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Katoku-Kikyo N, Lim S, Yuan C, Koroth J, Nakagawa Y, Bradley EW, Kikyo N. The circadian regulator PER1 promotes cell reprogramming by inhibiting inflammatory signaling from macrophages. PLoS Biol 2023; 21:e3002419. [PMID: 38048364 PMCID: PMC10721173 DOI: 10.1371/journal.pbio.3002419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 12/14/2023] [Accepted: 11/03/2023] [Indexed: 12/06/2023] Open
Abstract
Circadian regulation of gene expression is prevalent and plays critical roles in cell differentiation. However, its roles in the reprogramming of differentiated cells remain largely unknown. Here, we found that one of the master circadian regulators PER1 promoted virus-mediated reprogramming of mouse embryonic fibroblasts (MEFs) to induced neurons (iNs) and induced pluripotent stem cells (iPSCs). Unexpectedly, PER1 achieved this by repressing inflammatory activation of contaminating macrophages in the MEF culture, rather than by directly modulating the reprogrammability of MEFs. More specifically, we found that transduced viruses activated inflammatory genes in macrophages, such as Tnf encoding TNFα, one of the central inflammatory regulators and an autocrine activator of macrophages. TNFα inhibited iN reprogramming, whereas a TNFα inhibitor promoted iN reprogramming, connecting the inflammatory responses to iN reprogramming. In addition, macrophages were induced to proliferate and mature by non-macrophage cells serving as feeders, which also supported up-regulation of TNFα in macrophages without virus transduction. Furthermore, the 2 inflammatory responses were repressed by the circadian regulator PER1 in macrophages, making reprogrammability dependent on time-of-day of virus transduction. Similar results were obtained with iPSC reprogramming, suggesting a wide occurrence of macrophage-mediated inhibition of cell reprogramming. This study uncovers mechanistic links between cell reprogramming, bystander inflammatory macrophages, and circadian rhythms, which are particularly relevant to in vivo reprogramming and organoid formation incorporating immune cells.
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Affiliation(s)
- Nobuko Katoku-Kikyo
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Seunghyun Lim
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ce Yuan
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jinsha Koroth
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Orthopedic Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Yasushi Nakagawa
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Elizabeth W. Bradley
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Orthopedic Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Nobuaki Kikyo
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
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2
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Gršković P, Korać P. Circadian Gene Variants in Diseases. Genes (Basel) 2023; 14:1703. [PMID: 37761843 PMCID: PMC10531145 DOI: 10.3390/genes14091703] [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: 07/22/2023] [Revised: 08/19/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
The circadian rhythm is a self-sustaining 24 h cycle that regulates physiological processes within the body, including cycles of alertness and sleepiness. Cells have their own intrinsic clock, which consists of several proteins that regulate the circadian rhythm of each individual cell. The core of the molecular clock in human cells consists of four main circadian proteins that work in pairs. The CLOCK-BMAL1 heterodimer and the PER-CRY heterodimer each regulate the other pair's expression, forming a negative feedback loop. Several other proteins are involved in regulating the expression of the main circadian genes, and can therefore also influence the circadian rhythm of cells. This review focuses on the existing knowledge regarding circadian gene variants in both the main and secondary circadian genes, and their association with various diseases, such as tumors, metabolic diseases, cardiovascular diseases, and sleep disorders.
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Affiliation(s)
| | - Petra Korać
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10 000 Zagreb, Croatia;
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3
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Lesicka M, Nedoszytko B, Reszka E. Disruptions of Circadian Genes in Cutaneous Melanoma-An In Silico Analysis of Transcriptome Databases. Int J Mol Sci 2023; 24:10140. [PMID: 37373286 DOI: 10.3390/ijms241210140] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Circadian genes are a set of genes that regulate the body's internal clock and influence various physiological processes, including sleep-wake cycles, metabolism and immune function. Skin cutaneous melanoma (SKCM) is a type of skin cancer that arises from the pigment-producing cells in the skin and is the most deadly form of skin cancer. This study has investigated the relevance of circadian gene expression and immune infiltrations in the outcomes of cutaneous melanoma patients. In the present study, in silico methods based on the GEPIa, TIMER 2.0 and cBioPortal databases were performed, so as to investigate the transcript level and prognostic value of 24 circadian genes in SKCM and their relationship with the immune infiltration level. The in silico analysis showed that significantly more than half of the investigated circadian genes have an altered transcript pattern in cutaneous melanoma compared to normal skin. The mRNA levels of TIMELES and BHLHE41 were upregulated, whereas those of NFIL3, BMAL1, HLF, TEF, RORA, RORC, NR1D1, PER1, PER2, PER3, CRY2 and BHLHE40 were downregulated. The presented research shows that SKCM patients with at least one alteration of their circadian genes have decreased overall survival. Additionally, majority of the circadian genes are significantly corelated with the immune cells' infiltration level. The strongest correlation was found for neutrophils and was followed by circadian genes: NR1D2 r = 0.52 p < 0.0001, BMAL1 r = 0.509 p < 0.0001; CLOCK r = 0.45 p < 0.0001; CSNKA1A1 r = 0.45 p < 0.0001; RORA r = 0.44 p < 0.0001. The infiltration level of immune cells in skin tumors has been associated with patient prognosis and treatment response. Circadian regulation of immune cell infiltration may further contribute to these prognostic and predictive markers. Examining the correlation between circadian rhythm and immune cell infiltration can provide valuable insights into disease progression and guide personalized treatment decisions.
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Affiliation(s)
- Monika Lesicka
- Department of Translational Research, Nofer Institute of Occupational Medicine, 91-349 Lodz, Poland
| | - Bogusław Nedoszytko
- Department of Dermatology, Venerology and Allergology Medical University of Gdansk, 80-211 Gdansk, Poland
- Molecular Laboratory, Invicta Fertility and Reproductive Centre, Polna 64, 81-740 Sopot, Poland
| | - Edyta Reszka
- Department of Translational Research, Nofer Institute of Occupational Medicine, 91-349 Lodz, Poland
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4
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Felten M, Ferencik S, Teixeira Alves LG, Letsiou E, Lienau J, Müller-Redetzky HC, Langenhagen AK, Voß A, Dietert K, Kershaw O, Gruber AD, Michalick L, Kuebler WM, Ananthasubramaniam B, Maier B, Uhlenhaut H, Kramer A, Witzenrath M. Ventilator-induced Lung Injury Is Modulated by the Circadian Clock. Am J Respir Crit Care Med 2023; 207:1464-1474. [PMID: 36480958 DOI: 10.1164/rccm.202202-0320oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Rationale: Mechanical ventilation (MV) is life-saving but may evoke ventilator-induced lung injury (VILI). Objectives: To explore how the circadian clock modulates severity of murine VILI via the core clock component BMAL1 (basic helix-loop-helix ARNT like 1) in myeloid cells. Methods: Myeloid cell BMAL1-deficient (LysM (lysozyme 2 promoter/enhancer driving cre recombinase expression)Bmal1-/-) or wild-type control (LysMBmal1+/+) mice were subjected to 4 hours MV (34 ml/kg body weight) to induce lung injury. Ventilation was initiated at dawn or dusk or in complete darkness (circadian time [CT] 0 or CT12) to determine diurnal and circadian effects. Lung injury was quantified by lung function, pulmonary permeability, blood gas analysis, neutrophil recruitment, inflammatory markers, and histology. Neutrophil activation and oxidative burst were analyzed ex vivo. Measurements and Main Results: In diurnal experiments, mice ventilated at dawn exhibited higher permeability and neutrophil recruitment compared with dusk. Experiments at CT showed deterioration of pulmonary function, worsening of oxygenation, and increased mortality at CT0 compared with CT12. Wild-type neutrophils isolated at dawn showed higher activation and reactive oxygen species production compared with dusk, whereas these day-night differences were dampened in LysMBmal1-/- neutrophils. In LysMBmal1-/- mice, circadian variations in VILI severity were dampened and VILI-induced mortality at CT0 was reduced compared with LysMBmal1+/+ mice. Conclusions: Inflammatory response and lung barrier dysfunction upon MV exhibit diurnal variations, regulated by the circadian clock. LysMBmal1-/- mice are less susceptible to ventilation-induced pathology and lack circadian variation of severity compared with LysMBmal1+/+ mice. Our data suggest that the internal clock in myeloid cells is an important modulator of VILI.
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Affiliation(s)
- Matthias Felten
- Department of Infectious Diseases, Respiratory Medicine and Critical Care
| | - Sebastian Ferencik
- Department of Infectious Diseases, Respiratory Medicine and Critical Care
| | | | - Eleftheria Letsiou
- Division of Pulmonary, Critical Care, Sleep, and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Jasmin Lienau
- Department of Infectious Diseases, Respiratory Medicine and Critical Care
| | | | | | - Anne Voß
- Department of Veterinary Pathology and
| | - Kristina Dietert
- Department of Veterinary Pathology and
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | | | | | - Laura Michalick
- Institute of Physiology
- German Centre for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Wolfgang M Kuebler
- Institute of Physiology
- German Centre for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Giessen, Germany; and
| | | | - Bert Maier
- Laboratory of Chronobiology, Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Henriette Uhlenhaut
- Metabolic Programming, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases, Respiratory Medicine and Critical Care
- German Center for Lung Research (DZL), Giessen, Germany; and
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5
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Waddell H, Stevenson TJ, Mole DJ. The role of the circadian rhythms in critical illness with a focus on acute pancreatitis. Heliyon 2023; 9:e15335. [PMID: 37089281 PMCID: PMC10119767 DOI: 10.1016/j.heliyon.2023.e15335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/20/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023] Open
Abstract
Circadian rhythms are responsible for governing various physiological processes, including hormone secretion, immune responses, metabolism, and the sleep/wake cycle. In critical illnesses such as acute pancreatitis (AP), circadian rhythms can become dysregulated due to disease. Evidence suggests that time of onset of disease, coupled with peripheral inflammation brought about by AP will impact on the circadian rhythms generated in the central pacemaker and peripheral tissues. Cells of the innate and adaptive immune system are governed by circadian rhythms and the diurnal pattern of expression can be disrupted during disease. Peak circadian immune cell release and gene expression can coincide with AP onset, that may increase pancreatic injury, tissue damage and the potential for systemic inflammation and multiple organ failure to develop. Here, we provide an overview of the role of circadian rhythms in AP and the underpinning inflammatory mechanisms to contextualise ongoing research into the chronobiology and chronotherapeutics of AP.
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Affiliation(s)
- Heather Waddell
- Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Tyler J. Stevenson
- Institute of Biodiversity and Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Damian J. Mole
- Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, EH16 4TJ, UK
- Clinical Surgery, School of Clinical Sciences and Community Health, The University of Edinburgh, Edinburgh, EH16 4SB, UK
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6
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Stanton D, Justin HS, Reitzel AM. Step in Time: Conservation of Circadian Clock Genes in Animal Evolution. Integr Comp Biol 2022; 62:1503-1518. [PMID: 36073444 DOI: 10.1093/icb/icac140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 01/05/2023] Open
Abstract
Over the past few decades, the molecular mechanisms responsible for circadian phenotypes of animals have been studied in increasing detail in mammals, some insects, and other invertebrates. Particular circadian proteins and their interactions are shared across evolutionary distant animals, resulting in a hypothesis for the canonical circadian clock of animals. As the number of species for which the circadian clockwork has been described increases, the circadian clock in animals driving cyclical phenotypes becomes less similar. Our focus in this review is to develop and synthesize the current literature to better understand the antiquity and evolution of the animal circadian clockwork. Here, we provide an updated understanding of circadian clock evolution in animals, largely through the lens of conserved genes characterized in the circadian clock identified in bilaterian species. These comparisons reveal extensive variation within the likely composition of the core clock mechanism, including losses of many genes, and that the ancestral clock of animals does not equate to the bilaterian clock. Despite the loss of these core genes, these species retain circadian behaviors and physiology, suggesting novel clocks have evolved repeatedly. Additionally, we highlight highly conserved cellular processes (e.g., cell division, nutrition) that intersect with the circadian clock of some animals. The conservation of these processes throughout the animal tree remains essentially unknown, but understanding their role in the evolution and maintenance of the circadian clock will provide important areas for future study.
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Affiliation(s)
- Daniel Stanton
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
| | - Hannah S Justin
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte NC 28223, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte NC 28223, USA
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7
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Lee EY, Wilcox ME. Sleep in the intensive care unit. Curr Opin Pulm Med 2022; 28:515-521. [PMID: 36101905 DOI: 10.1097/mcp.0000000000000912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Sleep is particularly important for critically ill patients. Here, we review the latest evidence on how sleep and circadian disruption in the intensive care unit (ICU) affects physiology and clinical outcomes, as well as the most recent advances in sleep and circadian rhythm promoting interventions including therapeutics. RECENT FINDINGS On a molecular level, clock genes dysrhythmia and altered immunity are clearly linked, particularly in sepsis. Melatonin may also be associated with insulin sensitivity in ICU patients. Clinically, changes in sleep architecture are associated with delirium, and sleep-promoting interventions in the form of multifaceted care bundles may reduce its incidence. Regarding medications, one recent randomized controlled trial (RCT) on melatonin showed no difference in sleep quality or incidence of delirium. SUMMARY Further investigation is needed to establish the clinical relevance of sleep and circadian disruption in the ICU. For interventions, standardized protocols of sleep promotion bundles require validation by larger multicenter trials. Administratively, such protocols should be individualized to both organizational and independent patient needs. Incorporating pharmacotherapy such as melatonin and nocturnal dexmedetomidine requires further evaluation in large RCTs.
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Affiliation(s)
- Eugenia Y Lee
- Interdepartmental Division of Critical Care Medicine, University of Toronto
| | - M Elizabeth Wilcox
- Interdepartmental Division of Critical Care Medicine, University of Toronto
- Department of Medicine, University Health Network, Toronto, Canada
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8
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Manella G, Ezagouri S, Champigneulle B, Gaucher J, Mendelson M, Lemarie E, Stauffer E, Pichon A, Howe CA, Doutreleau S, Golik M, Verges S, Asher G. The human blood transcriptome exhibits time-of-day-dependent response to hypoxia: Lessons from the highest city in the world. Cell Rep 2022; 40:111213. [PMID: 35977481 PMCID: PMC9396531 DOI: 10.1016/j.celrep.2022.111213] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/27/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
Abstract
High altitude exposes humans to hypobaric hypoxia, which induces various physiological and molecular changes. Recent studies point toward interaction between circadian rhythms and the hypoxic response, yet their human relevance is lacking. Here, we examine the effect of different high altitudes in conjunction with time of day on human whole-blood transcriptome upon an expedition to the highest city in the world, La Rinconada, Peru, which is 5,100 m above sea level. We find that high altitude vastly affects the blood transcriptome and, unexpectedly, does not necessarily follow a monotonic response to altitude elevation. Importantly, we observe daily variance in gene expression, especially immune-related genes, which is largely altitude dependent. Moreover, using a digital cytometry approach, we estimate relative changes in abundance of different cell types and find that the response of several immune cell types is time- and altitude dependent. Taken together, our data provide evidence for interaction between the transcriptional response to hypoxia and the time of day in humans. Low oxygen availability upon high altitude vastly affects human blood transcriptome The transcriptomic changes upon altitude elevation are not necessarily monotonic The daily variance in gene expression is dependent on altitude The response of several immune cell types is time- and altitude dependent
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Affiliation(s)
- Gal Manella
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Saar Ezagouri
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Benoit Champigneulle
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France
| | - Jonathan Gaucher
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France
| | - Monique Mendelson
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France
| | - Emeline Lemarie
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France
| | - Emeric Stauffer
- Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Team "Biologie vasculaire et du globule rouge", Université Claude Bernard Lyon 1, Université de Lyon, France; Laboratoire d'Excellence du Globule Rouge (Labex GR-Ex), PRES Sorbonne, Paris, France
| | - Aurélien Pichon
- Laboratoire MOVE, STAPS, Université de Poitiers, Poitiers, France
| | - Connor A Howe
- Centre for Heart, Lung and Vascular Health, School of Health and Exercise Sciences, University of British Columbia - Okanagan, Kelowna, BC, Canada
| | - Stéphane Doutreleau
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France
| | - Marina Golik
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Samuel Verges
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France.
| | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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9
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Oster H, Ray DW. Chronoimmunology: from preclinical assessments to clinical applications. Semin Immunopathol 2022; 44:149-151. [PMID: 35257251 DOI: 10.1007/s00281-022-00923-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Henrik Oster
- Institute of Neurobiology, University of Lübeck, Lübeck, DE, Germany.
- Centre of Brain, Behaviour & Metabolism (CBBM), University of Lübeck, Lübeck, DE, Germany.
| | - David W Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.
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