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Identification of Human Cell Cycle Phase Markers Based on Single-Cell RNA-Seq Data by Using Machine Learning Methods. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2516653. [PMID: 36004205 PMCID: PMC9393965 DOI: 10.1155/2022/2516653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 12/17/2022]
Abstract
The cell cycle is composed of a series of ordered, highly regulated processes through which a cell grows and duplicates its genome and eventually divides into two daughter cells. According to the complex changes in cell structure and biosynthesis, the cell cycle is divided into four phases: gap 1 (G1), DNA synthesis (S), gap 2 (G2), and mitosis (M). Determining which cell cycle phases a cell is in is critical to the research of cancer development and pharmacy for targeting cell cycle. However, current detection methods have the following problems: (1) they are complicated and time consuming to perform, and (2) they cannot detect the cell cycle on a large scale. Rapid developments in single-cell technology have made dissecting cells on a large scale possible with unprecedented resolution. In the present research, we construct efficient classifiers and identify essential gene biomarkers based on single-cell RNA sequencing data through Boruta and three feature ranking algorithms (e.g., mRMR, MCFS, and SHAP by LightGBM) by utilizing four advanced classification algorithms. Meanwhile, we mine a series of classification rules that can distinguish different cell cycle phases. Collectively, we have provided a novel method for determining the cell cycle and identified new potential cell cycle-related genes, thereby contributing to the understanding of the processes that regulate the cell cycle.
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Mihelakis M, Ndikung J, Oelgeschläger M, Ertych N. The 4th dimension of in vitro systems - Time to level up. ENVIRONMENT INTERNATIONAL 2022; 164:107256. [PMID: 35472563 DOI: 10.1016/j.envint.2022.107256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
Various in vitro model systems have been established over the last decades to understand physiological processes, the causalities of diseases and the response of humans to environmental and industrial chemicals or therapeutic drugs. Common to all is a limited biological significance due to the impairment of functionality, for instance by the lack of physiological 3D tissue architecture or the loss of fundamental regulatory mechanisms including the circadian rhythm. The circadian rhythm is an adaption of living organisms to rhythmic environmental changes of the day-night cycle and coordinates behavior as well as various crucial physiological processes in a 24-hour pattern. Here, we discuss the impact of integrating circadian regulation in experimental approaches and toxicological assessments to improve the biological relevance of the obtained results. In particular, it is known for some time that an ongoing disruption of the circadian rhythmicity is associated with an increased risk for cardiovascular disease, metabolic dysfunction or cancer. In the context of health recovery, the importance of circadian control mechanism is recognized by chronopharmacological concepts to increase the efficiency of pharmacological treatment strategies. Despite the undeniable circadian dependency and the biological relevance of manifold cellular and molecular processes, the impact of circadian regulation is hardly considered in a wide range of biomedical and toxicological research areas. Reactivating the circadian regulation holds the promise to enhance the biological relevance and reliability of in vitro approaches. In the context of human health protection the implementation of a circadian regulation will subsequently generate advanced physiologically relevant in vitro approaches and allows an improved toxicological assessment of health risks. In addition, the establishment of circadian disruption as a novel toxicological endpoint will provide a better understanding of toxicological mode of actions of environmental and industrial chemicals or drugs and enlarge the knowledge of disease development.
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Affiliation(s)
- Melina Mihelakis
- German Federal Institute for Risk Assessment, German Centre for the Protection of Laboratory Animals (Bf3R), Diedersdorfer Weg 1, 12277 Berlin, Germany
| | - Johanna Ndikung
- German Federal Institute for Risk Assessment, German Centre for the Protection of Laboratory Animals (Bf3R), Diedersdorfer Weg 1, 12277 Berlin, Germany
| | - Michael Oelgeschläger
- German Federal Institute for Risk Assessment, German Centre for the Protection of Laboratory Animals (Bf3R), Diedersdorfer Weg 1, 12277 Berlin, Germany
| | - Norman Ertych
- German Federal Institute for Risk Assessment, German Centre for the Protection of Laboratory Animals (Bf3R), Diedersdorfer Weg 1, 12277 Berlin, Germany.
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Georgakis MK, Bernhagen J, Heitman LH, Weber C, Dichgans M. Targeting the CCL2-CCR2 axis for atheroprotection. Eur Heart J 2022; 43:1799-1808. [PMID: 35567558 DOI: 10.1093/eurheartj/ehac094] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/22/2021] [Accepted: 02/15/2022] [Indexed: 11/12/2022] Open
Abstract
Decades of research have established atherosclerosis as an inflammatory disease. Only recently though, clinical trials provided proof-of-concept evidence for the efficacy of anti-inflammatory strategies with respect to cardiovascular events, thus offering a new paradigm for lowering residual vascular risk. Efforts to target the inflammasome-interleukin-1β-interleukin-6 pathway have been highly successful, but inter-individual variations in drug response, a lack of reduction in all-cause mortality, and a higher rate of infections also highlight the need for a second generation of anti-inflammatory agents targeting atherosclerosis-specific immune mechanisms while minimizing systemic side effects. CC-motif chemokine ligand 2/monocyte-chemoattractant protein-1 (CCL2/MCP-1) orchestrates inflammatory monocyte trafficking between the bone marrow, circulation, and atherosclerotic plaques by binding to its cognate receptor CCR2. Adding to a strong body of data from experimental atherosclerosis models, a coherent series of recent large-scale genetic and observational epidemiological studies along with data from human atherosclerotic plaques highlight the relevance and therapeutic potential of the CCL2-CCR2 axis in human atherosclerosis. Here, we summarize experimental and human data pinpointing the CCL2-CCR2 pathway as an emerging drug target in cardiovascular disease. Furthermore, we contextualize previous efforts to interfere with this pathway, scrutinize approaches of ligand targeting vs. receptor targeting, and discuss possible pathway-intrinsic opportunities and challenges related to pharmacological targeting of the CCL2-CCR2 axis in human atherosclerotic disease.
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Affiliation(s)
- Marios K Georgakis
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, D-81377 Munich, Germany
- Center of Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jürgen Bernhagen
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, D-81377 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Christian Weber
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU) Munich, Germany
- Institute for Genetic and Biomedical Research, UoS of Milan, National Research Council, Milan, Italy
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, D-81377 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Munich, Germany
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Damato AR, Katumba RGN, Luo J, Atluri H, Talcott GR, Govindan A, Slat EA, Weilbaecher KN, Tao Y, Huang J, Butt OH, Ansstas G, Johanns TM, Chheda MG, Herzog ED, Rubin JB, Campian JL. A randomized feasibility study evaluating temozolomide circadian medicine in patients with glioma. Neurooncol Pract 2022; 9:193-200. [PMID: 35601970 PMCID: PMC9113320 DOI: 10.1093/nop/npac003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Background Gliomas are the most common primary brain tumor in adults. Current treatments involve surgery, radiation, and temozolomide (TMZ) chemotherapy; however, prognosis remains poor and new approaches are required. Circadian medicine aims to maximize treatment efficacy and/or minimize toxicity by timed delivery of medications in accordance with the daily rhythms of the patient. We published a retrospective study showing greater anti-tumor efficacy for the morning, relative to the evening, administration of TMZ in patients with glioblastoma. We conducted this prospective randomized trial to determine the feasibility, and potential clinical impact, of TMZ chronotherapy in patients with gliomas (NCT02781792). Methods Adult patients with gliomas (WHO grade II-IV) were enrolled prior to initiation of monthly TMZ therapy and were randomized to receive TMZ either in the morning (AM) before 10 am or in the evening (PM) after 8 pm. Pill diaries were recorded to measure compliance and FACT-Br quality of life (QoL) surveys were completed throughout treatment. Study compliance, adverse events (AE), and overall survival were compared between the two arms. Results A total of 35 evaluable patients, including 21 with GBM, were analyzed (18 AM patients and 17 PM patients). Compliance data demonstrated the feasibility of timed TMZ dosing. There were no significant differences in AEs, QoL, or survival between the arms. Conclusions Chronotherapy with TMZ is feasible. A larger study is needed to validate the effect of chronotherapy on clinical efficacy.
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Affiliation(s)
- Anna R Damato
- Department of Biology, Washington University, St Louis, Missouri, USA
| | - Ruth G N Katumba
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Jingqin Luo
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
- Siteman Cancer Center Biostatistics Core, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Himachandana Atluri
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Grayson R Talcott
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Ashwin Govindan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
- John T. Milliken Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Emily A Slat
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri, USA
| | - Katherine N Weilbaecher
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Yu Tao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
- Siteman Cancer Center Biostatistics Core, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jiayi Huang
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Omar H Butt
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - George Ansstas
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Tanner M Johanns
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Milan G Chheda
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Erik D Herzog
- Department of Biology, Washington University, St Louis, Missouri, USA
- Department of Neuroscience, Washington University School of Medicine, St Louis, Missouri, USA
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, USA
- Department of Neuroscience, Washington University School of Medicine, St Louis, Missouri, USA
| | - Jian L Campian
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
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Lee S, Hong CI. Organoids as Model Systems to Investigate Circadian Clock-Related Diseases and Treatments. Front Genet 2022; 13:874288. [PMID: 35559029 PMCID: PMC9086274 DOI: 10.3389/fgene.2022.874288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Circadian rhythms exist in most cell types in mammals regulating temporal organization of numerous cellular and physiological processes ranging from cell cycle to metabolism. The master clock, suprachiasmatic nucleus (SCN) in the hypothalamus, processes light input and coordinates peripheral clocks optimizing organisms' survival and functions aligning with external conditions. Intriguingly, it was demonstrated that circadian rhythms in the mouse liver can be decoupled from the master clock under time-restricted feeding regimen when food was provided during their inactive phase. Furthermore, mouse liver showed clock-controlled gene expression even in the absence of the master clock demonstrating independent functions of peripheral clocks apart from the SCN. These findings suggest a dynamic relationship between the master and peripheral clocks and highlight potential functions of peripheral clocks independent of the master clock. Importantly, disruption of circadian rhythms correlates with numerous human ailments including cancer and metabolic diseases, suggesting that diseases may be exacerbated by disruption of circadian rhythms in the SCN and/or peripheral clocks. However, molecular mechanisms providing causative links between circadian rhythms and human diseases remain largely unknown. Recent technical advances highlighted PCS- and tissue-derived 3-dimensional organoids as in vitro organs that possess numerous applications ranging from disease modeling to drug screening. In this mini-review, we highlight recent findings on the importance and contributions of peripheral clocks and potential uses of 3D organoids investigating complex circadian clock-related diseases.
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Affiliation(s)
| | - Christian I. Hong
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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Kim E, Kim YJ, Ji Z, Kang JM, Wirianto M, Paudel KR, Smith JA, Ono K, Kim JA, Eckel-Mahan K, Zhou X, Lee HK, Yoo JY, Yoo SH, Chen Z. ROR activation by Nobiletin enhances antitumor efficacy via suppression of IκB/NF-κB signaling in triple-negative breast cancer. Cell Death Dis 2022; 13:374. [PMID: 35440077 PMCID: PMC9018867 DOI: 10.1038/s41419-022-04826-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/19/2022] [Accepted: 04/04/2022] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease characterized by poor response to standard therapies and therefore unfavorable clinical outcomes. Better understanding of TNBC and new therapeutic strategies are urgently needed. ROR nuclear receptors are multifunctional transcription factors with important roles in circadian pathways and other processes including immunity and tumorigenesis. Nobiletin (NOB) is a natural compound known to display anticancer effects, and our previous studies showed that NOB activates RORs to enhance circadian rhythms and promote physiological fitness in mice. Here, we identified several TNBC cell lines being sensitive to NOB, by itself or in combination. Cell and xenograft experiments showed that NOB significantly inhibited TNBC cell proliferation and motility in vitro and in vivo. ROR loss- and gain-of-function studies showed concordant effects of the NOB–ROR axis on MDA-MB-231 cell growth. Mechanistically, we found that NOB activates ROR binding to the ROR response elements (RRE) of the IκBα promoter, and NOB strongly inhibited p65 nuclear translocation. Consistent with transcriptomic analysis indicating cancer and NF-κB signaling as major pathways altered by NOB, p65-inducible expression abolished NOB effects, illustrating a requisite role of NF-κB suppression mediating the anti-TNBC effect of NOB. Finally, in vivo mouse xenograft studies showed that NOB enhanced the antitumor efficacy in mammary fat pad implanted TNBC, as a single agent or in combination with the chemotherapy agent Docetaxel. Together, our study highlights an anti-TNBC mechanism of ROR-NOB via suppression of NF-κB signaling, suggesting novel preventive and chemotherapeutic strategies against this devastating disease. ![]()
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Affiliation(s)
- Eunju Kim
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Yoon-Jin Kim
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Zhiwei Ji
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Jin Muk Kang
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Marvin Wirianto
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Keshav Raj Paudel
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Joshua A Smith
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Kaori Ono
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Jin-Ah Kim
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kristin Eckel-Mahan
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Hyun Kyoung Lee
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Ji Young Yoo
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA.
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA.
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Tyson JJ, Csikasz-Nagy A, Gonze D, Kim JK, Santos S, Wolf J. Time-keeping and decision-making in living cells: Part I. Interface Focus 2022. [PMCID: PMC9010849 DOI: 10.1098/rsfs.2022.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To survive and reproduce, a cell must process information from its environment and its own internal state and respond accordingly, in terms of metabolic activity, gene expression, movement, growth, division and differentiation. These signal–response decisions are made by complex networks of interacting genes and proteins, which function as biochemical switches and clocks, and other recognizable information-processing circuitry. This theme issue of Interface Focus (in two parts) brings together articles on time-keeping and decision-making in living cells—work that uses precise mathematical modelling of underlying molecular regulatory networks to understand important features of cell physiology. Part I focuses on time-keeping: mechanisms and dynamics of biological oscillators and modes of synchronization and entrainment of oscillators, with special attention to circadian clocks.
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Affiliation(s)
- John J. Tyson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Attila Csikasz-Nagy
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, 1088 Budapest, Hungary
| | - Didier Gonze
- Unit of Theoretical Chronobiology, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Jae Kyoung Kim
- Department of Mathematical Sciences, KAIST, Daejeon 34141, South Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, South Korea
| | - Silvia Santos
- Quantitative Stem Cell Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Jana Wolf
- Mathematical Modeling of Cellular Processes, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Department of Mathematics and Computer Science, Free University, 14195 Berlin, Germany
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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.
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Mylona I, Floros GD. Blue Light Blocking Treatment for the Treatment of Bipolar Disorder: Directions for Research and Practice. J Clin Med 2022; 11:jcm11051380. [PMID: 35268469 PMCID: PMC8911317 DOI: 10.3390/jcm11051380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/16/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
Recent results from a small number of clinical studies have resulted in the suggestion that the process of blocking the transmission of shorter-wavelength light (‘blue light’ with a wave length of 450 nm to 470 nm) may have a beneficial role in the treatment of bipolar disorder. This critical review will appraise the quality of evidence so far as to these claims, assess the neurobiology that could be implicated in the underlying processes while introducing a common set of research criteria for the field.
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Affiliation(s)
- Ioanna Mylona
- 2nd Department of Ophthalmology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
| | - Georgios D. Floros
- 2nd Department of Psychiatry, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
- Correspondence: ; Tel.: +30-69-4432-4565
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Abstract
The circadian clock is an evolutionarily highly conserved endogenous timing program that structures physiology and behavior according to the time of day. Disruption of circadian rhythms is associated with many common pathologies. The emerging field of circadian medicine aims to exploit the mechanisms of circadian physiology and clock-disease interaction for clinical diagnosis, treatment, and prevention. In this Essay, we outline the principle approaches of circadian medicine, highlight the development of the field in selected areas, and point out open questions and challenges. Circadian medicine has unambiguous health benefits over standard care but is rarely utilized. It is time for clock biology to become an integrated part of translational research.
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Affiliation(s)
- Achim Kramer
- Charité –Universitätsmedizin Berlin, Laboratory of Chronobiology, Berlin, Germany
- * E-mail: (AK); (HO)
| | - Tanja Lange
- University of Lübeck, Department of Rheumatology & Clinical Immunology, Center of Brain, Behavior and Metabolism, Lübeck, Germany
| | - Claudia Spies
- Charité –Universitätsmedizin Berlin, Department of Anesthesiology and Intensive Care Medicine, Berlin, Germany
| | - Anna-Marie Finger
- Charité –Universitätsmedizin Berlin, Laboratory of Chronobiology, Berlin, Germany
| | - Daniela Berg
- Christian-Albrechts-University Kiel, Department of Neurology, Kiel, Germany
| | - Henrik Oster
- University of Lübeck, Institute of Neurobiology, Center of Brain, Behavior and Metabolism, Lübeck, Germany
- * E-mail: (AK); (HO)
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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.
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Liu J, Yang M, Zhao W, Zhou X. CCPE: cell cycle pseudotime estimation for single cell RNA-seq data. Nucleic Acids Res 2022; 50:704-716. [PMID: 34931240 PMCID: PMC8789092 DOI: 10.1093/nar/gkab1236] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/22/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
Pseudotime analysis from scRNA-seq data enables to characterize the continuous progression of various biological processes, such as the cell cycle. Cell cycle plays an important role in cell fate decisions and differentiation and is often regarded as a confounder in scRNA-seq data analysis when analyzing the role of other factors. Therefore, accurate prediction of cell cycle pseudotime and identification of cell cycle stages are important steps for characterizing the development-related biological processes. Here, we develop CCPE, a novel cell cycle pseudotime estimation method to characterize cell cycle timing and identify cell cycle phases from scRNA-seq data. CCPE uses a discriminative helix to characterize the circular process of the cell cycle and estimates each cell's pseudotime along the cell cycle. We evaluated the performance of CCPE based on a variety of simulated and real scRNA-seq datasets. Our results indicate that CCPE is an effective method for cell cycle estimation and competitive in various applications compared with other existing methods. CCPE successfully identified cell cycle marker genes and is robust to dropout events in scRNA-seq data. Accurate prediction of the cell cycle using CCPE can also effectively facilitate the removal of cell cycle effects across cell types or conditions.
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Affiliation(s)
- Jiajia Liu
- College of Electronic and Information Engineering, Tongji University, Shanghai, Shanghai 201804, China
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Mengyuan Yang
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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63
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Lin CR, Bahmed K, Kosmider B. Dysregulated Cell Signaling in Pulmonary Emphysema. Front Med (Lausanne) 2022; 8:762878. [PMID: 35047522 PMCID: PMC8762198 DOI: 10.3389/fmed.2021.762878] [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: 08/23/2021] [Accepted: 12/06/2021] [Indexed: 01/19/2023] Open
Abstract
Pulmonary emphysema is characterized by the destruction of alveolar septa and irreversible airflow limitation. Cigarette smoking is the primary cause of this disease development. It induces oxidative stress and disturbs lung physiology and tissue homeostasis. Alveolar type II (ATII) cells have stem cell potential and can repair the denuded epithelium after injury; however, their dysfunction is evident in emphysema. There is no effective treatment available for this disease. Challenges in this field involve the large complexity of lung pathophysiological processes and gaps in our knowledge on the mechanisms of emphysema progression. It implicates dysregulation of various signaling pathways, including aberrant inflammatory and oxidative responses, defective antioxidant defense system, surfactant dysfunction, altered proteostasis, disrupted circadian rhythms, mitochondrial damage, increased cell senescence, apoptosis, and abnormal proliferation and differentiation. Also, genetic predispositions are involved in this disease development. Here, we comprehensively review studies regarding dysregulated cell signaling, especially in ATII cells, and their contribution to alveolar wall destruction in emphysema. Relevant preclinical and clinical interventions are also described.
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Affiliation(s)
- Chih-Ru Lin
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States
| | - Karim Bahmed
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA, United States
| | - Beata Kosmider
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States
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64
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Wucher V, Sodaei R, Amador R, Irimia M, Guigó R. Day-night and seasonal variation of human gene expression across tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.02.28.433266. [PMID: 33688644 PMCID: PMC7941615 DOI: 10.1101/2021.02.28.433266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate transcriptomic changes associated with those cycles across multiple tissues. Overall, most variation across tissues during day-night and among seasons was unique to each cycle. Although all tissues remodeled their transcriptomes, brain and gonadal tissues exhibited the highest seasonality, whereas those in the thoracic cavity showed stronger day-night regulation. Core clock genes displayed marked day-night differences across multiple tissues, which were largely conserved in baboon and mouse, but adapted to their nocturnal or diurnal habits. Seasonal variation of expression affected multiple pathways and it was enriched among genes associated with the immune response, consistent with the seasonality of viral infections. Furthermore, they unveiled cytoarchitectural changes in brain regions. Altogether, our results provide the first combined atlas of how transcriptomes from human tissues adapt to major cycling environmental conditions.
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Affiliation(s)
- Valentin Wucher
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- NeuroMyogene Institute, SynatAc Team, INSERM U1217/UMR CNRS 5310, Lyon, France
- French Reference Center on Paraneoplastic Neurological Syndrome, Hospices Civils de Lyon, Lyon, France
- University of Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Reza Sodaei
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Raziel Amador
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
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65
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Boots R, Mead G, Rawashdeh O, Bellapart J, Townsend S, Paratz J, Garner N, Clement P, Oddy D. Temperature Profile and Adverse Outcomes After Discharge From the Intensive Care Unit. Am J Crit Care 2022; 31:e1-e9. [PMID: 34972850 DOI: 10.4037/ajcc2022223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND A predictive model that uses the rhythmicity of core body temperature (CBT) could be an easily accessible clinical tool to ultimately improve outcomes among critically ill patients. OBJECTIVES To assess the relation between the 24-hour CBT profile (CBT-24) before intensive care unit (ICU) discharge and clinical events in the step-down unit within 7 days of ICU discharge. METHODS This retrospective cohort study in a tertiary ICU at a single center included adult patients requiring acute invasive ventilation for more than 48 hours and assessed major clinical adverse events (MCAEs) and rapid response system activations (RRSAs) within 7 days of ICU discharge (MCAE-7 and RRSA-7, respectively). RESULTS The 291 enrolled patients had a median mechanical ventilation duration of 139 hours (IQR, 50-862 hours) and at admission had a median Acute Physiology and Chronic Health Evaluation II score of 22 (IQR, 7-42). At least 1 MCAE or RRSA occurred in 64% and 22% of patients, respectively. Independent predictors of an MCAE-7 were absence of CBT-24 rhythmicity (odds ratio, 1.78 [95% CI, 1.07-2.98]; P = .03), Sequential Organ Failure Assessment score at ICU discharge (1.10 [1.00-1.21]; P = .05), male sex (1.72 [1.04-2.86]; P = .04), age (1.02 [1.00-1.04]; P = .02), and Charlson Comorbidity Index (0.87 [0.76-0.99]; P = .03). Age (1.03 [1.01-1.05]; P = .006), sepsis at ICU admission (2.02 [1.13-3.63]; P = .02), and Charlson Comorbidity Index (1.18 [1.02-1.36]; P = .02) were independent predictors of an RRSA-7. CONCLUSIONS Use of CBT-24 rhythmicity can assist in stratifying a patient's risk of subsequent deterioration during general care within 7 days of ICU discharge.
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Affiliation(s)
- Rob Boots
- Rob Boots is an associate professor, Thoracic Medicine, Royal Brisbane and Women’s Hospital, and Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Gabrielle Mead
- Gabrielle Mead is an honors student, School of Biomedical Sciences, Faculty of Medicine, The University of Queensland
| | - Oliver Rawashdeh
- Oliver Rawashdeh is a senior lecturer,, School of Biomedical Sciences, Faculty of Medicine, The University of Queensland
| | - Judith Bellapart
- Judith Bellapart is a senior specialist, Department of Intensive Care Medicine, Royal Brisbane and Women’s Hospital, and Burns, Trauma and Critical Care, The University of Queensland
| | - Shane Townsend
- Shane Townsend is director, Intensive Care Services, Royal Brisbane and Women’s Hospital
| | - Jenny Paratz
- Jenny Paratz is an associate professor and a senior research fellow, Burns, Trauma and Critical Care Research Centre, The University of Queensland School of Medicine
| | - Nicholas Garner
- Nicholas Garner is a PhD student, School of Biomedical Sciences, Faculty of Medicine, The University of Queensland
| | - Pierre Clement
- Pierre Clement is the clinical information systems manager, Department of Intensive Care Services, Royal Brisbane and Women’s Hospital
| | - David Oddy
- David Oddy is the clinical data manager, Department of Intensive Care Services, Royal Brisbane and Women’s Hospital
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66
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Wu X, Cheng Q. Algorithmic Stability and Generalization of an Unsupervised Feature Selection Algorithm. ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 2021; 34:19860-19875. [PMID: 36187051 PMCID: PMC9524443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Feature selection, as a vital dimension reduction technique, reduces data dimension by identifying an essential subset of input features, which can facilitate interpretable insights into learning and inference processes. Algorithmic stability is a key characteristic of an algorithm regarding its sensitivity to perturbations of input samples. In this paper, we propose an innovative unsupervised feature selection algorithm attaining this stability with provable guarantees. The architecture of our algorithm consists of a feature scorer and a feature selector. The scorer trains a neural network (NN) to globally score all the features, and the selector adopts a dependent sub-NN to locally evaluate the representation abilities for selecting features. Further, we present algorithmic stability analysis and show that our algorithm has a performance guarantee via a generalization error bound. Extensive experimental results on real-world datasets demonstrate superior generalization performance of our proposed algorithm to strong baseline methods. Also, the properties revealed by our theoretical analysis and the stability of our algorithm-selected features are empirically confirmed.
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67
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Abstract
Circadian clocks are biological timing mechanisms that generate 24-h rhythms of physiology and behavior, exemplified by cycles of sleep/wake, hormone release, and metabolism. The adaptive value of clocks is evident when internal body clocks and daily environmental cycles are mismatched, such as in the case of shift work and jet lag or even mistimed eating, all of which are associated with physiological disruption and disease. Studies with animal and human models have also unraveled an important role of functional circadian clocks in modulating cellular and organismal responses to physiological cues (ex., food intake, exercise), pathological insults (e.g. virus and parasite infections), and medical interventions (e.g. medication). With growing knowledge of the molecular and cellular mechanisms underlying circadian physiology and pathophysiology, it is becoming possible to target circadian rhythms for disease prevention and treatment. In this review, we discuss recent advances in circadian research and the potential for therapeutic applications that take patient circadian rhythms into account in treating disease.
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Affiliation(s)
- Yool Lee
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington
| | - Jeffrey M. Field
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amita Sehgal
- Howard Hughes Medical Institute, Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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68
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Li MD. Clock-modulated checkpoints in time-restricted eating. Trends Mol Med 2021; 28:25-35. [PMID: 34801412 DOI: 10.1016/j.molmed.2021.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Time-restricted eating (TRE), which limits the daily meal timing to a window of 6-12 h, has been shown to reduce the risks of cardiometabolic diseases through consolidating circadian rhythms of metabolism and physiology. Recent advances indicate that canonical circadian clocks are dispensable for the actions of TRE in the liver, and that meal timing entrains circadian rhythms in peripheral tissues in a tissue-specific manner (e.g., the liver and fat are readily entrainable, whereas the heart and kidneys are resistant). Here, we propose that TRE engages clock-modulated checkpoints (CCPs) to reset circadian rhythms of tissue functions. Elucidation of CCPs would reveal the mechanistic basis of tissue responsiveness to TRE, and facilitate the use of TRE in precision medicine for cardiometabolic diseases.
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Affiliation(s)
- Min-Dian Li
- Department of Cardiology and the Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Army Medical University, Chongqing, 400038, China.
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69
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Rong B, Wu Q, Saeed M, Sun C. Gut microbiota-a positive contributor in the process of intermittent fasting-mediated obesity control. ACTA ACUST UNITED AC 2021; 7:1283-1295. [PMID: 34786501 PMCID: PMC8567329 DOI: 10.1016/j.aninu.2021.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 09/12/2021] [Accepted: 09/25/2021] [Indexed: 12/12/2022]
Abstract
Historically, intermittent fasting (IF) has been considered as an effective strategy for controlling the weight of athletes before competition. Along with excellent insight into its application in various spaces by numerous studies, increasing IF-mediated positive effects have been reported, including anti-aging, neuroprotection, especially obesity control. Recently, the gut microbiota has been considered as an essential manipulator for host energy metabolism and its structure has been reported to be sensitive to dietary structure and habits, indicating that there is a potential and strong association between IF and gut microbiota. In this paper, we focus on the crosstalk between these symbionts and energy metabolism during IF which hold the promise to optimize host energy metabolism at various physical positions, including adipose tissue, liver and intestines, and further improve milieu internal homeostasis. Moreover, this paper also discusses the positive function of a potential recommendatory strain (Akkermansia muciniphila) based on the observational data for IF-mediated alternated pattern of gut microbiota and a hopefully regulatory pathway (circadian rhythm) for gut microbiota in IF-involved improvement on host energy metabolism. Finally, this review addresses the limitation and perspective originating from these studies, such as the association with tissue-specific bio-clock and single strain research, which may continuously reveal novel viewpoints and mechanisms to understand the energy metabolism and develop new strategies for treating obesity, diabetes, and metabolic disorders.
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Affiliation(s)
- Bohan Rong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qiong Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Pathophysiology, Qinghai University Medical College, Xining, Qinghai, China
| | - Muhammad Saeed
- Faculty of Animal Production & Technology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
| | - Chao Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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70
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Wu G, Francey LJ, Ruben MD, Hogenesch JB. Normalized coefficient of variation (nCV): a method to evaluate circadian clock robustness in population scale data. Bioinformatics 2021; 37:4581-4583. [PMID: 34726689 PMCID: PMC8652017 DOI: 10.1093/bioinformatics/btab731] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/22/2021] [Accepted: 10/27/2021] [Indexed: 12/05/2022] Open
Abstract
Summary Robust oscillation of clock genes is a core feature of the circadian system. Relative amplitude (rAMP) measures the robustness of clock gene oscillations but only works for longitudinal samples. We lack a method for estimating robust oscillations from human samples without labeled time. We show that the normalized coefficient of variation (nCV) of 10 clock genes is linearly correlated with their normalized rAMP, independent of time labels. We found that the mean nCV of clock genes are consistently decreased in tumors compared to nontumors, suggesting a new therapeutic target in cancer treatment by enhancing clock robustness. nCV can provide a simple measure of the clock robustness in population-level datasets. Availability and implementation The nCV package (https://github.com/gangwug/nCV) and web application (https://github.com/gangwug/nCVapp) are available on the GitHub repository. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gang Wu
- Divisions of Human Genetics and Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH, 45229
| | - Lauren J Francey
- Divisions of Human Genetics and Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH, 45229
| | - Marc D Ruben
- Divisions of Human Genetics and Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH, 45229
| | - John B Hogenesch
- Divisions of Human Genetics and Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH, 45229
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71
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Delisle BP, George AL, Nerbonne JM, Bass JT, Ripplinger CM, Jain MK, Hermanstyne TO, Young ME, Kannankeril PJ, Duffy JF, Goldhaber JI, Hall MH, Somers VK, Smolensky MH, Garnett CE, Anafi RC, Scheer FA, Shivkumar K, Shea SA, Balijepalli RC. Understanding Circadian Mechanisms of Sudden Cardiac Death: A Report From the National Heart, Lung, and Blood Institute Workshop, Part 2: Population and Clinical Considerations. Circ Arrhythm Electrophysiol 2021; 14:e010190. [PMID: 34719257 PMCID: PMC8865094 DOI: 10.1161/circep.121.010190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Sudden cardiac death (SCD) is the sudden, unexpected death due to abrupt loss of heart function secondary to cardiovascular disease. In certain populations living with cardiovascular disease, SCD follows a distinct 24-hour pattern in occurrence, suggesting day/night rhythms in behavior, the environment, and endogenous circadian rhythms result in daily spans of increased vulnerability. The National Heart, Lung, and Blood Institute convened a workshop, Understanding Circadian Mechanisms of Sudden Cardiac Death to identify fundamental questions regarding the role of the circadian rhythms in SCD. Part 2 summarizes research gaps and opportunities in the areas of population and clinical research identified in the workshop. Established research supports a complex interaction between circadian rhythms and physiological responses that increase the risk for SCD. Moreover, these physiological responses themselves are influenced by several biological variables, including the type of cardiovascular disease, sex, age, and genetics, as well as environmental factors. The emergence of new noninvasive biotechnological tools that continuously measure key cardiovascular variables, as well as the identification of biomarkers to assess circadian rhythms, hold promise for generating large-scale human data sets that will delineate which subsets of individuals are most vulnerable to SCD. Additionally, these data will improve our understanding of how people who suffer from circadian disruptions develop cardiovascular diseases that increase the risk for SCD. Emerging strategies to identify new biomarkers that can quantify circadian health (eg, environmental, behavioral, and internal misalignment) may lead to new interventions and therapeutic targets to prevent the progression of cardiovascular diseases that cause SCD.
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Affiliation(s)
| | - Alfred L. George
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Jeanne M. Nerbonne
- Departments of Medicine, Cardiovascular Division, and Developmental Biology, Washington University School of Medicine, St. Louis, MO
| | - Joseph T. Bass
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | | | - Mukesh K. Jain
- Department of Medicine, Case Western Reserve University, Cleveland, OH
| | - Tracey O. Hermanstyne
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO
| | - Martin E. Young
- Department of Medicine, University of Alabama, Birmingham, AL
| | | | | | | | - Martica H. Hall
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | | | | | | | - Ron C. Anafi
- Department of Medicine and Center for Sleep and Circadian Neurobiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | - Kalyanam Shivkumar
- Departement of Medicine, David Greffen School of Medicine at UCLA, Los Angeles, CA
| | - Steven A. Shea
- Oregon Institute of Occupational Health Sciences, Oregon Health and Science University, Portland, OR
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72
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Abstract
Neurodegenerative diseases encompass a large group of conditions that are clinically and pathologically diverse yet are linked by a shared pathology of misfolded proteins. The accumulation of insoluble aggregates is accompanied by a progressive loss of vulnerable neurons. For some patients, the symptoms are motor focused (ataxias), while others experience cognitive and psychiatric symptoms (dementias). Among the shared symptoms of neurodegenerative diseases is a disruption of the sleep/wake cycle that occurs early in the trajectory of the disease and may be a risk factor for disease development. In many cases, the disruption in the timing of sleep and other rhythmic physiological markers immediately raises the possibility of neurodegeneration-driven disruption of the circadian timing system. The aim of this Review is to summarize the evidence supporting the hypothesis that circadian disruption is a core symptom within neurodegenerative diseases, including Alzheimer's disease, Huntington's disease, and Parkinson's disease, and to discuss the latest progress in this field. The Review discusses evidence that neurodegenerative processes may disrupt the structure and function of the circadian system and describes circadian-based interventions as well as timed drug treatments that may improve a wide range of symptoms associated with neurodegenerative disorders. It also identifies key gaps in our knowledge.
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73
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Li MD, Xin H, Yuan Y, Yang X, Li H, Tian D, Zhang H, Zhang Z, Han TL, Chen Q, Duan G, Ju D, Chen K, Deng F, He W. Circadian Clock-Controlled Checkpoints in the Pathogenesis of Complex Disease. Front Genet 2021; 12:721231. [PMID: 34557221 PMCID: PMC8452875 DOI: 10.3389/fgene.2021.721231] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/16/2021] [Indexed: 12/26/2022] Open
Abstract
The circadian clock coordinates physiology, metabolism, and behavior with the 24-h cycles of environmental light. Fundamental mechanisms of how the circadian clock regulates organ physiology and metabolism have been elucidated at a rapid speed in the past two decades. Here we review circadian networks in more than six organ systems associated with complex disease, which cluster around metabolic disorders, and seek to propose critical regulatory molecules controlled by the circadian clock (named clock-controlled checkpoints) in the pathogenesis of complex disease. These include clock-controlled checkpoints such as circadian nuclear receptors in liver and muscle tissues, chemokines and adhesion molecules in the vasculature. Although the progress is encouraging, many gaps in the mechanisms remain unaddressed. Future studies should focus on devising time-dependent strategies for drug delivery and engagement in well-characterized organs such as the liver, and elucidating fundamental circadian biology in so far less characterized organ systems, including the heart, blood, peripheral neurons, and reproductive systems.
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Affiliation(s)
- Min-Dian Li
- Department of Cardiology and the Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Haoran Xin
- Department of Cardiology and the Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yinglin Yuan
- Medical Center of Hematology, The Xinqiao Hospital of Army Medical University, Chongqing, China
| | - Xinqing Yang
- Department of Anesthesiology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hongli Li
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dingyuan Tian
- Department of Cardiology and the Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Hua Zhang
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhihui Zhang
- Department of Cardiology and the Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Ting-Li Han
- Department of Obstetrics and Gynaecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qing Chen
- Key Lab of Medical Protection for Electromagnetic Radiation, Ministry of Education of China, Institute of Toxicology, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China
| | - Guangyou Duan
- Department of Anesthesiology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Dapeng Ju
- Department of Anesthesiology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ka Chen
- Research Center for Nutrition and Food Safety, Institute of Military Preventive Medicine, Army Medical University, Chongqing, China
| | - Fang Deng
- Key Laboratory of Extreme Environmental Medicine, Department of Pathophysiology, College of High Altitude Military Medicine, Ministry of Education of China, Army Medical University (Third Military Medical University), Chongqing, China.,Key Laboratory of High Altitude Medicine, PLA, Army Medical University (Third Military Medical University), Chongqing, China
| | - Wenyan He
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Abstract
The objective of chronotherapy is to optimize medical treatments taking into account the body's circadian rhythms. Chronotherapy is referred to and practiced in two different ways: (1) to alter the sleep-wake rhythms of patients to improve the sequels of several pathologies; (2) to take into account the circadian rhythms of patients to improve therapeutics. Even minor dysfunction of the biological clock can greatly affect sleep/wake physiology causing excessive diurnal somnolence, increase in sleep onset latency, phase delays or advances in sleep onset, frequent night awakenings, reduced sleep efficiency, delayed and shortened rapid eye movement sleep, or increased periodic leg movements. Chronotherapy aims to restore the proper circadian pattern of the sleep-wake cycle, through adequate sleep hygiene, timed light exposure, and the use of chronobiotic medications, such as melatonin, that affect the output phase of circadian rhythms, thus controlling the clock. Concerning the second use of chronotherapy, therapeutic outcomes as diverse as the survival after open-heart surgery or the efficacy and tolerance to chemotherapy vary according to the time of day. However, humans are heterogeneous concerning the timing of their internal clocks. Not only different chronotypes exist but also the endogenous human circadian period (τ) is not a stable trait as it depends on many internal and external factors. If any scheduled therapeutic intervention is going to be optimized, a tool is needed for simple diagnostic and objectively measurement of an individual's internal time at any given time. Methodologic advances like the use of single-sample gene expression and metabolomics are discussed.
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Affiliation(s)
- Daniel P Cardinali
- Faculty of Medical Sciences, Pontificia Universidad Católica Argentina, Buenos Aires, Argentina
| | - Gregory M Brown
- Department of Psychiatry, Centre for Addiction and Mental Health, University of Toronto, Toronto, ON, Canada
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75
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Burchett JB, Knudsen-Clark AM, Altman BJ. MYC Ran Up the Clock: The Complex Interplay between MYC and the Molecular Circadian Clock in Cancer. Int J Mol Sci 2021; 22:7761. [PMID: 34299381 PMCID: PMC8305799 DOI: 10.3390/ijms22147761] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/02/2021] [Accepted: 07/14/2021] [Indexed: 12/13/2022] Open
Abstract
The MYC oncoprotein and its family members N-MYC and L-MYC are known to drive a wide variety of human cancers. Emerging evidence suggests that MYC has a bi-directional relationship with the molecular clock in cancer. The molecular clock is responsible for circadian (~24 h) rhythms in most eukaryotic cells and organisms, as a mechanism to adapt to light/dark cycles. Disruption of human circadian rhythms, such as through shift work, may serve as a risk factor for cancer, but connections with oncogenic drivers such as MYC were previously not well understood. In this review, we examine recent evidence that MYC in cancer cells can disrupt the molecular clock; and conversely, that molecular clock disruption in cancer can deregulate and elevate MYC. Since MYC and the molecular clock control many of the same processes, we then consider competition between MYC and the molecular clock in several select aspects of tumor biology, including chromatin state, global transcriptional profile, metabolic rewiring, and immune infiltrate in the tumor. Finally, we discuss how the molecular clock can be monitored or diagnosed in human tumors, and how MYC inhibition could potentially restore molecular clock function. Further study of the relationship between the molecular clock and MYC in cancer may reveal previously unsuspected vulnerabilities which could lead to new treatment strategies.
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Affiliation(s)
- Jamison B. Burchett
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Amelia M. Knudsen-Clark
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Brian J. Altman
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA;
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
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76
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Circadian Clock and Liver Cancer. Cancers (Basel) 2021; 13:cancers13143631. [PMID: 34298842 PMCID: PMC8306099 DOI: 10.3390/cancers13143631] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 07/15/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary The circadian coordination of metabolism is tightly regulated, and its alteration can trigger several diseases, including liver steatohepatitis and cancer. Many factors (such as diet and jet lag) shape both the liver molecular clock and the circadian transcription/translation of genes related to different metabolic pathways. Here, we summarize our current knowledge about the molecular mechanisms that control this circadian regulation of liver metabolism. Abstract Circadian clocks control several homeostatic processes in mammals through internal molecular mechanisms. Chronic perturbation of circadian rhythms is associated with metabolic diseases and increased cancer risk, including liver cancer. The hepatic physiology follows a daily rhythm, driven by clock genes that control the expression of several proteins involved in distinct metabolic pathways. Alteration of the liver clock results in metabolic disorders, such as non-alcoholic fatty liver diseases (NAFLD) and impaired glucose metabolism, that can trigger the activation of oncogenic pathways, inducing spontaneous hepatocarcinoma (HCC). In this review, we provide an overview of the role of the liver clock in the metabolic and oncogenic changes that lead to HCC and discuss new potentially useful targets for prevention and management of HCC.
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77
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Liu J, Fan Z, Zhao W, Zhou X. Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges. Front Genet 2021; 12:655536. [PMID: 34135939 PMCID: PMC8203333 DOI: 10.3389/fgene.2021.655536] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
The rapid development of single-cell technologies allows for dissecting cellular heterogeneity at different omics layers with an unprecedented resolution. In-dep analysis of cellular heterogeneity will boost our understanding of complex biological systems or processes, including cancer, immune system and chronic diseases, thereby providing valuable insights for clinical and translational research. In this review, we will focus on the application of machine learning methods in single-cell multi-omics data analysis. We will start with the pre-processing of single-cell RNA sequencing (scRNA-seq) data, including data imputation, cross-platform batch effect removal, and cell cycle and cell-type identification. Next, we will introduce advanced data analysis tools and methods used for copy number variance estimate, single-cell pseudo-time trajectory analysis, phylogenetic tree inference, cell-cell interaction, regulatory network inference, and integrated analysis of scRNA-seq and spatial transcriptome data. Finally, we will present the latest analyzing challenges, such as multi-omics integration and integrated analysis of scRNA-seq data.
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Affiliation(s)
- Jiajia Liu
- College of Electronic and Information Engineering, Tongji University, Shanghai, China
- School of Biomedical Informatics, The University of Texas Health Science Centre at Houston, Houston, TX, United States
| | - Zhiwei Fan
- School of Biomedical Informatics, The University of Texas Health Science Centre at Houston, Houston, TX, United States
- West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Weiling Zhao
- School of Biomedical Informatics, The University of Texas Health Science Centre at Houston, Houston, TX, United States
| | - Xiaobo Zhou
- School of Biomedical Informatics, The University of Texas Health Science Centre at Houston, Houston, TX, United States
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78
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Acosta-Rodríguez VA, Rijo-Ferreira F, Green CB, Takahashi JS. Importance of circadian timing for aging and longevity. Nat Commun 2021; 12:2862. [PMID: 34001884 PMCID: PMC8129076 DOI: 10.1038/s41467-021-22922-6] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/29/2021] [Indexed: 12/21/2022] Open
Abstract
Dietary restriction (DR) decreases body weight, improves health, and extends lifespan. DR can be achieved by controlling how much and/or when food is provided, as well as by adjusting nutritional composition. Because these factors are often combined during DR, it is unclear which are necessary for beneficial effects. Several drugs have been utilized that target nutrient-sensing gene pathways, many of which change expression throughout the day, suggesting that the timing of drug administration is critical. Here, we discuss how dietary and pharmacological interventions promote a healthy lifespan by influencing energy intake and circadian rhythms. Circadian clocks link physiologic processes to environmental conditions and a mismatch between internal and external rhythms has negative effects on organismal health. In this review, the authors discuss the interactions between circadian clocks and dietary interventions targeted to promote healthy aging.
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Affiliation(s)
- Victoria A Acosta-Rodríguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Filipa Rijo-Ferreira
- Department of Neuroscience, 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
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joseph S Takahashi
- Department of Neuroscience, 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.
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79
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Bar N, Sobel JA, Penzel T, Shamay Y, Behar JA. From sleep medicine to medicine during sleep-a clinical perspective. Physiol Meas 2021; 42. [PMID: 33794516 DOI: 10.1088/1361-6579/abf47c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/01/2021] [Indexed: 01/01/2023]
Abstract
Objective. In this perspective paper, we aim to highlight the potential of sleep as an auspicious time for diagnosis, management and therapy of non-sleep-specific pathologies.Approach. Sleep has a profound influence on the physiology of body systems and biological processes. Molecular studies have shown circadian-regulated shifts in protein expression patterns across human tissues, further emphasizing the unique functional, behavioral and pharmacokinetic landscape of sleep. Thus, many pathological processes are also expected to exhibit sleep-specific manifestations. Modern advances in biosensor technologies have enabled remote, non-invasive recording of a growing number of physiologic parameters and biomarkers promoting the detection and study of such processes.Main results. Here, we introduce key clinical studies in selected medical fields, which leveraged novel technologies and the advantageous period of sleep to diagnose, monitor and treat pathologies. Studies demonstrate that sleep is an ideal time frame for the collection of long and clean physiological time series data which can then be analyzed using data-driven algorithms such as deep learning.Significance.This new paradigm proposes opportunities to further harness modern technologies to explore human health and disease during sleep and to advance the development of novel clinical applications - from sleep medicine to medicine during sleep.
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Affiliation(s)
- Nitai Bar
- Israel Department of Radiology, Rambam Health Care Campus, Haifa, Israel
| | - Jonathan A Sobel
- Biomedical Engineering Faculty, Technion-Israel Institute of Technology, Haifa, Israel
| | - Thomas Penzel
- Interdisciplinary Center of Sleep Medicine, Charite University Medicine Berlin, Chariteplatz 1, D-10117 Berlin, Germany.,Saratov State University, Saratov, Russia
| | - Yosi Shamay
- Biomedical Engineering Faculty, Technion-Israel Institute of Technology, Haifa, Israel
| | - Joachim A Behar
- Biomedical Engineering Faculty, Technion-Israel Institute of Technology, Haifa, Israel
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80
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Cash E, Sephton S, Woolley C, Elbehi AM, R I A, Ekine-Afolabi B, Kok VC. The role of the circadian clock in cancer hallmark acquisition and immune-based cancer therapeutics. J Exp Clin Cancer Res 2021; 40:119. [PMID: 33794967 PMCID: PMC8017624 DOI: 10.1186/s13046-021-01919-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
The circadian system temporally regulates physiology to maintain homeostasis. Co-opting and disrupting circadian signals appear to be distinct attributes that are functionally important for the development of a tumor and can enable or give rise to the hallmarks that tumors use to facilitate their initiation, growth and progression. Because circadian signals are also strong regulators of immune cell proliferation, trafficking and exhaustion states, they play a role in how tumors respond to immune-based cancer therapeutics. While immuno-oncology has heralded a paradigm shift in cancer therapeutics, greater accuracy is needed to increase our capability of predicting who will respond favorably to, or who is likely to experience the troubling adverse effects of, immunotherapy. Insights into circadian signals may further refine our understanding of biological determinants of response and help answer the fundamental question of whether certain perturbations in circadian signals interfere with the activity of immune checkpoint inhibitors. Here we review the body of literature highlighting circadian disruption as a cancer promoter and synthesize the burgeoning evidence suggesting circadian signals play a role in how tumors respond to immune-based anti-cancer therapeutics. The goal is to develop a framework to advance our understanding of the relationships between circadian markers, cancer biology, and immunotherapeutics. Bolstered by this new understanding, these relationships may then be pursued in future clinical studies to improve our ability to predict which patients will respond favorably to, and avoid the adverse effects of, traditional and immune-based cancer therapeutics.
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Affiliation(s)
- Elizabeth Cash
- Department of Otolaryngology and Communicative Disorders, University of Louisville School of Medicine, James Graham Brown Cancer Center, 529 S Jackson Street, Louisville, KY, 40202, USA.
| | - Sandra Sephton
- Department of Psychological & Brain Sciences, University of Louisville, Louisville, KY, USA
| | - Cassandra Woolley
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Attia M Elbehi
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Anu R I
- Department of Clinical Biochemistry, MVR Cancer Center and Research Institute, Kerala, India
| | - Bene Ekine-Afolabi
- ZEAB Therapeutic Ltd, London, UK
- Department of Health, Sport & Bioscience, University of East London, Stratford, UK
| | - Victor C Kok
- Department of Medical Oncology, Kuang Tien General Hospital Cancer Center, Taichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University Taiwan, Taichung, Taiwan
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81
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Abstract
Circadian rhythms describe physiological systems that repeat themselves with a cycle of approximately 24 h. Our understanding of the cellular and molecular origins of these oscillations has improved dramatically, allowing us to appreciate the significant role these oscillations play in maintaining physiological homeostasis. Circadian rhythms allow living organisms to predict and efficiently respond to a dynamically changing environment, set by repetitive day/night cycles. Since circadian rhythms underlie almost every aspect of human physiology, it is unsurprising that they also influence the response of a living organism to disease, stress, and therapeutics. Therefore, not only do the mechanisms that maintain health and disrupt homeostasis depend on our internal circadian clock, but also the way drugs are perceived and function depends on these physiological rhythms. We present a holistic view of the therapeutic process, discussing components such as disease state, pharmacokinetics, and pharmacodynamics, as well as adverse reactions that are critically affected by circadian rhythms. We outline challenges and opportunities in moving toward personalized medicine approaches that explore and capitalize on circadian rhythms for the benefit of the patient.
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Affiliation(s)
- Yaakov Nahmias
- Center for Bioengineering, School of Computer Science and Engineering, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ioannis P Androulakis
- Department of Biomedical Engineering and Department of Chemical & Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, USA; .,Department of Surgery, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, USA
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82
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Mavroudis PD, Jusko WJ. Mathematical modeling of mammalian circadian clocks affecting drug and disease responses. J Pharmacokinet Pharmacodyn 2021; 48:375-386. [PMID: 33725238 DOI: 10.1007/s10928-021-09746-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/26/2021] [Indexed: 12/28/2022]
Abstract
To align with daily environmental changes, most physiological processes in mammals exhibit a time-of-day rhythmicity. This circadian control of physiology is intrinsically driven by a cell-autonomous clock gene network present in almost all cells of the body that drives rhythmic expression of genes that regulate numerous molecular and cellular processes. Accordingly, many aspects of pharmacology and toxicology also oscillate in a time-of-day manner giving rise to diverse effects on pharmacokinetics and pharmacodynamics. Genome-wide studies and mathematical modeling are available tools that have significantly improved our understanding of these nonlinear aspects of physiology and therapeutics. In this manuscript current literature and our prior work on the model-based approaches that have been used to explore circadian genomic systems of mammals are reviewed. Such basic understanding and having an integrative approach may provide new strategies for chronotherapeutic drug treatments and yield new insights for the restoration of the circadian system when altered by diseases.
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Affiliation(s)
- Panteleimon D Mavroudis
- Quantitative Pharmacology, DMPK, Sanofi, Waltham, MA, 02451, USA. .,State University of New York, School of Pharmacy and Pharmaceutical Sciences, University of Buffalo, Buffalo, NY, USA.
| | - William J Jusko
- State University of New York, School of Pharmacy and Pharmaceutical Sciences, University of Buffalo, Buffalo, NY, USA
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83
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Bartman CM, Matveyenko A, Pabelick C, Prakash YS. Cellular clocks in hyperoxia effects on [Ca 2+] i regulation in developing human airway smooth muscle. Am J Physiol Lung Cell Mol Physiol 2021; 320:L451-L466. [PMID: 33404366 PMCID: PMC8294620 DOI: 10.1152/ajplung.00406.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 01/06/2023] Open
Abstract
Supplemental O2 (hyperoxia) is necessary for preterm infant survival but is associated with development of bronchial airway hyperreactivity and childhood asthma. Understanding early mechanisms that link hyperoxia to altered airway structure and function are key to developing advanced therapies. We previously showed that even moderate hyperoxia (50% O2) enhances intracellular calcium ([Ca2+]i) and proliferation of human fetal airway smooth muscle (fASM), thereby facilitating bronchoconstriction and remodeling. Here, we introduce cellular clock biology as a novel mechanism linking early oxygen exposure to airway biology. Peripheral, intracellular clocks are a network of transcription-translation feedback loops that produce circadian oscillations with downstream targets highly relevant to airway function and asthma. Premature infants suffer circadian disruption whereas entrainment strategies improve outcomes, highlighting the need to understand relationships between clocks and developing airways. We hypothesized that hyperoxia impacts clock function in fASM and that the clock can be leveraged to attenuate deleterious effects of O2 on the developing airway. We report that human fASM express core clock machinery (PER1, PER2, CRY1, ARNTL/BMAL1, CLOCK) that is responsive to dexamethasone (Dex) and altered by O2. Disruption of the clock via siRNA-mediated PER1 or ARNTL knockdown alters store-operated calcium entry (SOCE) and [Ca2+]i response to histamine in hyperoxia. Effects of O2 on [Ca2+]i are rescued by driving expression of clock proteins, via effects on the Ca2+ channels IP3R and Orai1. These data reveal a functional fASM clock that modulates [Ca2+]i regulation, particularly in hyperoxia. Harnessing clock biology may be a novel therapeutic consideration for neonatal airway diseases following prematurity.
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Affiliation(s)
- Colleen M Bartman
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota
| | - Aleksey Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| | - Christina Pabelick
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| | - Y S Prakash
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
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84
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Ruan W, Yuan X, Eltzschig HK. Circadian rhythm as a therapeutic target. Nat Rev Drug Discov 2021; 20:287-307. [PMID: 33589815 DOI: 10.1038/s41573-020-00109-w] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 12/20/2022]
Abstract
The circadian clock evolved in diverse organisms to integrate external environmental changes and internal physiology. The clock endows the host with temporal precision and robust adaptation to the surrounding environment. When circadian rhythms are perturbed or misaligned, as a result of jet lag, shiftwork or other lifestyle factors, adverse health consequences arise, and the risks of diseases such as cancer, cardiovascular diseases or metabolic disorders increase. Although the negative impact of circadian rhythm disruption is now well established, it remains underappreciated how to take advantage of biological timing, or correct it, for health benefits. In this Review, we provide an updated account of the circadian system and highlight several key disease areas with altered circadian signalling. We discuss environmental and lifestyle modifications of circadian rhythm and clock-based therapeutic strategies, including chronotherapy, in which dosing time is deliberately optimized for maximum therapeutic index, and pharmacological agents that target core clock components and proximal regulators. Promising progress in research, disease models and clinical applications should encourage a concerted effort towards a new era of circadian medicine.
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Affiliation(s)
- Wei Ruan
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoyi Yuan
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Holger K Eltzschig
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
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85
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Patel SA, Kondratov RV. Clock at the Core of Cancer Development. BIOLOGY 2021; 10:150. [PMID: 33672910 PMCID: PMC7918730 DOI: 10.3390/biology10020150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/29/2022]
Abstract
To synchronize various biological processes with the day and night cycle, most organisms have developed circadian clocks. This evolutionarily conserved system is important in the temporal regulation of behavior, physiology and metabolism. Multiple pathological changes associated with circadian disruption support the importance of the clocks in mammals. Emerging links have revealed interplay between circadian clocks and signaling networks in cancer. Understanding the cross-talk between the circadian clock and tumorigenesis is imperative for its prevention, management and development of effective treatment options. In this review, we summarize the role of the circadian clock in regulation of one important metabolic pathway, insulin/IGF1/PI3K/mTOR signaling, and how dysregulation of this metabolic pathway could lead to uncontrolled cancer cell proliferation and growth. Targeting the circadian clock and rhythms either with recently discovered pharmaceutical agents or through environmental cues is a new direction in cancer chronotherapy. Combining the circadian approach with traditional methods, such as radiation, chemotherapy or the recently developed, immunotherapy, may improve tumor response, while simultaneously minimizing the adverse effects commonly associated with cancer therapies.
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Affiliation(s)
- Sonal A. Patel
- Fusion Pharmaceuticals Inc., Hamilton, ON L8P 0A6, Canada;
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Roman V. Kondratov
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
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86
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Astone M, Santoro MM. Time to fight: targeting the circadian clock molecular machinery in cancer therapy. Drug Discov Today 2021; 26:1164-1184. [PMID: 33549826 DOI: 10.1016/j.drudis.2021.01.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/23/2020] [Accepted: 01/22/2021] [Indexed: 02/06/2023]
Abstract
The circadian clock regulates a wide range of molecular pathways and biological processes. The expression of clock genes is often altered in cancer, fostering tumor initiation and progression. Inhibition and activation of core circadian clock genes, as well as treatments that restore circadian rhythmicity, have been successful in counteracting tumor growth in different experimental models. Here, we provide an up-to-date overview of studies that show the therapeutic effects of targeting the clock molecular machinery in cancer, both genetically and pharmacologically. We also highlight future areas for progress that offer a promising path towards innovative anticancer strategies. Substantial limitations in the current understanding of the complex interplay between the circadian clock and cancer in vivo need to be addressed in order to allow clock-targeting therapies in cancer.
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Affiliation(s)
- Matteo Astone
- Department of Biology, University of Padova, I-35131, Italy
| | - Massimo M Santoro
- Department of Biology, University of Padova, I-35131, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35129 Padova, Italy.
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87
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Sion B, Bégou M. Can chronopharmacology improve the therapeutic management of neurological diseases? Fundam Clin Pharmacol 2021; 35:564-581. [PMID: 33539566 DOI: 10.1111/fcp.12659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/04/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022]
Abstract
The importance of circadian rhythm dysfunctions in the pathophysiology of neurological diseases has been highlighted recently. Chronopharmacology principles imply that tailoring the timing of treatments to the circadian rhythm of individual patients could optimize therapeutic management. According to these principles, chronopharmacology takes into account the individual differences in patients' clocks, the rhythmic changes in the organism sensitivity to therapeutic and side effects of drugs, and the predictable time variations of disease. This review examines the current literature on chronopharmacology of neurological diseases focusing its scope on epilepsy, Alzheimer and Parkinson diseases, and neuropathic pain, even if other neurological diseases could have been analyzed. While the results of the studies discussed in this review point to a potential therapeutic benefit of chronopharmacology in neurological diseases, the field is still in its infancy. Studies including a sufficiently large number of patients and measuring gold standard markers of the circadian rhythmicity are still needed to evaluate the beneficial effect of administration times over the 24-hour day but also of clock modulating drugs.
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Affiliation(s)
- Benoit Sion
- Université Clermont Auvergne, INSERM U1107, NEURO-DOL, Clermont-Ferrand, France
| | - Mélina Bégou
- Université Clermont Auvergne, INSERM U1107, NEURO-DOL, Clermont-Ferrand, France
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88
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Alamoudi AA. Why do cancer cells break from host circadian rhythm? Insights from unicellular organisms. Bioessays 2021; 43:e2000205. [PMID: 33533033 DOI: 10.1002/bies.202000205] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/30/2020] [Accepted: 12/17/2020] [Indexed: 12/12/2022]
Abstract
It is not clear why cancer cells choose to disrupt their circadian clock rhythms, and whether such disruption governs a selective fitness and a survival advantage. In this review, I focus on understanding the impacts of clock gene disruption on a simpler model, such as the unicellular cyanobacterium, in order to explain how cancer cells may alter the circadian rhythm to reprogram their metabolism based on their needs and status. It appears to be that the activation of the oxidative pentose phosphate pathway (OPPP) and production of NADPH, the preferred molecule for detoxification of reactive oxygen species, is a critical process for night survival in unicellular organisms. The circadian clock acts as a gatekeeper that controls how the organism will utilize its sugar, shifting sugar influx between glycolysis and OPPP. The circadian clock can thus act as a gatekeeper between an anabolic, proliferative mode and a homeostatic, survival mode.
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Affiliation(s)
- Aliaa A Alamoudi
- Clinical Biochemistry Department, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Stem Cell Unit, King Fahad Medical Research Center, Jeddah, Saudi Arabia
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89
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Haspel J, Kim M, Zee P, Schwarzmeier T, Montagnese S, Panda S, Albani A, Merrow M. A Timely Call to Arms: COVID-19, the Circadian Clock, and Critical Care. J Biol Rhythms 2021; 36:55-70. [PMID: 33573430 PMCID: PMC7882674 DOI: 10.1177/0748730421992587] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We currently find ourselves in the midst of a global coronavirus disease 2019 (COVID-19) pandemic, caused by the highly infectious novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we discuss aspects of SARS-CoV-2 biology and pathology and how these might interact with the circadian clock of the host. We further focus on the severe manifestation of the illness, leading to hospitalization in an intensive care unit. The most common severe complications of COVID-19 relate to clock-regulated human physiology. We speculate on how the pandemic might be used to gain insights on the circadian clock but, more importantly, on how knowledge of the circadian clock might be used to mitigate the disease expression and the clinical course of COVID-19.
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Affiliation(s)
- Jeffrey Haspel
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Minjee Kim
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Phyllis Zee
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tanja Schwarzmeier
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Munich, Germany
| | | | | | - Adriana Albani
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Munich, Germany
- Department of Medicine IV, LMU Munich, Munich, Germany
| | - Martha Merrow
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Munich, Germany
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90
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Abstract
The liver is a "front line" in the homeostatic defenses against variation in nutrient intake. It orchestrates metabolic responses to feeding by secreting factors essential for maintaining metabolic homeostasis, converting carbohydrates to triglycerides for storage, and releasing lipids packaged as lipoproteins for distribution to other tissues. Between meals, it provides fuel to the body by releasing glucose produced from glucogenic precursors and ketones from fatty acids and ketogenic amino acids. Modern diets enriched in sugars and saturated fats increase lipid accumulation in hepatocytes (nonalcoholic fatty liver disease). If untreated, this can progress to liver inflammation (nonalcoholic steatohepatitis), fibrosis, cirrhosis, and hepatocellular carcinoma. Dysregulation of liver metabolism is also relatively common in modern societies. Increased hepatic glucose production underlies fasting hyperglycemia that defines type 2 diabetes, while increased production of atherogenic, large, triglyceride-rich, very low-density lipoproteins raises the risk of cardiovascular disease. Evidence has accrued of a strong connection between meal timing, the liver clock, and metabolic homeostasis. Metabolic programming of the liver transcriptome and posttranslation modifications of proteins is strongly influenced by the daily rhythms in nutrient intake governed by the circadian clock. Importantly, whereas cell-autonomous clocks have been identified in the liver, the complete circadian programing of the liver transcriptome and posttranslational modifications of essential metabolic proteins is strongly dependent on nutrient flux and circadian signals from outside the liver. The purpose of this review is to provide a basic understanding of liver circadian physiology, drawing attention to recent research on the relationships between circadian biology and liver function.
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Affiliation(s)
- Kyle S McCommis
- Department of Biochemistry & Molecular Biology, Center for Cardiovascular Research, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Andrew A Butler
- Department of Pharmacology and Physiology, Center for Cardiovascular Research, The Henry and Amelia Nasrallah Center for Neuroscience, School of Medicine and the Henry and Amelia Nasrallah Center for Neuroscience, St Louis University, St Louis, Missouri, USA
- Correspondence: Andrew A. Butler, PhD, Department of Pharmacology and Physiology, Center for Cardiovascular Research, The Henry and Amelia Nasrallah Center for Neuroscience, School of Medicine and the Henry and Amelia Nasrallah Center for Neuroscience, St Louis University, 1402 S Grand Blvd, St Louis, MO 63104, USA.
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91
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Wu X, Cheng Q. Fractal Autoencoders for Feature Selection. PROCEEDINGS OF THE ... AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE. AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE 2021; 2021:10370-10378. [PMID: 35391993 PMCID: PMC8985126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Feature selection reduces the dimensionality of data by identifying a subset of the most informative features. In this paper, we propose an innovative framework for unsupervised feature selection, called fractal autoencoders (FAE). It trains a neural network to pinpoint informative features for global exploring of representability and for local excavating of diversity. Architecturally, FAE extends autoencoders by adding a one-to-one scoring layer and a small sub-neural network for feature selection in an unsupervised fashion. With such a concise architecture, FAE achieves state-of-the-art performances; extensive experimental results on fourteen datasets, including very high-dimensional data, have demonstrated the superiority of FAE over existing contemporary methods for unsupervised feature selection. In particular, FAE exhibits substantial advantages on gene expression data exploration, reducing measurement cost by about 15% over the widely used L1000 landmark genes. Further, we show that the FAE framework is easily extensible with an application.
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92
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Sengupta S, Ince L, Sartor F, Borrmann H, Zhuang X, Naik A, Curtis A, McKeating JA. Clocks, Viruses, and Immunity: Lessons for the COVID-19 Pandemic. J Biol Rhythms 2021; 36:23-34. [PMID: 33480287 PMCID: PMC7970201 DOI: 10.1177/0748730420987669] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Circadian rhythms are evolutionarily conserved anticipatory systems that
allow the host to prepare and respond to threats in its environment.
This article summarizes a European Biological Rhythms Society (EBRS)
workshop held in July 2020 to review current knowledge of the
interplay between the circadian clock and viral infections to inform
therapeutic strategies against SARS-CoV-2 and COVID-19. A large body
of work supports the role of the circadian clock in regulating various
aspects of viral replication, host responses, and associated
pathogenesis. We review the evidence describing the multifaceted role
of the circadian clock, spanning host susceptibility, antiviral
mechanisms, and host resilience. Finally, we define the most pressing
research questions and how our knowledge of chronobiology can inform
key translational research priorities.
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Affiliation(s)
- Shaon Sengupta
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louise Ince
- Departement de Pathologie et Immunologie, Geneva, Switzerland
| | - Francesca Sartor
- Institute of Medical Psychology, Medical Faculty, Ludwig Maximilian University of Munich, Munich, Germany
| | - Helene Borrmann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amruta Naik
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Annie Curtis
- School of Pharmacy and Biomolecular Sciences, Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jane A McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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93
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Javeed N, Brown MR, Rakshit K, Her T, Sen SK, Matveyenko AV. Proinflammatory Cytokine Interleukin 1β Disrupts β-cell Circadian Clock Function and Regulation of Insulin Secretion. Endocrinology 2021; 162:bqaa084. [PMID: 32455427 PMCID: PMC7692023 DOI: 10.1210/endocr/bqaa084] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/21/2020] [Indexed: 12/24/2022]
Abstract
Intrinsic β-cell circadian clocks are important regulators of insulin secretion and overall glucose homeostasis. Whether the circadian clock in β-cells is perturbed following exposure to prodiabetogenic stressors such as proinflammatory cytokines, and whether these perturbations are featured during the development of diabetes, remains unknown. To address this, we examined the effects of cytokine-mediated inflammation common to the pathophysiology of diabetes, on the physiological and molecular regulation of the β-cell circadian clock. Specifically, we provide evidence that the key diabetogenic cytokine IL-1β disrupts functionality of the β-cell circadian clock and impairs circadian regulation of glucose-stimulated insulin secretion. The deleterious effects of IL-1β on the circadian clock were attributed to impaired expression of key circadian transcription factor Bmal1, and its regulator, the NAD-dependent deacetylase, Sirtuin 1 (SIRT1). Moreover, we also identified that Type 2 diabetes in humans is associated with reduced immunoreactivity of β-cell BMAL1 and SIRT1, suggestive of a potential causative link between islet inflammation, circadian clock disruption, and β-cell failure. These data suggest that the circadian clock in β-cells is perturbed following exposure to proinflammatory stressors and highlights the potential for therapeutic targeting of the circadian system for treatment for β-cell failure in diabetes.
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Affiliation(s)
- Naureen Javeed
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Matthew R Brown
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Kuntol Rakshit
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Tracy Her
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Satish K Sen
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Aleksey V Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
- Department of Medicine, Division of Endocrinology, Metabolism, Diabetes, and Nutrition, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
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94
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Cal-Kayitmazbatir S, Kulkoyluoglu-Cotul E, Growe J, Selby CP, Rhoades SD, Malik D, Oner H, Asimgil H, Francey LJ, Sancar A, Kruger WD, Hogenesch JB, Weljie A, Anafi RC, Kavakli IH. CRY1-CBS binding regulates circadian clock function and metabolism. FEBS J 2021; 288:614-639. [PMID: 32383312 PMCID: PMC7648728 DOI: 10.1111/febs.15360] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/09/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022]
Abstract
Circadian disruption influences metabolic health. Metabolism modulates circadian function. However, the mechanisms coupling circadian rhythms and metabolism remain poorly understood. Here, we report that cystathionine β-synthase (CBS), a central enzyme in one-carbon metabolism, functionally interacts with the core circadian protein cryptochrome 1 (CRY1). In cells, CBS augments CRY1-mediated repression of the CLOCK/BMAL1 complex and shortens circadian period. Notably, we find that mutant CBS-I278T protein, the most common cause of homocystinuria, does not bind CRY1 or regulate its repressor activity. Transgenic CbsZn/Zn mice, while maintaining circadian locomotor activity period, exhibit reduced circadian power and increased expression of E-BOX outputs. CBS function is reciprocally influenced by CRY1 binding. CRY1 modulates enzymatic activity of the CBS. Liver extracts from Cry1-/- mice show reduced CBS activity that normalizes after the addition of exogenous wild-type (WT) CRY1. Metabolomic analysis of WT, CbsZn/Zn , Cry1-/- , and Cry2-/- samples highlights the metabolic importance of endogenous CRY1. We observed temporal variation in one-carbon and transsulfuration pathways attributable to CRY1-induced CBS activation. CBS-CRY1 binding provides a post-translational switch to modulate cellular circadian physiology and metabolic control.
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Affiliation(s)
- Sibel Cal-Kayitmazbatir
- Department Molecular Biology and Genetics, Koc University
Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Eylem Kulkoyluoglu-Cotul
- Department Chemical and Biological Engineering Koc
University Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Jacqueline Growe
- Systems Pharmacology and Translational Therapeutics,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christopher P. Selby
- Department of Biochemistry and Biophysics, University of
North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Seth D. Rhoades
- Systems Pharmacology and Translational Therapeutics,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Dania Malik
- Systems Pharmacology and Translational Therapeutics,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hasimcan Oner
- Department Chemical and Biological Engineering Koc
University Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Hande Asimgil
- Department Chemical and Biological Engineering Koc
University Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Lauren J. Francey
- Divisions of Human Genetics and Immunobiology, Cincinnati
Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of
North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Warren D. Kruger
- Cancer Biology Program, Fox Chase Cancer Center,
Philadelphia, PA, USA
| | - John B. Hogenesch
- Systems Pharmacology and Translational Therapeutics,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Divisions of Human Genetics and Immunobiology, Cincinnati
Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Aalim Weljie
- Systems Pharmacology and Translational Therapeutics,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ron C. Anafi
- Department of Medicine, Chronobiology and Sleep Institute,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ibrahim Halil Kavakli
- Department Molecular Biology and Genetics, Koc University
Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
- Department Chemical and Biological Engineering Koc
University Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
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95
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Crnko S, Schutte H, Doevendans PA, Sluijter JPG, van Laake LW. Minimally Invasive Ways of Determining Circadian Rhythms in Humans. Physiology (Bethesda) 2021; 36:7-20. [DOI: 10.1152/physiol.00018.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Circadian rhythm exerts a critical role in mammalian health and disease. A malfunctioning circadian clock can be a consequence, as well as the cause of several pathophysiologies. Clinical therapies and research may also be influenced by the clock. Since the most suitable manner of revealing this rhythm in humans is not yet established, we discuss existing methods and seek to determine the most feasible ones.
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Affiliation(s)
- Sandra Crnko
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, Circulatory Health Laboratory, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Hilde Schutte
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Pieter A. Doevendans
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
- Central Military Hospital, Utrecht, The Netherlands
| | - Joost P. G. Sluijter
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, Circulatory Health Laboratory, University Medical Centre Utrecht, Utrecht, The Netherlands
- Utrecht University, Utrecht, The Netherlands
| | - Linda W. van Laake
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, Circulatory Health Laboratory, University Medical Centre Utrecht, Utrecht, The Netherlands
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96
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Wang F, Li N, Wang C, Xing G, Cao S, Xu Q, Zhang Y, Hu M, Zhang G. DPL: a comprehensive database on sequences, structures, sources and functions of peptide ligands. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5979899. [PMID: 33216893 PMCID: PMC7678785 DOI: 10.1093/database/baaa089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/02/2020] [Accepted: 09/11/2020] [Indexed: 12/02/2022]
Abstract
DPL (http://www.peptide-ligand.cn/) is a comprehensive database of peptide ligand (DPL). DPL1.0 holds 1044 peptide ligand entries and provides references for the study of the polypeptide platform. The data were collected from PubMed-NCBI, PDB, APD3, CAMPR3, etc. The lengths of the base sequences are varied from 3 to78. DPL database has 923 linear peptides and 88 cyclic peptides. The functions of peptides collected by DPL are very wide. It includes 540 entries of antiviral peptides (including SARS-CoV-2), 55 entries of signal peptides, 48 entries of protease inhibitors, 45 entries of anti-hypertension, 37 entries of anticancer peptides, etc. There are 270 different kinds of peptide targets. All peptides in DPL have clear binding targets. Most of the peptides and receptors have 3D structures experimentally verified or predicted by CYCLOPS, I-TASSER and SWISS-MODEL. With the rapid development of the COVID-2019 epidemic, this database also collects the research progress of peptides against coronavirus. In conclusion, DPL is a unique resource, which allows users easily to explore the targets, different structures as well as properties of peptides.
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Affiliation(s)
- Fangyu Wang
- Henan Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou, Henan Province, 450002, China.,College of Food Science and Technology, Henan Agricultural University, 63#Agricultural Road, Zhengzhou, Henan Province, 450000, PR China
| | - Ning Li
- College of Food Science and Technology, Henan Agricultural University, 63#Agricultural Road, Zhengzhou, Henan Province, 450000, PR China
| | - Chunfeng Wang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, 1# Mianfang Street, Zhengzhou, Henan Province, 450052, China
| | - Guangxu Xing
- Henan Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou, Henan Province, 450002, China
| | - Shuai Cao
- College of Food Science and Technology, Henan Agricultural University, 63#Agricultural Road, Zhengzhou, Henan Province, 450000, PR China
| | - Qian Xu
- Henan Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou, Henan Province, 450002, China
| | - Yunshang Zhang
- Henan Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou, Henan Province, 450002, China
| | - Man Hu
- Henan Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou, Henan Province, 450002, China
| | - Gaiping Zhang
- Henan Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou, Henan Province, 450002, China.,College of Food Science and Technology, Henan Agricultural University, 63#Agricultural Road, Zhengzhou, Henan Province, 450000, PR China
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97
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Abstract
Circadian rhythms govern a large array of physiological and metabolic functions. Perturbations of the daily cycle have been linked to elevated risk of developing cancer as well as poor prognosis in patients with cancer. Also, expression of core clock genes or proteins is remarkably attenuated particularly in tumours of a higher stage or that are more aggressive, possibly linking the circadian clock to cellular differentiation. Emerging evidence indicates that metabolic control by the circadian clock underpins specific hallmarks of cancer metabolism. Indeed, to support cell proliferation and biomass production, the clock may direct metabolic processes of cancer cells in concert with non-clock transcription factors to control how nutrients and metabolites are utilized in a time-specific manner. We hypothesize that the metabolic switch between differentiation or stemness of cancer may be coupled to the molecular clockwork. Moreover, circadian rhythms of host organisms appear to dictate tumour growth and proliferation. This Review outlines recent discoveries of the interplay between circadian rhythms, proliferative metabolism and cancer, highlighting potential opportunities in the development of future therapeutic strategies.
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Affiliation(s)
- Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
- Department of Endocrinology, Metabolism, and Nephrology, School of Medicine, Keio University, Tokyo, Japan.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
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98
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Moškon M. CosinorPy: a python package for cosinor-based rhythmometry. BMC Bioinformatics 2020; 21:485. [PMID: 33121431 PMCID: PMC7597035 DOI: 10.1186/s12859-020-03830-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/21/2020] [Indexed: 11/25/2022] Open
Abstract
Background Even though several computational methods for rhythmicity detection and analysis of biological data have been proposed in recent years, classical trigonometric regression based on cosinor still has several advantages over these methods and is still widely used. Different software packages for cosinor-based rhythmometry exist, but lack certain functionalities and require data in different, non-unified input formats. Results We present CosinorPy, a Python implementation of cosinor-based methods for rhythmicity detection and analysis. CosinorPy merges and extends the functionalities of existing cosinor packages. It supports the analysis of rhythmic data using single- or multi-component cosinor models, automatic selection of the best model, population-mean cosinor regression, and differential rhythmicity assessment. Moreover, it implements functions that can be used in a design of experiments, a synthetic data generator, and import and export of data in different formats. Conclusion CosinorPy is an easy-to-use Python package for straightforward detection and analysis of rhythmicity requiring minimal statistical knowledge, and produces publication-ready figures. Its code, examples, and documentation are available to download from https://github.com/mmoskon/CosinorPy. CosinorPy can be installed manually or by using pip, the package manager for Python packages. The implementation reported in this paper corresponds to the software release v1.1.
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Affiliation(s)
- Miha Moškon
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, 1000, Ljubljana, Slovenia.
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99
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Hesse J, Malhan D, Yalҫin M, Aboumanify O, Basti A, Relógio A. An Optimal Time for Treatment-Predicting Circadian Time by Machine Learning and Mathematical Modelling. Cancers (Basel) 2020; 12:cancers12113103. [PMID: 33114254 PMCID: PMC7690897 DOI: 10.3390/cancers12113103] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023] Open
Abstract
Tailoring medical interventions to a particular patient and pathology has been termed personalized medicine. The outcome of cancer treatments is improved when the intervention is timed in accordance with the patient's internal time. Yet, one challenge of personalized medicine is how to consider the biological time of the patient. Prerequisite for this so-called chronotherapy is an accurate characterization of the internal circadian time of the patient. As an alternative to time-consuming measurements in a sleep-laboratory, recent studies in chronobiology predict circadian time by applying machine learning approaches and mathematical modelling to easier accessible observables such as gene expression. Embedding these results into the mathematical dynamics between clock and cancer in mammals, we review the precision of predictions and the potential usage with respect to cancer treatment and discuss whether the patient's internal time and circadian observables, may provide an additional indication for individualized treatment timing. Besides the health improvement, timing treatment may imply financial advantages, by ameliorating side effects of treatments, thus reducing costs. Summarizing the advances of recent years, this review brings together the current clinical standard for measuring biological time, the general assessment of circadian rhythmicity, the usage of rhythmic variables to predict biological time and models of circadian rhythmicity.
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Affiliation(s)
- Janina Hesse
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Deeksha Malhan
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Müge Yalҫin
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Ouda Aboumanify
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Alireza Basti
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
- Department of Human Medicine, Institute for Systems Medicine and Bioinformatics, MSH Medical School Hamburg—University of Applied Sciences and Medical University, 20457 Hamburg, Germany
- Correspondence: or
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100
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Zhu B. Decoding the function and regulation of the mammalian 12-h clock. J Mol Cell Biol 2020; 12:752-758. [PMID: 32384155 PMCID: PMC7816679 DOI: 10.1093/jmcb/mjaa021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/16/2020] [Accepted: 04/24/2020] [Indexed: 11/26/2022] Open
Affiliation(s)
- Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA.,Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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