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Jeppe K, Ftouni S, Nijagal B, Grant LK, Lockley SW, Rajaratnam SMW, Phillips AJK, McConville MJ, Tull D, Anderson C. Accurate detection of acute sleep deprivation using a metabolomic biomarker-A machine learning approach. SCIENCE ADVANCES 2024; 10:eadj6834. [PMID: 38457492 PMCID: PMC11094653 DOI: 10.1126/sciadv.adj6834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/02/2024] [Indexed: 03/10/2024]
Abstract
Sleep deprivation enhances risk for serious injury and fatality on the roads and in workplaces. To facilitate future management of these risks through advanced detection, we developed and validated a metabolomic biomarker of sleep deprivation in healthy, young participants, across three experiments. Bi-hourly plasma samples from 2 × 40-hour extended wake protocols (for train/test models) and 1 × 40-hour protocol with an 8-hour overnight sleep interval were analyzed by untargeted liquid chromatography-mass spectrometry. Using a knowledge-based machine learning approach, five consistently important variables were used to build predictive models. Sleep deprivation (24 to 38 hours awake) was predicted accurately in classification models [versus well-rested (0 to 16 hours)] (accuracy = 94.7%/AUC 99.2%, 79.3%/AUC 89.1%) and to a lesser extent in regression (R2 = 86.1 and 47.8%) models for within- and between-participant models, respectively. Metabolites were identified for replicability/future deployment. This approach for detecting acute sleep deprivation offers potential to reduce accidents through "fitness for duty" or "post-accident analysis" assessments.
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Affiliation(s)
- Katherine Jeppe
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia
| | - Suzanne Ftouni
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia
| | - Brunda Nijagal
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia
| | - Leilah K. Grant
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Steven W. Lockley
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Shantha M. W. Rajaratnam
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrew J. K. Phillips
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
| | - Malcolm J. McConville
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia
| | - Clare Anderson
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia
- Centre for Human Brain Health, School of Psychology, University of Birmingham, Edgbaston, UK
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Depner CM. Biomarkers linking habitual short sleep duration with risk of cardiometabolic disease: current progress and future directions. FRONTIERS IN SLEEP 2023; 2:1293941. [PMID: 39041043 PMCID: PMC11262587 DOI: 10.3389/frsle.2023.1293941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Approximately one in three adults in the United States sleeps less than the recommended 7 h per night. Decades of epidemiological data and data from experimental sleep restriction studies demonstrate short sleep duration is associated with adverse cardiometabolic risk, including risk of type 2 diabetes and cardiovascular disease. However, the precise mechanisms underlying this risk are not fully elucidated and there is a lack of sleep-based interventions designed to mitigate such risk. One strategy to overcome these limitations is to develop biomarkers that link habitual short sleep duration with adverse cardiometabolic risk. Such biomarkers could inform biochemical mechanisms, identify new targets for interventions, support precision medicine by identifying individuals most likely to benefit from sleep-based interventions, and ultimately lead to improved cardiometabolic health in people with habitual short sleep durations. Early progress demonstrates proof-of-principle that omics-based technologies are a viable approach to create biochemical signatures (biomarkers) of short sleep duration, primarily derived from acute studies of experimental sleep restriction. Yet, much work remains. Notably, studies that translate early findings from experimental sleep restriction to free-living adults with habitual short sleep duration have high potential to advance the field. Such studies also create an exciting opportunity for larger randomized controlled trials that simultaneously identify biomarkers of habitual short sleep duration and evaluate the efficacy of sleep-based interventions. Ultimately, early progress in developing molecular biomarkers of short sleep duration combined with the prior decades of progress in the sleep and metabolism fields provide the foundation for exciting progress in the biomarker development space.
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Affiliation(s)
- Christopher M. Depner
- Department of Health and Kinesiology, University of Utah, Salt Lake City, UT, United States
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3
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Russell KL, Rodman HR, Pak VM. Sleep insufficiency, circadian rhythms, and metabolomics: the connection between metabolic and sleep disorders. Sleep Breath 2023; 27:2139-2153. [PMID: 37147557 DOI: 10.1007/s11325-023-02828-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/06/2023] [Accepted: 04/05/2023] [Indexed: 05/07/2023]
Abstract
PURPOSE US adults who report experiencing insufficient sleep are more likely to suffer from metabolic disorders such as hyperlipidemia, diabetes, and obesity than those with sufficient sleep. Less is understood about the underlying molecular mechanisms connecting these phenomena. A systematic, qualitative review of metabolomics studies exploring metabolic changes in response to sleep insufficiency, sleep deprivation, or circadian disruption was conducted in accordance with PRISMA guidelines. METHODS An electronic literature review in the PubMed database was performed considering publications through May 2021 and screening and eligibility criteria were applied to articles retrieved. The following keywords were used: "metabolomics" and "sleep disorders" or "sleep deprivation" or "sleep disturbance" or "circadian rhythm." After screening and addition of studies included from reference lists of retrieved studies, 16 records were identified for review. RESULTS Consistent changes in metabolites were observed across studies between individuals experiencing sleep deprivation compared to non-sleep deprived controls. Significant increases in phosphatidylcholines, acylcarnitines, sphingolipids, and other lipids were consistent across studies. Increased levels of amino acids such as tryptophan and phenylalanine were also noted. However, studies were limited to small samples of young, healthy, mostly male participants conducted in short inpatient sessions, limiting generalizability. CONCLUSION Changes in lipid and amino acid metabolites accompanying sleep deprivation and/or circadian rhythms may indicate cellular membrane and protein breakdown underlying the connection between sleep disturbance, hyperlipidemia, and other metabolic disorders. Larger epidemiological studies examining changes in the human metabolome in response to chronic insufficient sleep would help elucidate this relationship.
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Affiliation(s)
| | | | - Victoria M Pak
- Emory Nell Hodgson School of Nursing, Atlanta, GA, USA.
- Emory Rollins School of Public Health, Atlanta, GA, USA.
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Vaquer-Alicea A, Yu J, Liu H, Lucey BP. Plasma and cerebrospinal fluid proteomic signatures of acutely sleep-deprived humans: an exploratory study. SLEEP ADVANCES : A JOURNAL OF THE SLEEP RESEARCH SOCIETY 2023; 4:zpad047. [PMID: 38046221 PMCID: PMC10691441 DOI: 10.1093/sleepadvances/zpad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/06/2023] [Indexed: 12/05/2023]
Abstract
Study Objectives Acute sleep deprivation affects both central and peripheral biological processes. Prior research has mainly focused on specific proteins or biological pathways that are dysregulated in the setting of sustained wakefulness. This exploratory study aimed to provide a comprehensive view of the biological processes and proteins impacted by acute sleep deprivation in both plasma and cerebrospinal fluid (CSF). Methods We collected plasma and CSF from human participants during one night of sleep deprivation and controlled normal sleep conditions. One thousand and three hundred proteins were measured at hour 0 and hour 24 using a high-scale aptamer-based proteomics platform (SOMAscan) and a systematic biological database tool (Metascape) was used to reveal altered biological pathways. Results Acute sleep deprivation decreased the number of upregulated and downregulated biological pathways and proteins in plasma but increased upregulated and downregulated biological pathways and proteins in CSF. Predominantly affected proteins and pathways were associated with immune response, inflammation, phosphorylation, membrane signaling, cell-cell adhesion, and extracellular matrix organization. Conclusions The identified modifications across biofluids add to evidence that acute sleep deprivation has important impacts on biological pathways and proteins that can negatively affect human health. As a hypothesis-driving study, these findings may help with the exploration of novel mechanisms that mediate sleep loss and associated conditions, drive the discovery of new sleep loss biomarkers, and ultimately aid in the identification of new targets for intervention to human diseases.
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Affiliation(s)
- Ana Vaquer-Alicea
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Jinsheng Yu
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Haiyan Liu
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Brendan P Lucey
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
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Souto-Maior C, Serrano Negron YL, Harbison ST. Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration. PLoS Comput Biol 2023; 19:e1011389. [PMID: 37561813 PMCID: PMC10443883 DOI: 10.1371/journal.pcbi.1011389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/22/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
All but the simplest phenotypes are believed to result from interactions between two or more genes forming complex networks of gene regulation. Sleep is a complex trait known to depend on the system of feedback loops of the circadian clock, and on many other genes; however, the main components regulating the phenotype and how they interact remain an unsolved puzzle. Genomic and transcriptomic data may well provide part of the answer, but a full account requires a suitable quantitative framework. Here we conducted an artificial selection experiment for sleep duration with RNA-seq data acquired each generation. The phenotypic results are robust across replicates and previous experiments, and the transcription data provides a high-resolution, time-course data set for the evolution of sleep-related gene expression. In addition to a Hierarchical Generalized Linear Model analysis of differential expression that accounts for experimental replicates we develop a flexible Gaussian Process model that estimates interactions between genes. 145 gene pairs are found to have interactions that are different from controls. Our method appears to be not only more specific than standard correlation metrics but also more sensitive, finding correlations not significant by other methods. Statistical predictions were compared to experimental data from public databases on gene interactions. Mutations of candidate genes implicated by our results affected night sleep, and gene expression profiles largely met predicted gene-gene interactions.
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Affiliation(s)
- Caetano Souto-Maior
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Yazmin L. Serrano Negron
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Susan T. Harbison
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, Maryland, United States of America
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Qi D, Li J, Quarles CC, Fonkem E, Wu E. Assessment and prediction of glioblastoma therapy response: challenges and opportunities. Brain 2023; 146:1281-1298. [PMID: 36445396 PMCID: PMC10319779 DOI: 10.1093/brain/awac450] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
Glioblastoma is the most aggressive type of primary adult brain tumour. The median survival of patients with glioblastoma remains approximately 15 months, and the 5-year survival rate is <10%. Current treatment options are limited, and the standard of care has remained relatively constant since 2011. Over the last decade, a range of different treatment regimens have been investigated with very limited success. Tumour recurrence is almost inevitable with the current treatment strategies, as glioblastoma tumours are highly heterogeneous and invasive. Additionally, another challenging issue facing patients with glioblastoma is how to distinguish between tumour progression and treatment effects, especially when relying on routine diagnostic imaging techniques in the clinic. The specificity of routine imaging for identifying tumour progression early or in a timely manner is poor due to the appearance similarity of post-treatment effects. Here, we concisely describe the current status and challenges in the assessment and early prediction of therapy response and the early detection of tumour progression or recurrence. We also summarize and discuss studies of advanced approaches such as quantitative imaging, liquid biomarker discovery and machine intelligence that hold exceptional potential to aid in the therapy monitoring of this malignancy and early prediction of therapy response, which may decisively transform the conventional detection methods in the era of precision medicine.
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Affiliation(s)
- Dan Qi
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
| | - Jing Li
- School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - C Chad Quarles
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ekokobe Fonkem
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Medical Education, School of Medicine, Texas A&M University, Bryan, TX 77807, USA
| | - Erxi Wu
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Medical Education, School of Medicine, Texas A&M University, Bryan, TX 77807, USA
- Department of Pharmaceutical Sciences, Irma Lerma Rangel School of Pharmacy, Texas A&M University, College Station, TX 77843, USA
- Department of Oncology and LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
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Li C, Gao Z, Su B, Xu G, Lin X. Data analysis methods for defining biomarkers from omics data. Anal Bioanal Chem 2021; 414:235-250. [PMID: 34951658 DOI: 10.1007/s00216-021-03813-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 02/01/2023]
Abstract
Omics mainly includes genomics, epigenomics, transcriptomics, proteomics and metabolomics. The rapid development of omics technology has opened up new ways to study disease diagnosis and prognosis and to define prospective information of complex diseases. Since omics data are usually large and complex, the method used to analyze the data and to define important information is crucial in omics study. In this review, we focus on advances in biomarker discovery methods based on omics data in the last decade, and categorize them as individual feature analysis, combinatorial feature analysis and network analysis. We also discuss the challenges and perspectives in this field.
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Affiliation(s)
- Chao Li
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China
| | - Zhenbo Gao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Benzhe Su
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China
| | - Xiaohui Lin
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.
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Garbarino S, Lanteri P, Bragazzi NL, Magnavita N, Scoditti E. Role of sleep deprivation in immune-related disease risk and outcomes. Commun Biol 2021; 4:1304. [PMID: 34795404 PMCID: PMC8602722 DOI: 10.1038/s42003-021-02825-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 10/26/2021] [Indexed: 12/11/2022] Open
Abstract
Modern societies are experiencing an increasing trend of reduced sleep duration, with nocturnal sleeping time below the recommended ranges for health. Epidemiological and laboratory studies have demonstrated detrimental effects of sleep deprivation on health. Sleep exerts an immune-supportive function, promoting host defense against infection and inflammatory insults. Sleep deprivation has been associated with alterations of innate and adaptive immune parameters, leading to a chronic inflammatory state and an increased risk for infectious/inflammatory pathologies, including cardiometabolic, neoplastic, autoimmune and neurodegenerative diseases. Here, we review recent advancements on the immune responses to sleep deprivation as evidenced by experimental and epidemiological studies, the pathophysiology, and the role for the sleep deprivation-induced immune changes in increasing the risk for chronic diseases. Gaps in knowledge and methodological pitfalls still remain. Further understanding of the causal relationship between sleep deprivation and immune deregulation would help to identify individuals at risk for disease and to prevent adverse health outcomes.
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Affiliation(s)
- Sergio Garbarino
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal/Child Sciences, University of Genoa, 16132, Genoa, Italy.
| | - Paola Lanteri
- Neurophysiology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Nicola Luigi Bragazzi
- Laboratory for Industrial and Applied Mathematics (LIAM), Department of Mathematics and Statistics, York University, Toronto, ON, M3J 1P3, Canada
| | - Nicola Magnavita
- Postgraduate School of Occupational Medicine, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Department of Woman/Child and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168, Rome, Italy
| | - Egeria Scoditti
- National Research Council (CNR), Institute of Clinical Physiology (IFC), 73100, Lecce, Italy
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Depner CM, Rice JD, Tussey EJ, Eckel RH, Bergman BC, Higgins JA, Melanson EL, Kohrt WM, Wright KP, Swanson CM. Bone turnover marker responses to sleep restriction and weekend recovery sleep. Bone 2021; 152:116096. [PMID: 34216838 PMCID: PMC8316414 DOI: 10.1016/j.bone.2021.116096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/28/2021] [Accepted: 06/25/2021] [Indexed: 01/29/2023]
Abstract
BACKGROUND Prior data demonstrated three weeks of sleep restriction and concurrent circadian disruption uncoupled bone turnover markers (BTMs), indicating decreased bone formation and no change or increased bone resorption. The effect of insufficient sleep with or without ad libitum weekend recovery sleep on BTMs is unknown. METHODS BTMs were measured in stored serum from 20 healthy adults randomized to one of three study groups consisting of a control group (N = 3 men; 9 h/night) or one of two nocturnal sleep restriction groups in an inpatient laboratory environment. One Sleep Restriction group ("SR"; N = 9; 4 women) had 5 h sleep opportunity per night for nine nights. The other sleep restriction group had an opportunity for ad libitum Weekend Recovery sleep ("WR"; N = 8; 4 women) after four nights of 5 h sleep opportunity per night. Food intake was energy balanced at baseline and ad libitum thereafter. Fasted morning BTM levels and hourly 24 h melatonin levels were obtained on study days 3 (baseline), 5 (after 1 night of sleep restriction for WR and SR), and 11 (after a sleep restricted workweek with weekend recovery sleep in WR or 7 nights of sleep restriction in SR). Linear mixed-effects modeling was used to examine the effect of study duration (e.g., change over time), study condition, age, and sex on BTMs. Pearson correlations were used to determine associations between changes in BTMs and changes in weight and morning circadian misalignment (i.e., duration of high melatonin levels after wake time). RESULTS There was no significant difference between the three study groups in change over time (p ≥ 0.4 for interaction between assigned group and time for all BTMs), adjusted for age and sex. There was no significant change in N-terminal propeptide of procollagen type I (P1NP), osteocalcin, or C-telopeptide of type I collagen (CTX) from baseline to day 11 (all p ≥ 0.3). In women <25 years old, there was a non-significant decline in P1NP from day 3 to day 5 (= -15.74 ± 7.80 ng/mL; p = 0.06). Change in weight and morning circadian misalignment from baseline to day 11 were correlated with statistically non-significant changes in BTMs (all p ≤ 0.05). CONCLUSION In this small secondary analysis, we showed that nine nights of prescribed sleep restriction with or without weekend recovery sleep and ad libitum food intake did not alter BTMs. It is possible that age, sex, weight change and morning circadian misalignment modify the effects of sleep restriction on bone metabolism.
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Affiliation(s)
- Christopher M Depner
- Sleep and Chronobiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA; Department of Health and Kinesiology, University of Utah, Salt Lake City, UT, USA
| | - John D Rice
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Emma J Tussey
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Robert H Eckel
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bryan C Bergman
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Janine A Higgins
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Edward L Melanson
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Division of Geriatric Medicine, University of Colorado Anschutz Medical Campus, and Eastern Colorado VA Geriatric, Research, Education, and Clinical Center (GRECC), Aurora, CO, USA
| | - Wendy M Kohrt
- Division of Geriatric Medicine, University of Colorado Anschutz Medical Campus, and Eastern Colorado VA Geriatric, Research, Education, and Clinical Center (GRECC), Aurora, CO, USA
| | - Kenneth P Wright
- Sleep and Chronobiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA; Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Christine M Swanson
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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Abstract
Wearable technology has a history in sleep research dating back to the 1970s. Because modern wearable technology is relatively cheap and widely used by the general population, this represents an opportunity to leverage wearable devices to advance sleep medicine and research. However, there is a lack of published validation studies designed to quantify device performance against accepted gold standards, especially across different populations. Recommendations for conducting performance assessments and using wearable devices are now published with the goal of standardizing wearable device implementation and advancing the field.
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Bjørkum AA, Carrasco Duran A, Frode B, Sinha Roy D, Rosendahl K, Birkeland E, Stuhr L. Human blood serum proteome changes after 6 hours of sleep deprivation at night. SLEEP SCIENCE AND PRACTICE 2021. [DOI: 10.1186/s41606-021-00066-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Abstract
Background
The aim of this study was to discover significantly changed proteins in human blood serum after loss of 6 h sleep at night. Furthermore, to reveal affected biological process- and molecular function categories that might be clinically relevant, by exploring systems biological databases.
Methods
Eight females were recruited by volunteer request. Peripheral venous whole blood was sampled at 04:00 am, after 6 h of sleep and after 6 h of sleep deprivation. We used within-subjects design (all subjects were their own control). Blood serum from each subject was depleted before protein digestion by trypsin and iTRAQ labeling. Labled peptides were analyzed by mass spectrometry (LTQ OritrapVelos Elite) connected to a LC system (Dionex Ultimate NCR-3000RS).
Results
We identified 725 proteins in human blood serum. 34 proteins were significantly differentially expressed after 6 h of sleep deprivation at night. Out of 34 proteins, 14 proteins were up-regulated, and 20 proteins were down-regulated. We emphasized the functionality of the 16 proteins commonly differentiated in all 8 subjects and the relation to pathological conditions. In addition, we discussed Histone H4 (H4) and protein S100-A6/Calcyclin (S10A6) that were upregulated more than 1.5-fold. Finally, we discussed affected biological process- and molecular function categories.
Conclusions
Overall, our study suggest that acute sleep deprivation, at least in females, affects several known biological processes- and molecular function categories and associates to proteins that also are changed under pathological conditions like impaired coagulation, oxidative stress, immune suppression, neurodegenerative related disorder, and cancer. Data are available via ProteomeXchange with identifier PXD021004.
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He J, Ren Z, Xia W, Zhou C, Bi B, Yu W, Zuo L. Identification of key genes and crucial pathways for major depressive disorder using peripheral blood samples and chronic unpredictable mild stress rat models. PeerJ 2021; 9:e11694. [PMID: 34414022 PMCID: PMC8344689 DOI: 10.7717/peerj.11694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/08/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Accurate diagnosis of major depressive disorder (MDD) remains difficult, and one of the key challenges in diagnosing MDD is the lack of reliable diagnostic biomarkers. The objective of this study was to explore gene networks and identify potential biomarkers for MDD. METHODS In the present study, we performed a comprehensive analysis of the mRNA expression profiles using blood samples of four patients with MDD and four controls by RNA sequencing. Differentially expressed genes (DEGs) were screened, and functional and pathway enrichment analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. All DEGs were inputted to the STRING database to build a PPI network, and the top 10 hub genes were screened using the cytoHubba plugin of the Cytoscape software. The relative expression of 10 key genes was identified by quantitative real-time polymerase chain reaction (qRT-PCR) of blood samples from 50 MDD patients and 50 controls. Plasma levels of SQSTM1 and TNFα were measured using an enzyme-linked immunosorbent assay in blood samples of 44 MDD patients and 44 controls. A sucrose preference test was used to evaluate depression-like behavior in chronic unpredictable mild stress (CUMS) model rats. Immunofluorescence assay and western blotting were performed to study the expression of proteins in the brain samples of CUMS model rats. RESULTS We identified 247 DEGs that were closely associated with MDD. Gene ontology analyses suggested that the DEGs were mainly enriched in negative regulation of transcription by RNA polymerase II promoter, cytoplasm, and protein binding. Moreover, Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that the DEGs were significantly enriched in the MAPK signaling pathway. Ten hub genes were screened through the PPI network, and qRT-PCR assay revealed that one and six genes were downregulated and upregulated, respectively; however, SMARCA2, PPP3CB, and RAB5C were not detected. Pathway enrichment analysis for the 10 genes showed that the mTOR signaling pathway was also enriched. A strong positive correlation was observed between SQSTM1 and TNFα protein levels in patients with MDD. LC3 II and SQSTM1 protein levels were increased in the CUMS rat model; however, p-mTOR protein levels were decreased. The sucrose preference values decreased in the CUMS rat model. CONCLUSIONS We identified 247 DEGs and constructed an MDD-specific network; thereafter, 10 hub genes were selected for further analysis. Our results provide novel insights into the pathogenesis of MDD. Moreover, SQSTM1, which is related to autophagy and inflammatory reactions, may play a key role in MDD. SQSTM1 may be used as a promising therapeutic target in MDD; additionally, more molecular mechanisms have been suggested that should be focused on in future in vivo and in vitro studies.
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Affiliation(s)
- Jun He
- Department of Immunology, School of Basic Medical Science, Guizhou Medical University, Guiyang, China
- Department of Laboratory Medicine, The Second People’s Hospital of Guizhou Province, Guiyang, China
| | - Zhenkui Ren
- Department of Laboratory Medicine, The Second People’s Hospital of Guizhou Province, Guiyang, China
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, School of Basic Medical Science, Guizhou Medical University, Guiyang, China
| | - Wansong Xia
- Department of Laboratory Medicine, The Second People’s Hospital of Guizhou Province, Guiyang, China
| | - Cao Zhou
- Psychosomatic Department, The Second People’s Hospital of Guizhou Province, Guiyang, China
| | - Bin Bi
- Psychosomatic Department, The Second People’s Hospital of Guizhou Province, Guiyang, China
| | - Wenfeng Yu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, School of Basic Medical Science, Guizhou Medical University, Guiyang, China
| | - Li Zuo
- Department of Immunology, School of Basic Medical Science, Guizhou Medical University, Guiyang, China
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13
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Liu X, Pamula Y, Immanuel S, Kennedy D, Martin J, Baumert M. Utilisation of machine learning to predict surgical candidates for the treatment of childhood upper airway obstruction. Sleep Breath 2021; 26:649-661. [PMID: 34273052 DOI: 10.1007/s11325-021-02425-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/24/2021] [Accepted: 06/21/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the effect of adenotonsillectomy on OSAS symptoms based on a data-driven approach and thereby identify criteria that may help avoid unnecessary surgery in children with OSAS. METHODS In 323 children enrolled in the Childhood Adenotonsillectomy Trial, randomised to undergo either early adenotonsillectomy (eAT; N = 165) or a strategy of watchful waiting with supportive care (WWSC; N = 158), the apnea-hypopnea index, heart period pattern dynamics, and thoraco-abdominal asynchrony measurements from overnight polysomnography (PSG) were measured. Using machine learning, all children were classified into one of two different clusters based on those features. The cluster transitions between follow-up and baseline PSG were investigated for each to predict those children who recovered spontaneously, following surgery and those who did not benefit from surgery. RESULTS The two clusters showed significant differences in OSAS symptoms, where children assigned in cluster A had fewer physiological and neurophysiological symptoms than cluster B. Whilst the majority of children were assigned to cluster A, those children who underwent surgery were more likely to stay in cluster A after seven months. Those children who were in cluster B at baseline PSG were more likely to have their symptoms reversed via surgery. Children who were assigned to cluster B at both baseline and 7 months after surgery had significantly higher end-tidal carbon dioxide at baseline. Children who spontaneously changed from cluster B to A presented highly problematic ratings in behaviour and emotional regulation at baseline. CONCLUSIONS Data-driven analysis demonstrated that AT helps to reverse and to prevent the worsening of the pathophysiological symptoms in children with OSAS. Multiple pathophysiological markers used with machine learning can capture more comprehensive information on childhood OSAS. Children with mild physiological and neurophysiological symptoms could avoid AT, and children who have UAO symptoms post AT may have sleep-related hypoventilation disease which requires further investigation. Furthermore, the findings may help surgeons more accurately predict children on whom they should perform AT.
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Affiliation(s)
- Xiao Liu
- School of Electrical and Electronic Engineering, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Yvonne Pamula
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, Adelaide, Australia
| | - Sarah Immanuel
- Centre for Artificial Intelligence Research and Optimisation, Torrens University, Adelaide, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Declan Kennedy
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, Adelaide, Australia.,Children's Research Centre, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, Australia
| | - James Martin
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, Adelaide, Australia
| | - Mathias Baumert
- School of Electrical and Electronic Engineering, The University of Adelaide, Adelaide, SA, 5005, Australia.
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14
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Xu W, Liu X, Leng F, Li W. Blood-based multi-tissue gene expression inference with Bayesian ridge regression. Bioinformatics 2020; 36:3788-3794. [PMID: 32277818 DOI: 10.1093/bioinformatics/btaa239] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 03/15/2020] [Accepted: 04/06/2020] [Indexed: 12/23/2022] Open
Abstract
MOTIVATION Gene expression profiling is widely used in basic and cancer research but still not feasible in many clinical applications because tissues, such as brain samples, are difficult and not ethnical to collect. Gene expression in uncollected tissues can be computationally inferred using genotype and expression quantitative trait loci. No methods can infer unmeasured gene expression of multiple tissues with single tissue gene expression profile as input. RESULTS Here, we present a Bayesian ridge regression-based method (B-GEX) to infer gene expression profiles of multiple tissues from blood gene expression profile. For each gene in a tissue, a low-dimensional feature vector was extracted from whole blood gene expression profile by feature selection. We used GTEx RNAseq data of 16 tissues to train inference models to capture the cross-tissue expression correlations between each target gene in a tissue and its preselected feature genes in peripheral blood. We compared B-GEX with least square regression, LASSO regression and ridge regression. B-GEX outperforms the other three models in most tissues in terms of mean absolute error, Pearson correlation coefficient and root-mean-squared error. Moreover, B-GEX infers expression level of tissue-specific genes as well as those of non-tissue-specific genes in all tissues. Unlike previous methods, which require genomic features or gene expression profiles of multiple tissues, our model only requires whole blood expression profile as input. B-GEX helps gain insights into gene expressions of uncollected tissues from more accessible data of blood. AVAILABILITY AND IMPLEMENTATION B-GEX is available at https://github.com/xuwenjian85/B-GEX. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wenjian Xu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Xuanshi Liu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Fei Leng
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
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15
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Kothari V, Cardona Z, Chirakalwasan N, Anothaisintawee T, Reutrakul S. Sleep interventions and glucose metabolism: systematic review and meta-analysis. Sleep Med 2020; 78:24-35. [PMID: 33383394 DOI: 10.1016/j.sleep.2020.11.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Sleep disturbances (insufficient or poor sleep quality) have been linked to abnormal glucose metabolism. This systematic review and meta-analysis aimed to explore the effects of behavioral and pharmacological sleep interventions on glucose metabolism. METHODS Medline and Embase were used for systematic search. Studies reporting behavioral or pharmacological interventions in population with sleep disturbances, with measured outcomes of glucose metabolism and sleep parameters were selected. RESULTS Twenty two studies were eligible for review (eight were conducted in people with type 2 diabetes). Studies were grouped into three types of intervention: sleep extension (n = 6), sleep education or cognitive behavioral therapy for insomnia (CBT-I, n = 6) and pharmacological interventions (n = 10). CBT-I and sleep education resulted in significantly improved self-reported sleep quality (Pittsburgh Sleep Quality Index, mean difference, MD, -1.31, 95% confidence interval (CI) -1.83, -0.80), non-significant reduction in hemoglobin A1c level (MD -0.35%, 95% CI -0.84, 0.13), and non-significant reduction in fasting glucose levels (MD -4.76 mg/dL, 95% CI -14.19, 4.67). Other studies were not eligible for meta-analysis due to heterogeneity of interventions or outcomes. Sleep extension was able to increase sleep duration by varying degrees in short sleepers, and five of six studies demonstrated relationships between the intervention and measures of insulin resistance. A majority of pharmacological intervention studies showed improved sleep but the effects on glucose metabolism were mixed. CONCLUSIONS Available sleep interventions were effective in improving sleep but the effects on glucose metabolism were inconclusive. Larger randomized studies with consistent outcome measurements are needed to demonstrate this potential causal relationship.
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Affiliation(s)
- Vallari Kothari
- Division of Endocrinology, Diabetes and Metabolism, University of Illinois at Chicago, Chicago, IL, USA
| | - Zulma Cardona
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Naricha Chirakalwasan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Sleep Disorders, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Thunyarat Anothaisintawee
- Department of Family Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand; Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sirimon Reutrakul
- Division of Endocrinology, Diabetes and Metabolism, University of Illinois at Chicago, Chicago, IL, USA.
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16
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Stocker LJ, Cagampang FR, Lu S, Ladyman T, Cheong YC. Is sleep deficit associated with infertility and recurrent pregnancy losses? Results from a prospective cohort study. Acta Obstet Gynecol Scand 2020; 100:302-313. [PMID: 32981061 DOI: 10.1111/aogs.14008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Biological rhythms, the innate cycle of changes in the body's physiological functions, are circadian if they have a 24-hour period. It is known that sleep is a key feature of human circadian rhythm but the relation between sleep and female fertility is largely unknown. This paucity of research is surprising given that circadian rhythms are paramount to human physiology and sleep is related to major female reproductive events. This study was designed to investigate whether there is a difference between the sleep and activity parameters of women with poor reproductive outcome compared with healthy, fertile parous women (comparator group) using subjective (questionnaires) and objective (actigraphy and light exposure) measures. MATERIAL AND METHODS A prospective cohort study in a tertiary in vitro fertilization referral center in the UK; composed of three study groups: women diagnosed with recurrent implantation failure, women with recurrent miscarriage (RM) and a comparison group (fertile women without endometrial pathology). Comparison women were selected gynecology patients without endometrial disease (ie perineal complaints or altruistic egg donors). Primary outcome was differences in objective length of sleep in each of the participant groups using actigraphy. Secondary outcomes were subjective sleep quality and quantity, using participant questionnaires, light exposure, and the feasibility of machine learning in activity-pattern interpretation. RESULTS Women with recurrent implantation failure slept daily on average for 7 hours 35 minutes (± 57 min), 53 minutes less than the comparison group (P = .03), although quality of their objective sleep, and quantity of their subjective sleep, were not significantly different. Women with recurrent miscarriage slept less that the comparison women (36 minutes less/night) but more than women with recurrent implantation failure (17 minutes more/night). No difference in light exposure was found between recurrent miscarriage and the recurrent implantation failure and comparison groups. CONCLUSIONS This study demonstrates an objective observation of sleep time reduction in women with subfertility, although it is not yet clear if this association is casual. Given our increased understanding of the internal body clock and circadian rhythm on fertility, our observation warrants further investigation.
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Affiliation(s)
- Linden Jane Stocker
- Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Felino Ramon Cagampang
- Institute of Developmental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Shilong Lu
- Department of Electronics and Computer and Sciences, University of Southampton, Southampton, UK
| | - Tom Ladyman
- Department of Electronics and Computer and Sciences, University of Southampton, Southampton, UK
| | - Ying Chin Cheong
- Complete Fertility Centre, Princess Anne Hospital, Southampton, UK
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17
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Abstract
The temporal organization of molecular and physiological processes is driven by environmental and behavioral cycles as well as by self-sustained molecular circadian oscillators. Quantification of phase, amplitude, period, and disruption of circadian oscillators is essential for understanding their contribution to sleep-wake disorders, social jet lag, interindividual differences in entrainment, and the development of chrono-therapeutics. Traditionally, assessment of the human circadian system, and the output of the SCN in particular, has required collection of long time series of univariate markers such as melatonin or core body temperature. Data were collected in specialized laboratory protocols designed to control for environmental and behavioral influences on rhythmicity. These protocols are time-consuming, expensive, and not practical for assessing circadian status in patients or in participants in epidemiologic studies. Novel approaches for assessment of circadian parameters of the SCN or peripheral oscillators have been developed. They are based on machine learning or mathematical model-informed analyses of features extracted from 1 or a few samples of high-dimensional data, such as transcriptomes, metabolomes, long-term simultaneous recording of activity, light exposure, skin temperature, and heart rate or in vitro approaches. Here, we review whether these approaches successfully quantify parameters of central and peripheral circadian oscillators as indexed by gold standard markers. Although several approaches perform well under entrained conditions when sleep occurs at night, the methods either perform worse in other conditions such as shift work or they have not been assessed under any conditions other than entrainment and thus we do not yet know how robust they are. Novel approaches for the assessment of circadian parameters hold promise for circadian medicine, chrono-therapeutics, and chrono-epidemiology. There remains a need to validate these approaches against gold standard markers, in individuals of all sexes and ages, in patient populations, and, in particular, under conditions in which behavioral cycles are displaced.
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Affiliation(s)
- Derk-Jan Dijk
- Surrey Sleep Research Centre, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.,UK Dementia Research Institute, University of Surrey
| | - Jeanne F Duffy
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, USA
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18
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Depner CM, Cogswell DT, Bisesi PJ, Markwald RR, Cruickshank-Quinn C, Quinn K, Melanson EL, Reisdorph N, Wright KP. Developing preliminary blood metabolomics-based biomarkers of insufficient sleep in humans. Sleep 2020; 43:zsz321. [PMID: 31894238 PMCID: PMC7355401 DOI: 10.1093/sleep/zsz321] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/27/2019] [Indexed: 01/20/2023] Open
Abstract
STUDY OBJECTIVE Identify small molecule biomarkers of insufficient sleep using untargeted plasma metabolomics in humans undergoing experimental insufficient sleep. METHODS We conducted a crossover laboratory study where 16 normal-weight participants (eight men; age 22 ± 5 years; body mass index < 25 kg/m2) completed three baseline days (9 hours sleep opportunity per night) followed by 5-day insufficient (5 hours sleep opportunity per night) and adequate (9 hours sleep opportunity per night) sleep conditions. Energy balanced diets were provided during baseline, with ad libitum energy intake provided during the insufficient and adequate sleep conditions. Untargeted plasma metabolomics analyses were performed using blood samples collected every 4 hours across the final 24 hours of each condition. Biomarker models were developed using logistic regression and linear support vector machine (SVM) algorithms. RESULTS The top-performing biomarker model was developed by linear SVM modeling, consisted of 65 compounds, and discriminated insufficient versus adequate sleep with 74% overall accuracy and a Matthew's Correlation Coefficient of 0.39. The compounds in the top-performing biomarker model were associated with ATP Binding Cassette Transporters in Lipid Homeostasis, Phospholipid Metabolic Process, Plasma Lipoprotein Remodeling, and sphingolipid metabolism. CONCLUSION We identified potential metabolomics-based biomarkers of insufficient sleep in humans. Although our current biomarkers require further development and validation using independent cohorts, they have potential to advance our understanding of the negative consequences of insufficient sleep, improve diagnosis of poor sleep health, and could eventually help identify targets for countermeasures designed to mitigate the negative health consequences of insufficient sleep.
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Affiliation(s)
- Christopher M Depner
- Sleep and Chronobiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - Dasha T Cogswell
- Sleep and Chronobiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - Paul J Bisesi
- Sleep and Chronobiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - Rachel R Markwald
- Sleep and Chronobiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | | | - Kevin Quinn
- Skaggs School of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Edward L Melanson
- Division of Endocrinology, Metabolism, and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
- Division of Geriatric Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
- Eastern Colorado Veterans Affairs Geriatric Research, Education, and Clinical Center, Denver, CO
| | - Nichole Reisdorph
- Skaggs School of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Kenneth P Wright
- Sleep and Chronobiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
- Division of Endocrinology, Metabolism, and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
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19
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Goecks J, Jalili V, Heiser LM, Gray JW. How Machine Learning Will Transform Biomedicine. Cell 2020; 181:92-101. [PMID: 32243801 PMCID: PMC7141410 DOI: 10.1016/j.cell.2020.03.022] [Citation(s) in RCA: 220] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/07/2020] [Accepted: 03/09/2020] [Indexed: 12/15/2022]
Abstract
This Perspective explores the application of machine learning toward improved diagnosis and treatment. We outline a vision for how machine learning can transform three broad areas of biomedicine: clinical diagnostics, precision treatments, and health monitoring, where the goal is to maintain health through a range of diseases and the normal aging process. For each area, early instances of successful machine learning applications are discussed, as well as opportunities and challenges for machine learning. When these challenges are met, machine learning promises a future of rigorous, outcomes-based medicine with detection, diagnosis, and treatment strategies that are continuously adapted to individual and environmental differences.
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Affiliation(s)
- Jeremy Goecks
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.
| | - Vahid Jalili
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Laura M Heiser
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
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20
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Hao S, You J, Chen L, Zhao H, Huang Y, Zheng L, Tian L, Maric I, Liu X, Li T, Bianco YK, Winn VD, Aghaeepour N, Gaudilliere B, Angst MS, Zhou X, Li YM, Mo L, Wong RJ, Shaw GM, Stevenson DK, Cohen HJ, Mcelhinney DB, Sylvester KG, Ling XB. Changes in pregnancy-related serum biomarkers early in gestation are associated with later development of preeclampsia. PLoS One 2020; 15:e0230000. [PMID: 32126118 PMCID: PMC7053753 DOI: 10.1371/journal.pone.0230000] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Background Placental protein expression plays a crucial role during pregnancy. We hypothesized that: (1) circulating levels of pregnancy-associated, placenta-related proteins throughout gestation reflect the temporal progression of the uncomplicated, full-term pregnancy, and can effectively estimate gestational ages (GAs); and (2) preeclampsia (PE) is associated with disruptions in these protein levels early in gestation; and can identify impending PE. We also compared gestational profiles of proteins in the human and mouse, using pregnant heme oxygenase-1 (HO-1) heterozygote (Het) mice, a mouse model reflecting PE-like symptoms. Methods Serum levels of placenta-related proteins–leptin (LEP), chorionic somatomammotropin hormone like 1 (CSHL1), elabela (ELA), activin A, soluble fms-like tyrosine kinase 1 (sFlt-1), and placental growth factor (PlGF)–were quantified by ELISA in blood serially collected throughout human pregnancies (20 normal subjects with 66 samples, and 20 subjects who developed PE with 61 samples). Multivariate analysis was performed to estimate the GA in normal pregnancy. Mean-squared errors of GA estimations were used to identify impending PE. The human protein profiles were then compared with those in the pregnant HO-1 Het mice. Results An elastic net-based gestational dating model was developed (R2 = 0.76) and validated (R2 = 0.61) using serum levels of the 6 proteins measured at various GAs from women with normal uncomplicated pregnancies. In women who developed PE, the model was not (R2 = -0.17) associated with GA. Deviations from the model estimations were observed in women who developed PE (P = 0.01). The model developed with 5 proteins (ELA excluded) performed similarly from sera from normal human (R2 = 0.68) and WT mouse (R2 = 0.85) pregnancies. Disruptions of this model were observed in both human PE-associated (R2 = 0.27) and mouse HO-1 Het (R2 = 0.30) pregnancies. LEP outperformed sFlt-1 and PlGF in differentiating impending PE at early human and late mouse GAs. Conclusions Serum placenta-related protein profiles are temporally regulated throughout normal pregnancies and significantly disrupted in women who develop PE. LEP changes earlier than the well-established biomarkers (sFlt-1 and PlGF). There may be evidence of a causative action of HO-1 deficiency in LEP upregulation in a PE-like murine model.
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Affiliation(s)
- Shiying Hao
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
- Clinical and Translational Research Program, Betty Irene Moore Children's Heart Center, Lucile Packard Children’s Hospital, Palo Alto, CA, United States of America
| | - Jin You
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Lin Chen
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Hui Zhao
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Yujuan Huang
- Department of Emergency, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Le Zheng
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
- Clinical and Translational Research Program, Betty Irene Moore Children's Heart Center, Lucile Packard Children’s Hospital, Palo Alto, CA, United States of America
| | - Lu Tian
- Department of Health Research and Policy, Stanford University, Stanford, CA, United States of America
| | - Ivana Maric
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Xin Liu
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Tian Li
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Ylayaly K. Bianco
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Virginia D. Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Xin Zhou
- Tianjin Key Laboratory of Cardiovascular Remodeling and Target Organ Injury, Pingjin Hospital Heart Center, Tianjin, China
| | - Yu-Ming Li
- Tianjin Key Laboratory of Cardiovascular Remodeling and Target Organ Injury, Pingjin Hospital Heart Center, Tianjin, China
| | - Lihong Mo
- Department of Obstetrics and Gynecology, University of California San Francisco-Fresno, Fresno, CA, United States of America
| | - Ronald J. Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - David K. Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Harvey J. Cohen
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Doff B. Mcelhinney
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
- Clinical and Translational Research Program, Betty Irene Moore Children's Heart Center, Lucile Packard Children’s Hospital, Palo Alto, CA, United States of America
| | - Karl G. Sylvester
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Xuefeng B. Ling
- Clinical and Translational Research Program, Betty Irene Moore Children's Heart Center, Lucile Packard Children’s Hospital, Palo Alto, CA, United States of America
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
- * E-mail:
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21
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Depner CM, Cheng PC, Devine JK, Khosla S, de Zambotti M, Robillard R, Vakulin A, Drummond SPA. Wearable technologies for developing sleep and circadian biomarkers: a summary of workshop discussions. Sleep 2020; 43:zsz254. [PMID: 31641776 PMCID: PMC7368340 DOI: 10.1093/sleep/zsz254] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/17/2019] [Indexed: 01/03/2023] Open
Abstract
The "International Biomarkers Workshop on Wearables in Sleep and Circadian Science" was held at the 2018 SLEEP Meeting of the Associated Professional Sleep Societies. The workshop brought together experts in consumer sleep technologies and medical devices, sleep and circadian physiology, clinical translational research, and clinical practice. The goals of the workshop were: (1) characterize the term "wearable" for use in sleep and circadian science and identify relevant sleep and circadian metrics for wearables to measure; (2) assess the current use of wearables in sleep and circadian science; (3) identify current barriers for applying wearables to sleep and circadian science; and (4) identify goals and opportunities for wearables to advance sleep and circadian science. For the purposes of biomarker development in the sleep and circadian fields, the workshop included the terms "wearables," "nearables," and "ingestibles." Given the state of the current science and technology, the limited validation of wearable devices against gold standard measurements is the primary factor limiting large-scale use of wearable technologies for sleep and circadian research. As such, the workshop committee proposed a set of best practices for validation studies and guidelines regarding how to choose a wearable device for research and clinical use. To complement validation studies, the workshop committee recommends the development of a public data repository for wearable data. Finally, sleep and circadian scientists must actively engage in the development and use of wearable devices to maintain the rigor of scientific findings and public health messages based on wearable technology.
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Affiliation(s)
- Christopher M Depner
- Sleep and Chronobiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - Philip C Cheng
- Sleep Disorders and Research Center, Division of Sleep Medicine, Henry Ford Health System, Detroit, MI
| | - Jaime K Devine
- Behavioral Biology Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | | | | | - Rébecca Robillard
- Sleep Research Unit, The Royal’s Institute for Mental Health Research, affiliated to the University of Ottawa, Ottawa, ON, Canada
| | - Andrew Vakulin
- Adelaide Institute for Sleep Health: Flinders Centre of Research Excellence, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
- NeuroSleep, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, University of Sydney, Glebe, NSW, Australia
| | - Sean P A Drummond
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, VIC, Australia
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22
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Vetter C. Circadian disruption: What do we actually mean? Eur J Neurosci 2020; 51:531-550. [PMID: 30402904 PMCID: PMC6504624 DOI: 10.1111/ejn.14255] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/14/2022]
Abstract
The circadian system regulates physiology and behavior. Acute challenges to the system, such as those experienced when traveling across time zones, will eventually result in re-synchronization to local environmental time cues, but this re-synchronization is oftentimes accompanied by adverse short-term consequences. When such challenges are experienced chronically, adaptation may not be achieved, as for example in the case of rotating night shift workers. The transient and chronic disturbance of the circadian system is most frequently referred to as "circadian disruption", but many other terms have been proposed and used to refer to similar situations. It is now beyond doubt that the circadian system contributes to health and disease, emphasizing the need for clear terminology when describing challenges to the circadian system and their consequences. The goal of this review is to provide an overview of the terms used to describe disruption of the circadian system, discuss proposed quantifications of disruption in experimental and observational settings with a focus on human research, and highlight limitations and challenges of currently available tools. For circadian research to advance as a translational science, clear, operationalizable, and scalable quantifications of circadian disruption are key, as they will enable improved assessment and reproducibility of results, ideally ranging from mechanistic settings, including animal research, to large-scale randomized clinical trials.
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Affiliation(s)
- Céline Vetter
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado
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Kirsch DB. Disruption in Health Care (and Sleep Medicine): "It's the End of the World as We Know it…and I Feel Fine.". J Clin Sleep Med 2019; 15:1185-1188. [PMID: 31538585 PMCID: PMC6760411 DOI: 10.5664/jcsm.7900] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 06/26/2019] [Accepted: 06/26/2019] [Indexed: 12/11/2022]
Abstract
CITATION Kirsch DB. Disruption in health care (and sleepmedicine): "it's the end of the world as we know it…and I feel fine.". J Clin Sleep Med. 2019;15(9):1185-1188.
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Besedovsky L, Lange T, Haack M. The Sleep-Immune Crosstalk in Health and Disease. Physiol Rev 2019; 99:1325-1380. [PMID: 30920354 PMCID: PMC6689741 DOI: 10.1152/physrev.00010.2018] [Citation(s) in RCA: 642] [Impact Index Per Article: 128.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 02/08/2023] Open
Abstract
Sleep and immunity are bidirectionally linked. Immune system activation alters sleep, and sleep in turn affects the innate and adaptive arm of our body's defense system. Stimulation of the immune system by microbial challenges triggers an inflammatory response, which, depending on its magnitude and time course, can induce an increase in sleep duration and intensity, but also a disruption of sleep. Enhancement of sleep during an infection is assumed to feedback to the immune system to promote host defense. Indeed, sleep affects various immune parameters, is associated with a reduced infection risk, and can improve infection outcome and vaccination responses. The induction of a hormonal constellation that supports immune functions is one likely mechanism underlying the immune-supporting effects of sleep. In the absence of an infectious challenge, sleep appears to promote inflammatory homeostasis through effects on several inflammatory mediators, such as cytokines. This notion is supported by findings that prolonged sleep deficiency (e.g., short sleep duration, sleep disturbance) can lead to chronic, systemic low-grade inflammation and is associated with various diseases that have an inflammatory component, like diabetes, atherosclerosis, and neurodegeneration. Here, we review available data on this regulatory sleep-immune crosstalk, point out methodological challenges, and suggest questions open for future research.
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Affiliation(s)
- Luciana Besedovsky
- Institute of Medical Psychology and Behavioral Neurobiology, University of Tübingen , Tübingen , Germany ; Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School , Boston, Massachusetts ; and Department of Rheumatology and Clinical Immunology, University of Lübeck , Lübeck , Germany
| | - Tanja Lange
- Institute of Medical Psychology and Behavioral Neurobiology, University of Tübingen , Tübingen , Germany ; Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School , Boston, Massachusetts ; and Department of Rheumatology and Clinical Immunology, University of Lübeck , Lübeck , Germany
| | - Monika Haack
- Institute of Medical Psychology and Behavioral Neurobiology, University of Tübingen , Tübingen , Germany ; Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School , Boston, Massachusetts ; and Department of Rheumatology and Clinical Immunology, University of Lübeck , Lübeck , Germany
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Grant LK, Ftouni S, Nijagal B, De Souza DP, Tull D, McConville MJ, Rajaratnam SMW, Lockley SW, Anderson C. Circadian and wake-dependent changes in human plasma polar metabolites during prolonged wakefulness: A preliminary analysis. Sci Rep 2019; 9:4428. [PMID: 30872634 PMCID: PMC6418225 DOI: 10.1038/s41598-019-40353-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 02/07/2019] [Indexed: 11/18/2022] Open
Abstract
Establishing circadian and wake-dependent changes in the human metabolome are critical for understanding and treating human diseases due to circadian misalignment or extended wake. Here, we assessed endogenous circadian rhythms and wake-dependent changes in plasma metabolites in 13 participants (4 females) studied during 40-hours of wakefulness. Four-hourly plasma samples were analyzed by hydrophilic interaction liquid chromatography (HILIC)-LC-MS for 1,740 metabolite signals. Group-averaged (relative to DLMO) and individual participant metabolite profiles were fitted with a combined cosinor and linear regression model. In group-level analyses, 22% of metabolites were rhythmic and 8% were linear, whereas in individual-level analyses, 14% of profiles were rhythmic and 4% were linear. We observed metabolites that were significant at the group-level but not significant in a single individual, and metabolites that were significant in approximately half of individuals but not group-significant. Of the group-rhythmic and group-linear metabolites, only 7% and 12% were also significantly rhythmic or linear, respectively, in ≥50% of participants. Owing to large inter-individual variation in rhythm timing and the magnitude and direction of linear change, acrophase and slope estimates also differed between group- and individual-level analyses. These preliminary findings have important implications for biomarker development and understanding of sleep and circadian regulation of metabolism.
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Affiliation(s)
- Leilah K Grant
- School of Psychological Sciences and Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Melbourne, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, USA
| | - Suzanne Ftouni
- School of Psychological Sciences and Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Melbourne, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia
| | - Brunda Nijagal
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia
| | - David P De Souza
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia
| | - Malcolm J McConville
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia
| | - Shantha M W Rajaratnam
- School of Psychological Sciences and Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Melbourne, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, USA
| | - Steven W Lockley
- School of Psychological Sciences and Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Melbourne, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, USA
| | - Clare Anderson
- School of Psychological Sciences and Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Melbourne, Australia.
- Cooperative Research Centre for Alertness, Safety and Productivity, Melbourne, Australia.
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, USA.
- Division of Sleep Medicine, Harvard Medical School, Boston, USA.
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26
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Abstract
Sleep and circadian rhythms are regulated across multiple functional, spatial and temporal levels: from genes to networks of coupled neurons and glial cells, to large scale brain dynamics and behaviour. The dynamics at each of these levels are complex and the interaction between the levels is even more so, so research have mostly focused on interactions within the levels to understand the underlying mechanisms—the so-called reductionist approach. Mathematical models were developed to test theories of sleep regulation and guide new experiments at each of these levels and have become an integral part of the field. The advantage of modelling, however, is that it allows us to simulate and test the dynamics of complex biological systems and thus provides a tool to investigate the connections between the different levels and study the system as a whole. In this paper I review key models of sleep developed at different physiological levels and discuss the potential for an integrated systems biology approach for sleep regulation across these levels. I also highlight the necessity of building mechanistic connections between models of sleep and circadian rhythms across these levels.
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Affiliation(s)
- Svetlana Postnova
- School of Physics, University of Sydney, Sydney 2006, NSW, Australia;
- Center of Excellence for Integrative Brain Function, University of Sydney, Sydney 2006, NSW, Australia
- Charles Perkins Center, University of Sydney, Sydney 2006, NSW, Australia
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REM sleep's unique associations with corticosterone regulation, apoptotic pathways, and behavior in chronic stress in mice. Proc Natl Acad Sci U S A 2019; 116:2733-2742. [PMID: 30683720 PMCID: PMC6377491 DOI: 10.1073/pnas.1816456116] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sleep disturbances are common in stress-related disorders but the nature of these sleep disturbances and how they relate to changes in the stress hormone corticosterone and changes in gene expression remained unknown. Here we demonstrate that in response to chronic mild stress, rapid–eye-movement sleep (REMS), a sleep state involved in emotion regulation and fear conditioning, changed first and more so than any other measured sleep characteristic. Transcriptomic profiles related to REMS continuity and theta oscillations overlapped with those for corticosterone, as well as with predictors for anhedonia, and were enriched for apoptotic pathways. These data highlight the central role of REMS in response to stress and warrant further investigation into REMS’s involvement in stress-related mental health disorders. One of sleep’s putative functions is mediation of adaptation to waking experiences. Chronic stress is a common waking experience; however, which specific aspect of sleep is most responsive, and how sleep changes relate to behavioral disturbances and molecular correlates remain unknown. We quantified sleep, physical, endocrine, and behavioral variables, as well as the brain and blood transcriptome in mice exposed to 9 weeks of unpredictable chronic mild stress (UCMS). Comparing 46 phenotypic variables revealed that rapid–eye-movement sleep (REMS), corticosterone regulation, and coat state were most responsive to UCMS. REMS theta oscillations were enhanced, whereas delta oscillations in non-REMS were unaffected. Transcripts affected by UCMS in the prefrontal cortex, hippocampus, hypothalamus, and blood were associated with inflammatory and immune responses. A machine-learning approach controlling for unspecific UCMS effects identified transcriptomic predictor sets for REMS parameters that were enriched in 193 pathways, including some involved in stem cells, immune response, and apoptosis and survival. Only three pathways were enriched in predictor sets for non-REMS. Transcriptomic predictor sets for variation in REMS continuity and theta activity shared many pathways with corticosterone regulation, in particular pathways implicated in apoptosis and survival, including mitochondrial apoptotic machinery. Predictor sets for REMS and anhedonia shared pathways involved in oxidative stress, cell proliferation, and apoptosis. These data identify REMS as a core and early element of the response to chronic stress, and identify apoptosis and survival pathways as a putative mechanism by which REMS may mediate the response to stressful waking experiences.
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Mullington JM. Please forgive our appearance while under biomarker construction. Sleep 2019; 42:5290258. [PMID: 30657993 DOI: 10.1093/sleep/zsy267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Janet M Mullington
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA
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