmonary Disease (COPD) and Lung Comorbidities. Int J Mol Sci 2023; 24:9140. [PMID: 37298092 PMCID: PMC10253051 DOI: 10.3390/ijms24119140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
People living with HIV (PLWH) have an elevated risk of chronic obstructive pulmonary disease (COPD) and are at a higher risk of asthma and worse outcomes. Even though the combination of antiretroviral therapy (cART) has significantly improved the life expectancy of HIV-infected patients, it still shows a higher incidence of COPD in patients as young as 40 years old. Circadian rhythms are endogenous 24 h oscillations that regulate physiological processes, including immune responses. Additionally, they play a significant role in health and diseases by regulating viral replication and its corresponding immune responses. Circadian genes play an essential role in lung pathology, especially in PLWH. The dysregulation of core clock and clock output genes plays an important role in chronic inflammation and aberrant peripheral circadian rhythmicity, particularly in PLWH. In this review, we explained the mechanism underlying circadian clock dysregulation in HIV and its effects on the development and progression of COPD. Furthermore, we discussed potential therapeutic approaches to reset the peripheral molecular clocks and mitigate airway inflammation.
Collapse
Affiliation(s)
- Kingshuk Panda
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA; (K.P.); (S.C.); (M.S.R.); (M.J.S.)
| | - Srinivasan Chinnapaiyan
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA; (K.P.); (S.C.); (M.S.R.); (M.J.S.)
| | - Md. Sohanur Rahman
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA; (K.P.); (S.C.); (M.S.R.); (M.J.S.)
| | - Maria J. Santiago
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA; (K.P.); (S.C.); (M.S.R.); (M.J.S.)
| | - Stephen M. Black
- Department of Cellular Biology & Pharmacology, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA;
| | - Hoshang J. Unwalla
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA; (K.P.); (S.C.); (M.S.R.); (M.J.S.)
| |
Collapse
|
2
|
Joshi K, Das M, Sarma A, Arora MK, SInghal M, Kumar B. Insight on Cardiac Chronobiology and Latest Developments of Chronotherapeutic Antihypertensive Interventions for Better Clinical Outcomes. Curr Hypertens Rev 2023; 19:106-122. [PMID: 36624649 DOI: 10.2174/1573402119666230109142156] [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: 04/23/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 01/11/2023]
Abstract
Cardiac circadian rhythms are an important regulator of body functions, including cardiac activities and blood pressure. Disturbance of circadian rhythm is known to trigger and aggravate various cardiovascular diseases. Thus, modulating the circadian rhythm can be used as a therapeutic approach to cardiovascular diseases. Through this work, we intend to discuss the current understanding of cardiac circadian rhythms, in terms of quantifiable parameters like BP and HR. We also elaborate on the molecular regulators and the molecular cascades along with their specific genetic aspects involved in modulating circadian rhythms, with specific reference to cardiovascular health and cardiovascular diseases. Along with this, we also presented the latest pharmacogenomic and metabolomics markers involved in chronobiological control of the cardiovascular system along with their possible utility in cardiovascular disease diagnosis and therapeutics. Finally, we reviewed the current expert opinions on chronotherapeutic approaches for utilizing the conventional as well as the new pharmacological molecules for antihypertensive chronotherapy.
Collapse
Affiliation(s)
- Kumud Joshi
- Department of Pharmacy, Lloyd Institute of Management and Technology, Greater Noida, India
| | - Madhubanti Das
- Department of Zoology, Gauhati University, Guwahati, Assam, India
| | - Anupam Sarma
- Advanced Drug Delivery Laboratory, GIPS, Girijananda Chowdhury University, Guwahati, Assam, India
| | - Mandeep K Arora
- School of Pharmacy and population health informatics, DIT University, Dehradun, India
| | - Manmohan SInghal
- School of Pharmacy and population health informatics, DIT University, Dehradun, India
| | - Bhavna Kumar
- School of Pharmacy and population health informatics, DIT University, Dehradun, India
| |
Collapse
|
3
|
Zhang Z, Liang Z, Gao W, Yu S, Hou Z, Li K, Zeng P. Identification of circadian clock genes as regulators of immune infiltration in Hepatocellular Carcinoma. J Cancer 2022; 13:3199-3208. [PMID: 36118525 PMCID: PMC9475357 DOI: 10.7150/jca.71925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Multiple studies have reported that the immune system is under the control of a circadian clock, especially in cancers, but how circadian clock genes shape tumor immune cell infiltration in hepatocellular carcinoma (HCC) remains unclear. Methods: The rhythmicity of circadian clock genes was investigated using the GETx database. The expression and methylation level of circadian clock genes in HCC and paracancerous was evaluated using the GETx and TCGA databases. The differential expression of circadian clock genes in HCC was analyzed using the “limma” package of the R 4.0.4 software. The prognosis of each circadian clock gene was accessed by Kaplan-Meier survival analysis and Cox proportional hazards regression analysis. Quantitative real-time PCR and immunohistochemistry (IHC) was carried out to confirm the results. The relationship between circadian rhythm and immune infiltration in HCC was evaluated using the TIMER database and the CIBERSORT algorithm. Results: In addition to RORA, RORB, and ARNTL2, there was a rhythmic expression of other circadian clock genes in liver tissue. The correlation between the expression of circadian clock genes differed when comparing HCC and liver tissue. HCC patients who express low levels of PER-1and CRY2 had a poor overall survival (OS). In contrast, patients with higher expression of NPAS2 had a poor prognosis. In HCC, the expression of the PER-1, CRY2, and NPAS2 genes was closely related to immune infiltration. Conclusion: Our study indicated the disruption of the expression of circadian clock-regulated genes in HCC and identified PER-1, CRY2, and NPAS2 as independent predictors of survival. These genes may be applied as candidate molecular targets for diagnosis and therapy of HCC.
Collapse
Affiliation(s)
- Zhen Zhang
- Department of Oncology, Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha 410006, P.R. China
| | - Zicheng Liang
- Department of Internal Medicine, College of Integrated Chinese and Western Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410208, P.R. China
| | - Wenhui Gao
- School of Chinese Medicine, Hunan University of Chinese Medicine, Changsha 410208, P.R. China
| | - Shuxian Yu
- Department of Oncology, Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha 410006, P.R. China
| | - Zongwei Hou
- Department of Oncology, Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha 410006, P.R. China
| | - Kexin Li
- Department of Oncology, Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha 410006, P.R. China
| | - Puhua Zeng
- Department of Oncology, Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha 410006, P.R. China
| |
Collapse
|
4
|
Pun TB, Phillips CL, Marshall NS, Comas M, Hoyos CM, D’Rozario AL, Bartlett DJ, Davis W, Hu W, Naismith SL, Cain S, Postnova S, Grunstein RR, Gordon CJ. The Effect of Light Therapy on Electroencephalographic Sleep in Sleep and Circadian Rhythm Disorders: A Scoping Review. Clocks Sleep 2022; 4:358-373. [PMID: 35997384 PMCID: PMC9397048 DOI: 10.3390/clockssleep4030030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 01/27/2023] Open
Abstract
Light therapy is used to treat sleep and circadian rhythm disorders, yet there are limited studies on whether light therapy impacts electroencephalographic (EEG) activity during sleep. Therefore, we aimed to provide an overview of research studies that examined the effects of light therapy on sleep macro- and micro-architecture in populations with sleep and circadian rhythm disorders. We searched for randomized controlled trials that used light therapy and included EEG sleep measures using MEDLINE, PubMed, CINAHL, PsycINFO and Cochrane Central Register of Controlled Trials databases. Five articles met the inclusion criteria of patients with either insomnia or delayed sleep−wake phase disorder (DSWPD). These trials reported sleep macro-architecture outcomes using EEG or polysomnography. Three insomnia trials showed no effect of the timing or intensity of light therapy on total sleep time, wake after sleep onset, sleep efficiency and sleep stage duration compared to controls. Only one insomnia trial reported significantly higher sleep efficiency after evening light therapy (>4000 lx between 21:00−23:00 h) compared with afternoon light therapy (>4000 lx between 15:00−17:00 h). In the only DSWPD trial, six multiple sleep latency tests were conducted across the day (09:00 and 19:00 h) and bright light (2500 lx) significantly lengthened sleep latency in the morning (09:00 and 11:00 h) compared to control light (300 lx). None of the five trials reported any sleep micro-architecture measures. Overall, there was limited research about the effect of light therapy on EEG sleep measures, and studies were confined to patients with insomnia and DSWPD only. More research is needed to better understand whether lighting interventions in clinical populations affect sleep macro- and micro-architecture and objective sleep timing and quality.
Collapse
Affiliation(s)
- Teha B. Pun
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Craig L. Phillips
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Nathaniel S. Marshall
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Maria Comas
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Camilla M. Hoyos
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- Healthy Brain Ageing Program, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW 2050, Australia
| | - Angela L. D’Rozario
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- Healthy Brain Ageing Program, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW 2050, Australia
| | - Delwyn J. Bartlett
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Wendy Davis
- School of Architecture, Design and Planning, The University of Sydney, Sydney, NSW 2008, Australia
| | - Wenye Hu
- School of Architecture, Design and Planning, The University of Sydney, Sydney, NSW 2008, Australia
| | - Sharon L. Naismith
- Healthy Brain Ageing Program, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW 2050, Australia
| | - Sean Cain
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, VIC 3800, Australia
| | - Svetlana Postnova
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- School of Physics, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ron R. Grunstein
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- Sleep and Severe Mental Illness Clinic, CPC-RPA Clinic, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Christopher J. Gordon
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- Correspondence: ; Tel.: +61-2-9351-0586
| |
Collapse
|
5
|
The role of cell-autonomous circadian oscillation of Cry transcription in circadian rhythm generation. Cell Rep 2022; 39:110703. [PMID: 35443162 DOI: 10.1016/j.celrep.2022.110703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/17/2022] [Accepted: 03/29/2022] [Indexed: 11/21/2022] Open
Abstract
The current model of the mammalian circadian clock describes cell-autonomous and negative feedback-driven circadian oscillation of Cry and Per transcription as the core circadian rhythm generator. However, the actual contribution of this oscillation to circadian rhythm generation remains undefined. Here we perform targeted disruption of cis elements indispensable for cell-autonomous Cry oscillation. Mice lacking overt cell-autonomous Cry oscillation show robust circadian rhythms in locomotor activity. In addition, tissue-autonomous circadian rhythms are robust in the absence of overt Cry oscillation. Unexpectedly, although the absence of overt Cry oscillation leads to severe attenuation of Per oscillation at the cell-autonomous level, circadian rhythms in Per2 accumulation remain robust. As a mechanism to explain this counterintuitive result, Per2 half-life shows cell-autonomous circadian rhythms independent of Cry and Per oscillation. The cell-autonomous circadian clock may therefore remain partially functional even in the absence of overt Cry and Per oscillation because of circadian oscillation in Per2 degradation.
Collapse
|
6
|
Circadian and Immunity Cycle Talk in Cancer Destination: From Biological Aspects to In Silico Analysis. Cancers (Basel) 2022; 14:cancers14061578. [PMID: 35326729 PMCID: PMC8945968 DOI: 10.3390/cancers14061578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary The circadian cycle is a natural cycle of the body repeated every 24 h, based on a day and night rhythm, and it affects many body processes. The present article reviews the importance and role of the circadian cycle in cancer and its association with the immune system and immunotherapy drugs at the cellular and molecular levels. It also examines the genes and cellular pathways involved in both circadian and immune systems. It offers possible computational solutions to increase the effectiveness of cancer treatment concerning the circadian cycle. Abstract Cancer is the leading cause of death and a major problem to increasing life expectancy worldwide. In recent years, various approaches such as surgery, chemotherapy, radiation, targeted therapies, and the newest pillar, immunotherapy, have been developed to treat cancer. Among key factors impacting the effectiveness of treatment, the administration of drugs based on the circadian rhythm in a person and within individuals can significantly elevate drug efficacy, reduce adverse effects, and prevent drug resistance. Circadian clocks also affect various physiological processes such as the sleep cycle, body temperature cycle, digestive and cardiovascular processes, and endocrine and immune systems. In recent years, to achieve precision patterns for drug administration using computational methods, the interaction of the effects of drugs and their cellular pathways has been considered more seriously. Integrated data-derived pathological images and genomics, transcriptomics, and proteomics analyses have provided an understanding of the molecular basis of cancer and dramatically revealed interactions between circadian and immunity cycles. Here, we describe crosstalk between the circadian cycle signaling pathway and immunity cycle in cancer and discuss how tumor microenvironment affects the influence on treatment process based on individuals’ genetic differences. Moreover, we highlight recent advances in computational modeling that pave the way for personalized immune chronotherapy.
Collapse
|
7
|
Circadian Clock Genes Are Correlated with Prognosis and Immune Cell Infiltration in Colon Adenocarcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:1709918. [PMID: 35116071 PMCID: PMC8807038 DOI: 10.1155/2022/1709918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/27/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022]
Abstract
Background Colon adenocarcinoma (COAD) is a malignancy with a high incidence and is associated with poor quality of life. Dysfunction of circadian clock genes and disruption of normal rhythms are associated with the occurrence and progression of many cancer types. However, studies that systematically describe the prognostic value and immune-related functions of circadian clock genes in COAD are lacking. Methods Genomic data obtained from The Cancer Genome Atlas (TCGA) database was analyzed for expression level, mutation status, potential biological functions, and prognostic performance of core circadian clock genes in COAD. Their correlations with immune infiltration and TMB/MSI score were analyzed by Spearman's correlation analysis. Pearson's correlation analysis was performed to analyze their associations with drug sensitivity. Lasso Cox regression analysis was performed to construct a prognosis signature. Moreover, an mRNA-miRNA-lncRNA regulatory axis was also detected by ceRNA network. Results In COAD tissues, the mRNA levels of CLOCK, CRY1, and NR1D1 were increased, while the mRNA levels of ARNTL, CRY2, PER1, PER3, and RORA were decreased. We also summarized the relative genetic mutation variation landscape. GO and KEGG pathway analyses demonstrated that these circadian clock genes were primarily correlated with the regulation of circadian rhythms and glucocorticoid receptor signaling pathways. COAD patients with high CRY2, NR1D1, and PER2 expression had worse prognosis. A prognostic model constructed based on the 9 core circadian clock genes predicted the COAD patients' overall survival with medium to high accuracy. A significant association between prognostic circadian clock genes and immune cell infiltration was found. Moreover, the lncRNA KCNQ1OT1/hsa-miRNA-32-5p/PER2/CRY2 regulatory axis in COAD was also detected through a mRNA-miRNA-lncRNA network. Conclusion Our results identified CRY2, NR1D1, and PER2 as potential prognostic biomarkers for COAD patients and correlated their expression with immune cell infiltration. The lncRNA KCNQ1OT1/hsa-miRNA-32-5p/PER2/CRY2 regulatory axis was detected in COAD and might play a vital role in the occurrence and progression of COAD.
Collapse
|
8
|
Zhu J, Zhou Q, Pan M, Zhou C. Multi-omics analysis of the prognosis and therapeutic significance of circadian clock in ovarian cancer. Gene 2021; 788:145644. [PMID: 33848579 DOI: 10.1016/j.gene.2021.145644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/14/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Ovarian cancer (OV) is one of the most common female malignancies with high morbidity and mortality, but its mechanism is not fully understood. The circadian clock is involved in the regulation of the immune system and the tumor microenvironment, regulating biological processes and behaviors in multiple ways. Circadian rhythm disorders are considered a risk factor for tumorigenesis. Multi-omics analysis was performed to comprehensively illustrate the roles of circadian clock genes in OV, we found that most of circadian clock genes undergo epigenetic alterations in OV and are strongly correlated with overall and progression-free patient survival. These clock genes are mainly involved in the inhibition of Apoptosis pathway, Cell Cycle pathway and DNA Damage Response pathway, as well as the activation of RAS/MAPK pathway and RTK pathway. Drug sensitivity model indicate that the expression of core clock genes may associate with drug resistance. Further, immune infiltrates analysis shows that different mutant forms of core genes can not only suppress immune infiltration, but also affect clinical outcome of ovarian cancer patients. Overall, our results may provide novel insights for the potential selection of immunotherapeutic targets.
Collapse
Affiliation(s)
- Jinyan Zhu
- Department of Gynecology, Maoming People's Hospital, Maoming, Guangdong 525000, China
| | - Qianyu Zhou
- Department of Gynecology, Huazhou Traditional Chinese Medicine Hospital, Maoming, Guangdong 525000, China
| | - Min Pan
- Department of Gynecology, Maoming People's Hospital, Maoming, Guangdong 525000, China.
| | - Cankun Zhou
- Department of Gynecology, Southern Medical University Affiliated Maternal & Child Health Hospital of Foshan, Foshan, Guangdong 528000, China.
| |
Collapse
|
9
|
Cox KH, Takahashi JS. Introduction to the Clock System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1344:3-20. [PMID: 34773223 DOI: 10.1007/978-3-030-81147-1_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Circadian (24-h) rhythms dictate almost everything we do, setting our clocks for specific times of sleeping and eating, as well as optimal times for many other basic functions. The physiological systems that coordinate circadian rhythms are intricate, but at their core, they all can be distilled down to cell-autonomous rhythms that are then synchronized within and among tissues. At first glance, these cell-autonomous rhythms may seem rather straight-forward, but years of research in the field has shown that they are strikingly complex, responding to many different external signals, often with remarkable tissue-specificity. To understand the cellular clock system, it is important to be familiar with the major players, which consist of pairs of proteins in a triad of transcriptional/translational feedback loops. In this chapter, we will go through each of the core protein pairs one-by-one, summarizing the literature as to their regulation and their broader impacts on circadian gene expression. We will conclude by briefly examining the human genetics literature, as well as providing perspectives on the future of the study of the molecular clock.
Collapse
Affiliation(s)
- Kimberly H Cox
- Department of Neuroscience and Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joseph S Takahashi
- Department of Neuroscience and Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
10
|
Zhou L, Luo Z, li Z, Huang Q. Circadian clock is associated with tumor microenvironment in kidney renal clear cell carcinoma. Aging (Albany NY) 2020; 12:14620-14632. [PMID: 32681792 PMCID: PMC7425457 DOI: 10.18632/aging.103509] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/04/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Kidney renal clear cell carcinoma (KIRC) is one of the most prevalent malignancies with high incidence and mortality. The circadian clock, which is also involved in the regulation of the immune system and tumor microenvironment, is an internal timing system that allows organisms to adjust biological processes and behaviors according to geophysical time. RESULT A wide range of circadian clock genes are epigenetically altered in KIRC, and associated with the overall survival and disease-free survival of patients. SNV analysis revealed missense mutation and splice site to be the most common variant types of circadian clock genes in KIRC. Several circadian clock genes were involved in the regulation of some cancer-related hallmark pathways, including apoptosis and cell cycle pathway. Further, immune infiltrates analysis not only revealed that the expression of circadian clock genes is associated with immune cell infiltrates, but also that somatic copy-number alteration of circadian clock genes could inhibit the immune infiltrates. Moreover, enrichment analysis implied that the circadian clock genes could regulate transcription factor activity and circadian rhythm in KIRC. CONCLUSION Our results demonstrate the potential of chrono-immunotherapy as a candidate option for the management of KIRC. METHOD Multi-omics analysis was performed to comprehensively determine the roles of core circadian clock genes in KIRC.
Collapse
MESH Headings
- Adenocarcinoma, Clear Cell/genetics
- Adenocarcinoma, Clear Cell/immunology
- Adenocarcinoma, Clear Cell/pathology
- Alternative Splicing
- Apoptosis/genetics
- Biomarkers, Tumor
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/pathology
- Circadian Rhythm
- Circadian Rhythm Signaling Peptides and Proteins/genetics
- Disease-Free Survival
- Epigenesis, Genetic
- Gene Dosage
- Genes, cdc/genetics
- Genetic Variation
- Humans
- Kidney Neoplasms/genetics
- Kidney Neoplasms/pathology
- Mutation, Missense
- Prognosis
- Survival Analysis
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
Collapse
Affiliation(s)
- Liangcheng Zhou
- Department of Nephrology, Maoming People’s Hospital, Maoming 525000, China
| | - Zhili Luo
- Department of Rehabilitative Medicine, Gaozhou People’s Hospital, Maoming 525200, China
| | - Zuwei li
- Department of Urology, Gaozhou People’s Hospital, Maoming 525200, China
| | - Qinying Huang
- Department of Ophthalmology, Shantou University Medical College, Shantou 515041, China
| |
Collapse
|
11
|
Yang Y, Yuan G, Xie H, Wei T, Zhu D, Cui J, Liu X, Shen R, Zhu Y, Yang X. Circadian clock associates with tumor microenvironment in thoracic cancers. Aging (Albany NY) 2019; 11:11814-11828. [PMID: 31881010 PMCID: PMC6949103 DOI: 10.18632/aging.102450] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 11/07/2019] [Indexed: 12/21/2022]
Abstract
The application of cancer chronotherapy is to treat cancers based on at specific times during circadian rhythms. Previous studies have characterized the impact of circadian clock on tumorigenesis and specific immune cells. Here, by using multi-omics computation techniques, we systematically characterized the distinct roles of core circadian clock genes in thoracic cancers including lung adenocarcinoma, lung squamous cell carcinoma, and esophageal carcinoma. Strikingly, a wide range of core clock genes are epigenetically altered in lung adenocarcinomas and lung squamous cell carcinomas but not esophageal carcinomas. Further cancer hallmark analysis reveals that several core clock genes highly correlate with apoptosis and cell cycle such as RORA and PER2. Interestingly, our results reveal that CD4 and CD8 T cells are correlated with core clock molecules especially in lung adenocarcinomas and lung squamous cell carcinomas, indicating that chrono-immunotherapy may serve as a candidate option for future cancer management.
Collapse
Affiliation(s)
- Yong Yang
- Department of Thoracic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Jiangsu 215001, China
| | - Guangda Yuan
- Department of Thoracic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Jiangsu 215001, China
| | - Hongya Xie
- Department of Thoracic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Jiangsu 215001, China
| | - Tengteng Wei
- Department of Thoracic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Jiangsu 215001, China
| | - Donglin Zhu
- Department of Thoracic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Jiangsu 215001, China
| | - Jianyong Cui
- Department of Thoracic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Jiangsu 215001, China
| | - Xiaoqiang Liu
- Department of Thoracic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Jiangsu 215001, China
| | - Rongming Shen
- Department of Thoracic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Jiangsu 215001, China
| | - Yimeng Zhu
- Department of Thoracic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Jiangsu 215001, China
| | - Xuefang Yang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Jiangsu 215001, China
| |
Collapse
|
12
|
The Phospho-Code Determining Circadian Feedback Loop Closure and Output in Neurospora. Mol Cell 2019; 74:771-784.e3. [PMID: 30954403 DOI: 10.1016/j.molcel.2019.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/07/2019] [Accepted: 03/01/2019] [Indexed: 10/27/2022]
Abstract
In the negative feedback loop driving fungal and animal circadian oscillators, negative elements (FREQUENCY [FRQ], PERIODS [PERs], and CRYPTOCHROMES [CRYs]) are understood to inhibit their own expression, in part by promoting the phosphorylation of their heterodimeric transcriptional activators (e.g., White Collar-1 [WC-1]-WC-2 [White Collar complex; WCC] and BMAL1/Circadian Locomotor Output Cycles Kaput [CLOCK]). However, correlations between heterodimer activity and phosphorylation are weak, contradictions exist, and mechanistic details are almost wholly lacking. We report mapping of 80 phosphosites on WC-1 and 15 on WC-2 and elucidation of the time-of-day-specific code, requiring both a group of phosphoevents on WC-1 and two distinct clusters on WC-2, that governs circadian repression, leading to feedback loop closure. Combinatorial control via phosphorylation also governs rhythmic WCC binding to the promoters of clock-controlled genes mediating the essential first step in circadian output, a group encoding both transcription factors and signaling proteins. These data provide a basic mechanistic understanding for fundamental events underlying circadian negative feedback and output, key aspects of circadian biology.
Collapse
|
13
|
Singh K, Jha NK, Thakur A. Spatiotemporal chromatin dynamics - A telltale of circadian epigenetic gene regulation. Life Sci 2019; 221:377-391. [PMID: 30721705 DOI: 10.1016/j.lfs.2019.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/27/2019] [Accepted: 02/01/2019] [Indexed: 01/08/2023]
Abstract
Over the course of evolution, nature has forced organisms under selection pressure to hardwire an internal time keeping device that defines 24 h of a daily cycle of physiological and behavioral rhythms, known as circadian rhythms. At the cellular level, the cycle is governed by significant fractions of transcriptomes, which are under the control of transcriptional and translational feedback loop of clock genes. Intriguingly, this feedback loop is regulated at multiple stratums such as at the transcriptional and translational levels, which direct a cell towards producing a robust rhythm by sustaining the repeated stoichiometry of protein products. Moreover, with the advent of state of the art paradigms, epigenetic regulation of circadian rhythms has been becoming more evident at present time. Light-induced recurring fluctuations in chromatin acetylation concurrent with the binding of RNA Pol II and integration of miRNAs monitor the chromatin modifiers or clock genes expression to drive temporal rhythmicity. Furthermore, CLOCK protein intrinsic histone acetyl transferase activity, the interaction of CLOCK-BMAL-1 with HAT enzymes, and the involvement of many histone deacetylases also maintain the rhythmic protein profile. Additionally, the critical role of the rhythmic methylation pattern of clock genes in battery of cancer and metabolic disorders also defines its importance. Therefore, in this review, we focused on accumulating all the present data available on epigenetics and circadian rhythms. Interestingly, we also gathered evidence from the available literature pinpointing towards the dynamic nature of chromatin architecture governed by long and short-range regulatory elements DNA contacts arising daily, that was thought to be steady otherwise.
Collapse
Affiliation(s)
- Kunal Singh
- Department of Biotechnology, Noida Institute of Engineering & Technology (NIET), Greater Noida, India.
| | - Niraj Kumar Jha
- Department of Biotechnology, Noida Institute of Engineering & Technology (NIET), Greater Noida, India
| | - Abhimanyu Thakur
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, India
| |
Collapse
|
14
|
Liberman AR, Halitjaha L, Ay A, Ingram KK. Modeling Strengthens Molecular Link between Circadian Polymorphisms and Major Mood Disorders. J Biol Rhythms 2018; 33:318-336. [PMID: 29614896 DOI: 10.1177/0748730418764540] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Anxiety and other mood disorders, such as major depressive disorder (MDD) and seasonal affective disorder (SAD), affect nearly one-fifth of the global population and disproportionately affect young adults. Individuals affected by mood disorders are frequently plagued by sleep and circadian problems, and recent genetic studies provide ample support for the association of circadian and sleep syndromes with depression and anxiety. Mathematical modeling has been crucial in understanding some of the essential features of the mammalian circadian clock and is now a vital tool for dissecting how circadian genes regulate the molecular mechanisms that influence mood. Here, we model the effect of five clock gene polymorphisms, previously linked to mood disorders, on circadian gene expression and, ultimately, on the period length and amplitude of the clock, two parameters that dictate the phase, or alignment, of the clock relative to the environment. We then test whether these gene variants are associated with circadian phenotypes (Horne-Ostberg Morningness-Eveningness scores) and well-established measures of depression (Beck Depression Inventory) and anxiety (State-Trait Anxiety Inventory) in a population of undergraduates ( n = 546). In this population, we find significant allelic and/or genotypic associations between CRY2 and two PER3 variants and diurnal preference. The PER3 length polymorphism (rs57875989) was significantly associated with depression in this sample, and individuals homozygous for the PER3 single nucleotide polymorphism (SNP) (rs228697) reported significantly higher anxiety. Our simple model satisfies available experimental knockdown conditions as well as existing data on clock polymorphisms associated with mood. In addition, our model enables us to predict circadian phenotypes (e.g., altered period length, amplitude) associated with mood disorders in order to identify critical effects of clock gene mutations on CRY/BMAL binding and to predict that the intronic SNPs studied represent gain-of-function mutations, causing increased transcription rate. Given the user-friendly structure of our model, we anticipate that it will be useful for further study of the relationships among clock polymorphisms, circadian misalignment, and mood disorders.
Collapse
Affiliation(s)
| | | | - Ahmet Ay
- Colgate University, Hamilton, New York
| | | |
Collapse
|
15
|
Montemurro C, Vadrevu S, Gurlo T, Butler AE, Vongbunyong KE, Petcherski A, Shirihai OS, Satin LS, Braas D, Butler PC, Tudzarova S. Cell cycle-related metabolism and mitochondrial dynamics in a replication-competent pancreatic beta-cell line. Cell Cycle 2017; 16:2086-2099. [PMID: 28820316 DOI: 10.1080/15384101.2017.1361069] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cell replication is a fundamental attribute of growth and repair in multicellular organisms. Pancreatic beta-cells in adults rarely enter cell cycle, hindering the capacity for regeneration in diabetes. Efforts to drive beta-cells into cell cycle have so far largely focused on regulatory molecules such as cyclins and cyclin-dependent kinases (CDKs). Investigations in cancer biology have uncovered that adaptive changes in metabolism, the mitochondrial network, and cellular Ca2+ are critical for permitting cells to progress through the cell cycle. Here, we investigated these parameters in the replication-competent beta-cell line INS 832/13. Cell cycle synchronization of this line permitted evaluation of cell metabolism, mitochondrial network, and cellular Ca2+ compartmentalization at key cell cycle stages. The mitochondrial network is interconnected and filamentous at G1/S but fragments during the S and G2/M phases, presumably to permit sorting to daughter cells. Pyruvate anaplerosis peaks at G1/S, consistent with generation of biomass for daughter cells, whereas mitochondrial Ca2+ and respiration increase during S and G2/M, consistent with increased energy requirements for DNA and lipid synthesis. This synchronization approach may be of value to investigators performing live cell imaging of Ca2+ or mitochondrial dynamics commonly undertaken in INS cell lines because without synchrony widely disparate data from cell to cell would be expected depending on position within cell cycle. Our findings also offer insight into why replicating beta-cells are relatively nonfunctional secreting insulin in response to glucose. They also provide guidance on metabolic requirements of beta-cells for the transition through the cell cycle that may complement the efforts currently restricted to manipulating cell cycle to drive beta-cells through cell cycle.
Collapse
Affiliation(s)
- Chiara Montemurro
- a Larry L. Hillblom Islet Research Center , University of California, Los Angeles, David Geffen School of Medicine , Los Angeles , CA , USA
| | - Suryakiran Vadrevu
- b Department of Pharmacology and Brehm Diabetes Research Center , University of Michigan , Ann Arbor , MI , USA
| | - Tatyana Gurlo
- a Larry L. Hillblom Islet Research Center , University of California, Los Angeles, David Geffen School of Medicine , Los Angeles , CA , USA
| | - Alexandra E Butler
- a Larry L. Hillblom Islet Research Center , University of California, Los Angeles, David Geffen School of Medicine , Los Angeles , CA , USA
| | - Kenny E Vongbunyong
- a Larry L. Hillblom Islet Research Center , University of California, Los Angeles, David Geffen School of Medicine , Los Angeles , CA , USA
| | - Anton Petcherski
- c Division of Endocrinology, Department of Medicine, David Geffen School of Medicine , University of California, Los Angeles , Los Angeles , CA , USA
| | - Orian S Shirihai
- c Division of Endocrinology, Department of Medicine, David Geffen School of Medicine , University of California, Los Angeles , Los Angeles , CA , USA
| | - Leslie S Satin
- b Department of Pharmacology and Brehm Diabetes Research Center , University of Michigan , Ann Arbor , MI , USA
| | - Daniel Braas
- d Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging , University of California, Los Angeles, David Geffen School of Medicine , Los Angeles , CA , USA ; UCLA Metabolomics Center , University of California, Los Angeles , Los Angeles , CA , USA
| | - Peter C Butler
- a Larry L. Hillblom Islet Research Center , University of California, Los Angeles, David Geffen School of Medicine , Los Angeles , CA , USA
| | - Slavica Tudzarova
- a Larry L. Hillblom Islet Research Center , University of California, Los Angeles, David Geffen School of Medicine , Los Angeles , CA , USA.,e Jonsson Comprehensive Cancer Center , University of California, Los Angeles, David Geffen School of Medicine , Los Angeles , CA , USA
| |
Collapse
|
16
|
Circadian Clock Model Supports Molecular Link Between PER3 and Human Anxiety. Sci Rep 2017; 7:9893. [PMID: 28860482 PMCID: PMC5579000 DOI: 10.1038/s41598-017-07957-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/06/2017] [Indexed: 01/17/2023] Open
Abstract
Generalized anxiety and major depression have become increasingly common in the United States, affecting 18.6 percent of the adult population. Mood disorders can be debilitating, and are often correlated with poor general health, life dissatisfaction, and the need for disability benefits due to inability to work. Recent evidence suggests that some mood disorders have a circadian component, and disruptions in circadian rhythms may even trigger the development of these disorders. However, the molecular mechanisms of this interaction are not well understood. Polymorphisms in a circadian clock-related gene, PER3, are associated with behavioral phenotypes (extreme diurnal preference in arousal and activity) and sleep/mood disorders, including seasonal affective disorder (SAD). Here we show that two PER3 mutations, a variable number tandem repeat (VNTR) allele and a single-nucleotide polymorphism (SNP), are associated with diurnal preference and higher Trait-Anxiety scores, supporting a role for PER3 in mood modulation. In addition, we explore a potential mechanism for how PER3 influences mood by utilizing a comprehensive circadian clock model that accurately predicts the changes in circadian period evident in knock-out phenotypes and individuals with PER3-related clock disorders.
Collapse
|
17
|
Hirano A, Fu YH, Ptáček LJ. The intricate dance of post-translational modifications in the rhythm of life. Nat Struct Mol Biol 2016; 23:1053-1060. [DOI: 10.1038/nsmb.3326] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/14/2016] [Indexed: 12/26/2022]
|
18
|
Shi G, Xie P, Qu Z, Zhang Z, Dong Z, An Y, Xing L, Liu Z, Dong Y, Xu G, Yang L, Liu Y, Xu Y. Distinct Roles of HDAC3 in the Core Circadian Negative Feedback Loop Are Critical for Clock Function. Cell Rep 2016; 14:823-834. [PMID: 26776516 DOI: 10.1016/j.celrep.2015.12.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 10/11/2015] [Accepted: 12/15/2015] [Indexed: 01/30/2023] Open
Abstract
In the core mammalian circadian negative feedback loop, the BMAL1-CLOCK complex activates the transcription of the genes Period (Per) and Cryptochrome (Cry). To close the negative feedback loop, the PER-CRY complex interacts with the BMAL1-CLOCK complex to repress its activity. These two processes are separated temporally to ensure clock function. Here, we show that histone deacetylase 3 (HDAC3) is a critical component of the circadian negative feedback loop by regulating both the activation and repression processes in a deacetylase activity-independent manner. Genetic depletion of Hdac3 results in low-amplitude circadian rhythms and dampened E-box-driven transcription. In subjective morning, HDAC3 is required for the efficient transcriptional activation process by regulating BMAL1 stability. In subjective night, however, HDAC3 blocks FBXL3-mediated CRY1 degradation and strongly promotes BMAL1 and CRY1 association. Therefore, these two opposing but temporally separated roles of HDAC3 in the negative feedback loop provide a mechanism for robust circadian gene expression.
Collapse
Affiliation(s)
- Guangsen Shi
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Pancheng Xie
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhipeng Qu
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhihui Zhang
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhen Dong
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Yang An
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Lijuan Xing
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Yingying Dong
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Guoqiang Xu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Ling Yang
- Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Ying Xu
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China; Cambridge-Suda Genomic Research Center, Soochow University, 199 Renai Road, Suzhou 215123, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China.
| |
Collapse
|
19
|
Dasgupta A, Fuller KK, Dunlap JC, Loros JJ. Seeing the world differently: variability in the photosensory mechanisms of two model fungi. Environ Microbiol 2015; 18:5-20. [PMID: 26373782 DOI: 10.1111/1462-2920.13055] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/01/2015] [Accepted: 09/12/2015] [Indexed: 12/14/2022]
Abstract
Light plays an important role for most organisms on this planet, serving either as a source of energy or information for the adaptation of biological processes to specific times of day. The fungal kingdom is estimated to contain well over a million species, possibly 10-fold more, and it is estimated that a majority of the fungi respond to light, eliciting changes in several physiological characteristics including pathogenesis, development and secondary metabolism. Two model organisms for photobiological studies have taken centre-stage over the last few decades--Neurospora crassa and Aspergillus nidulans. In this review, we will first discuss our understanding of the light response in N. crassa, about which the most is known, and will then juxtapose N. crassa with A. nidulans, which, as will be described below, provides an excellent template for understanding photosensory cross-talk. Finally, we will end with a commentary on the variability of the light response among other relevant fungi, and how our molecular understanding in the aforementioned model organisms still provides a strong base for dissecting light responses in such species.
Collapse
Affiliation(s)
- Arko Dasgupta
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Kevin K Fuller
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jay C Dunlap
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jennifer J Loros
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| |
Collapse
|
20
|
How is the inner circadian clock controlled by interactive clock proteins?: Structural analysis of clock proteins elucidates their physiological role. FEBS Lett 2015; 589:1516-29. [PMID: 25999309 DOI: 10.1016/j.febslet.2015.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 12/12/2022]
Abstract
Most internationally travelled researchers will have encountered jetlag. If not, working odd hours makes most of us feel somehow dysfunctional. How can all this be linked to circadian rhythms and circadian clocks? In this review, we define circadian clocks, their composition and underlying molecular mechanisms. We describe and discuss recent crystal structures of Drosophila and mammalian core clock components and the enormous impact they had on the understanding of circadian clock mechanisms. Finally, we highlight the importance of circadian clocks for the daily regulation of human/mammalian physiology and show connections to overall fitness, health and disease.
Collapse
|