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Escalante-Covarrubias Q, Mendoza-Viveros L, González-Suárez M, Sitten-Olea R, Velázquez-Villegas LA, Becerril-Pérez F, Pacheco-Bernal I, Carreño-Vázquez E, Mass-Sánchez P, Bustamante-Zepeda M, Orozco-Solís R, Aguilar-Arnal L. Time-of-day defines NAD + efficacy to treat diet-induced metabolic disease by synchronizing the hepatic clock in mice. Nat Commun 2023; 14:1685. [PMID: 36973248 PMCID: PMC10043291 DOI: 10.1038/s41467-023-37286-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
The circadian clock is an endogenous time-tracking system that anticipates daily environmental changes. Misalignment of the clock can cause obesity, which is accompanied by reduced levels of the clock-controlled, rhythmic metabolite NAD+. Increasing NAD+ is becoming a therapy for metabolic dysfunction; however, the impact of daily NAD+ fluctuations remains unknown. Here, we demonstrate that time-of-day determines the efficacy of NAD+ treatment for diet-induced metabolic disease in mice. Increasing NAD+ prior to the active phase in obese male mice ameliorated metabolic markers including body weight, glucose and insulin tolerance, hepatic inflammation and nutrient sensing pathways. However, raising NAD+ immediately before the rest phase selectively compromised these responses. Remarkably, timed NAD+ adjusted circadian oscillations of the liver clock until completely inverting its oscillatory phase when increased just before the rest period, resulting in misaligned molecular and behavioral rhythms in male and female mice. Our findings unveil the time-of-day dependence of NAD+-based therapies and support a chronobiology-based approach.
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Affiliation(s)
- Quetzalcoatl Escalante-Covarrubias
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Lucía Mendoza-Viveros
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
| | - Mirna González-Suárez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Román Sitten-Olea
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Laura A Velázquez-Villegas
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080, Mexico City, Mexico
| | - Fernando Becerril-Pérez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ignacio Pacheco-Bernal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Erick Carreño-Vázquez
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
| | - Paola Mass-Sánchez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Marcia Bustamante-Zepeda
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ricardo Orozco-Solís
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
- Centro de Investigación sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados, 14330, Mexico City, Mexico
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
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2
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Ness-Cohn E, Braun R. TimeCycle: Topology Inspired MEthod for the Detection of Cycling Transcripts in Circadian Time-Series Data. Bioinformatics 2021; 37:4405-4413. [PMID: 34175927 PMCID: PMC8652031 DOI: 10.1093/bioinformatics/btab476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/05/2021] [Accepted: 06/25/2021] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues. The recent revolution in high-throughput transcriptomics, coupled with the significant implications of the circadian clock for human health, has sparked an interest in circadian profiling studies to discover genes under circadian control. RESULT We present TimeCycle: a topology-based rhythm detection method designed to identify cycling transcripts. For a given time-series, the method reconstructs the state space using time-delay embedding, a data transformation technique from dynamical systems theory. In the embedded space, Takens' theorem proves that the dynamics of a rhythmic signal will exhibit circular patterns. The degree of circularity of the embedding is calculated as a persistence score using persistent homology, an algebraic method for discerning the topological features of data. By comparing the persistence scores to a bootstrapped null distribution, cycling genes are identified. Results in both synthetic and biological data highlight TimeCycle's ability to identify cycling genes across a range of sampling schemes, number of replicates, and missing data. Comparison to competing methods highlights their relative strengths, providing guidance as to the optimal choice of cycling detection method. AVAILABILITY A fully documented open-source R package implementing TimeCycle is available at: https://nesscoder.github.io/TimeCycle/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Elan Ness-Cohn
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.,Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Rosemary Braun
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.,Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA.,Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.,Northwestern Instutute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
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Ness-Cohn E, Iwanaszko M, Kath WL, Allada R, Braun R. TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Time-Series Data in Circadian Biology Research. J Biol Rhythms 2020; 35:439-451. [PMID: 32613882 PMCID: PMC7534021 DOI: 10.1177/0748730420934672] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues, coordinating physiological processes. The effect of this rhythm on health has generated increasing interest in discovering genes under circadian control by searching for periodic patterns in transcriptomic time-series experiments. While algorithms for detecting cycling transcripts have advanced, there remains little guidance quantifying the effect of experimental design and analysis choices on cycling detection accuracy. We present TimeTrial, a user-friendly benchmarking framework using both real and synthetic data to investigate cycle detection algorithms’ performance and improve circadian experimental design. Results show that the optimal choice of analysis method depends on the sampling scheme, noise level, and shape of the waveform of interest and provides guidance on the impact of sampling frequency and duration on cycling detection accuracy. The TimeTrial software is freely available for download and may also be accessed through a web interface. By supplying a tool to vary and optimize experimental design considerations, TimeTrial will enhance circadian transcriptomics studies.
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Affiliation(s)
- Elan Ness-Cohn
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA
| | - Marta Iwanaszko
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Silesian University of Technology, Department of Systems Biology and Engineering, Gliwice, Poland
| | - William L Kath
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.,Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Ravi Allada
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Rosemary Braun
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, USA
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4
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Braun R, Kath WL, Iwanaszko M, Kula-Eversole E, Abbott SM, Reid KJ, Zee PC, Allada R. Universal method for robust detection of circadian state from gene expression. Proc Natl Acad Sci U S A 2018; 115:E9247-E9256. [PMID: 30201705 PMCID: PMC6166804 DOI: 10.1073/pnas.1800314115] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Circadian clocks play a key role in regulating a vast array of biological processes, with significant implications for human health. Accurate assessment of physiological time using transcriptional biomarkers found in human blood can significantly improve diagnosis of circadian disorders and optimize the delivery time of therapeutic treatments. To be useful, such a test must be accurate, minimally burdensome to the patient, and readily generalizable to new data. A major obstacle in development of gene expression biomarker tests is the diversity of measurement platforms and the inherent variability of the data, often resulting in predictors that perform well in the original datasets but cannot be universally applied to new samples collected in other settings. Here, we introduce TimeSignature, an algorithm that robustly infers circadian time from gene expression. We demonstrate its application in data from three independent studies using distinct microarrays and further validate it against a new set of samples profiled by RNA-sequencing. Our results show that TimeSignature is more accurate and efficient than competing methods, estimating circadian time to within 2 h for the majority of samples. Importantly, we demonstrate that once trained on data from a single study, the resulting predictor can be universally applied to yield highly accurate results in new data from other studies independent of differences in study population, patient protocol, or assay platform without renormalizing the data or retraining. This feature is unique among expression-based predictors and addresses a major challenge in the development of generalizable, clinically useful tests.
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Affiliation(s)
- Rosemary Braun
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611;
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208
| | - William L Kath
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208
- Department of Neurobiology, Northwestern University, Evanston, IL 60208
| | - Marta Iwanaszko
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208
| | | | - Sabra M Abbott
- Department of Neurology, Northwestern University, Chicago, IL 60611
- the Center for Circadian and Sleep Medicine, Northwestern University, Chicago, IL 60611
| | - Kathryn J Reid
- Department of Neurology, Northwestern University, Chicago, IL 60611
- the Center for Circadian and Sleep Medicine, Northwestern University, Chicago, IL 60611
| | - Phyllis C Zee
- Department of Neurobiology, Northwestern University, Evanston, IL 60208
- Department of Neurology, Northwestern University, Chicago, IL 60611
| | - Ravi Allada
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208
- Department of Neurobiology, Northwestern University, Evanston, IL 60208
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5
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Sundar IK, Sellix MT, Rahman I. Redox regulation of circadian molecular clock in chronic airway diseases. Free Radic Biol Med 2018; 119:121-128. [PMID: 29097215 PMCID: PMC5910271 DOI: 10.1016/j.freeradbiomed.2017.10.383] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/12/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022]
Abstract
At the cellular level, circadian timing is maintained by the molecular clock, a family of interacting clock gene transcription factors, nuclear receptors and kinases called clock genes. Daily rhythms in pulmonary function are dictated by the circadian timing system, including rhythmic susceptibility to the harmful effects of airborne pollutants, exacerbations in patients with chronic airway disease and the immune-inflammatory response to infection. Further, evidence strongly suggests that the circadian molecular clock has a robust reciprocal interaction with redox signaling and plays a considerable role in the response to oxidative/carbonyl stress. Disruption of the circadian timing system, particularly in airway cells, impairs pulmonary rhythms and lung function, enhances oxidative stress due to airway inhaled pollutants like cigarette smoke and airborne particulate matter and leads to enhanced inflammosenescence, inflammasome activation, DNA damage and fibrosis. Herein, we briefly review recent evidence supporting the role of the lung molecular clock and redox signaling in regulating inflammation, oxidative stress, and DNA damage responses in lung diseases and their exacerbations. We further describe the potential for clock genes as novel biomarkers and therapeutic targets for the treatment of chronic lung diseases.
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Affiliation(s)
- Isaac K Sundar
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael T Sellix
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Rochester Medical Center, Rochester, NY, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA.
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Bartman CM, Oyama Y, Brodsky K, Khailova L, Walker L, Koeppen M, Eckle T. Intense light-elicited upregulation of miR-21 facilitates glycolysis and cardioprotection through Per2-dependent mechanisms. PLoS One 2017; 12:e0176243. [PMID: 28448534 PMCID: PMC5407766 DOI: 10.1371/journal.pone.0176243] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 03/21/2017] [Indexed: 12/12/2022] Open
Abstract
A wide search for ischemic preconditioning (IPC) mechanisms of cardioprotection identified the light elicited circadian rhythm protein Period 2 (Per2) to be cardioprotective. Studies on cardiac metabolism found a key role for light elicited Per2 in mediating metabolic dependence on carbohydrate metabolism. To profile Per2 mediated pathways following IPC of the mouse heart, we performed a genome array and identified 352 abundantly expressed and well-characterized Per2 dependent micro RNAs. One prominent result of our in silico analysis for cardiac Per2 dependent micro RNAs revealed a selective role for miR-21 in the regulation of hypoxia and metabolic pathways. Based on this Per2 dependency, we subsequently found a diurnal expression pattern for miR-21 with higher miR-21 expression levels at Zeitgeber time (ZT) 15 compared to ZT3. Gain or loss of function studies for miR-21 using miRNA mimics or miRNA inhibitors and a Seahorse Bioanalyzer uncovered a critical role of miR-21 for cellular glycolysis, glycolytic capacity, and glycolytic reserve. Exposing mice to intense light, a strategy to induce Per2, led to a robust induction of cardiac miR-21 tissue levels and decreased infarct sizes, which was abolished in miR-21-/- mice. Similarly, first translational studies in humans using intense blue light exposure for 5 days in healthy volunteers resulted in increased plasma miR-21 levels which was associated with increased phosphofructokinase activity, the rate-limiting enzyme in glycolysis. Together, we identified miR-21 as cardioprotective downstream target of Per2 and suggest intense light therapy as a potential strategy to enhance miR-21 activity and subsequent carbohydrate metabolism in humans.
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Affiliation(s)
- Colleen Marie Bartman
- Department of Anesthesiology, University of Colorado Denver School of Medicine, Aurora, CO, United States of America
- Department of Cell and Developmental Biology, University of Colorado Denver School of Medicine, Aurora, CO, United States of America
| | - Yoshimasa Oyama
- Department of Anesthesiology, University of Colorado Denver School of Medicine, Aurora, CO, United States of America
- Department of Anesthesiology and Intensive Care Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Kelley Brodsky
- Department of Anesthesiology, University of Colorado Denver School of Medicine, Aurora, CO, United States of America
- Division of Cardiology, Department of Medicine, University of Colorado Denver School of Medicine, Aurora, CO, United States of America
| | - Ludmila Khailova
- Department of Anesthesiology, University of Colorado Denver School of Medicine, Aurora, CO, United States of America
| | - Lori Walker
- Division of Cardiology, Department of Medicine, University of Colorado Denver School of Medicine, Aurora, CO, United States of America
| | - Michael Koeppen
- Department of Anesthesiology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Tobias Eckle
- Department of Anesthesiology, University of Colorado Denver School of Medicine, Aurora, CO, United States of America
- Department of Cell and Developmental Biology, University of Colorado Denver School of Medicine, Aurora, CO, United States of America
- Division of Cardiology, Department of Medicine, University of Colorado Denver School of Medicine, Aurora, CO, United States of America
- * E-mail:
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7
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Sundar IK, Yao H, Sellix MT, Rahman I. Circadian molecular clock in lung pathophysiology. Am J Physiol Lung Cell Mol Physiol 2015; 309:L1056-75. [PMID: 26361874 DOI: 10.1152/ajplung.00152.2015] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/08/2015] [Indexed: 02/06/2023] Open
Abstract
Disrupted daily or circadian rhythms of lung function and inflammatory responses are common features of chronic airway diseases. At the molecular level these circadian rhythms depend on the activity of an autoregulatory feedback loop oscillator of clock gene transcription factors, including the BMAL1:CLOCK activator complex and the repressors PERIOD and CRYPTOCHROME. The key nuclear receptors and transcription factors REV-ERBα and RORα regulate Bmal1 expression and provide stability to the oscillator. Circadian clock dysfunction is implicated in both immune and inflammatory responses to environmental, inflammatory, and infectious agents. Molecular clock function is altered by exposomes, tobacco smoke, lipopolysaccharide, hyperoxia, allergens, bleomycin, as well as bacterial and viral infections. The deacetylase Sirtuin 1 (SIRT1) regulates the timing of the clock through acetylation of BMAL1 and PER2 and controls the clock-dependent functions, which can also be affected by environmental stressors. Environmental agents and redox modulation may alter the levels of REV-ERBα and RORα in lung tissue in association with a heightened DNA damage response, cellular senescence, and inflammation. A reciprocal relationship exists between the molecular clock and immune/inflammatory responses in the lungs. Molecular clock function in lung cells may be used as a biomarker of disease severity and exacerbations or for assessing the efficacy of chronotherapy for disease management. Here, we provide a comprehensive overview of clock-controlled cellular and molecular functions in the lungs and highlight the repercussions of clock disruption on the pathophysiology of chronic airway diseases and their exacerbations. Furthermore, we highlight the potential for the molecular clock as a novel chronopharmacological target for the management of lung pathophysiology.
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Affiliation(s)
- Isaac K Sundar
- Department of Environmental Medicine, Lung Biology and Disease Program, University of Rochester Medical Center, Rochester, New York; and
| | - Hongwei Yao
- Department of Environmental Medicine, Lung Biology and Disease Program, University of Rochester Medical Center, Rochester, New York; and
| | - Michael T Sellix
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Rochester Medical Center, Rochester, New York
| | - Irfan Rahman
- Department of Environmental Medicine, Lung Biology and Disease Program, University of Rochester Medical Center, Rochester, New York; and
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