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Vázquez-Lizarraga R, Mendoza-Viveros L, Cid-Castro C, Ruiz-Montoya S, Carreño-Vázquez E, Orozco-Solis R. Hypothalamic circuits and aging: keeping the circadian clock updated. Neural Regen Res 2024; 19:1919-1928. [PMID: 38227516 DOI: 10.4103/1673-5374.389624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/20/2023] [Indexed: 01/17/2024] Open
Abstract
Over the past century, age-related diseases, such as cancer, type-2 diabetes, obesity, and mental illness, have shown a significant increase, negatively impacting overall quality of life. Studies on aged animal models have unveiled a progressive discoordination at multiple regulatory levels, including transcriptional, translational, and post-translational processes, resulting from cellular stress and circadian derangements. The circadian clock emerges as a key regulator, sustaining physiological homeostasis and promoting healthy aging through timely molecular coordination of pivotal cellular processes, such as stem-cell function, cellular stress responses, and inter-tissue communication, which become disrupted during aging. Given the crucial role of hypothalamic circuits in regulating organismal physiology, metabolic control, sleep homeostasis, and circadian rhythms, and their dependence on these processes, strategies aimed at enhancing hypothalamic and circadian function, including pharmacological and non-pharmacological approaches, offer systemic benefits for healthy aging. Intranasal brain-directed drug administration represents a promising avenue for effectively targeting specific brain regions, like the hypothalamus, while reducing side effects associated with systemic drug delivery, thereby presenting new therapeutic possibilities for diverse age-related conditions.
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Affiliation(s)
| | - Lucia Mendoza-Viveros
- Instituto Nacional de Medicina Genómica (INMEGEN), México City, México
- Centro de Investigacíon sobre el Envejecimiento, Centro de Investigacíon y de Estudios Avanzados (CIE-CINVESTAV), México City, México
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México UNAM, México City, México
| | - Carolina Cid-Castro
- Instituto Nacional de Medicina Genómica (INMEGEN), México City, México
- Centro de Investigacíon sobre el Envejecimiento, Centro de Investigacíon y de Estudios Avanzados (CIE-CINVESTAV), México City, México
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México UNAM, México City, México
| | | | | | - Ricardo Orozco-Solis
- Instituto Nacional de Medicina Genómica (INMEGEN), México City, México
- Centro de Investigacíon sobre el Envejecimiento, Centro de Investigacíon y de Estudios Avanzados (CIE-CINVESTAV), México City, México
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2
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Salminen A. Aryl hydrocarbon receptor impairs circadian regulation in Alzheimer's disease: Potential impact on glymphatic system dysfunction. Eur J Neurosci 2024. [PMID: 38924210 DOI: 10.1111/ejn.16450] [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: 01/17/2024] [Revised: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
Circadian clocks maintain diurnal rhythms of sleep-wake cycle of 24 h that regulate not only the metabolism of an organism but also many other periodical processes. There is substantial evidence that circadian regulation is impaired in Alzheimer's disease. Circadian clocks regulate many properties known to be disturbed in Alzheimer's patients, such as the integrity of the blood-brain barrier (BBB) as well as the diurnal glymphatic flow that controls waste clearance from the brain. Interestingly, an evolutionarily conserved transcription factor, that is, aryl hydrocarbon receptor (AhR), impairs the function of the core clock proteins and thus could disturb diurnal rhythmicity in the BBB. There is abundant evidence that the activation of AhR signalling inhibits the expression of the major core clock proteins, such as the brain and muscle arnt-like 1 (BMAL1), clock circadian regulator (CLOCK) and period circadian regulator 1 (PER1) in different experimental models. The expression of AhR is robustly increased in the brains of Alzheimer's patients, and protein level is enriched in astrocytes of the BBB. It seems that AhR signalling inhibits glymphatic flow since it is known that (i) activation of AhR impairs the function of the BBB, which is cooperatively interconnected with the glymphatic system in the brain, and (ii) neuroinflammation and dysbiosis of gut microbiota generate potent activators of AhR, which are able to impair glymphatic flow. I will examine current evidence indicating that activation of AhR signalling could disturb circadian functions of the BBB and impair glymphatic flow and thus be involved in the development of Alzheimer's pathology.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
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3
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Sheehan PW, Fass S, Sapkota D, Kang S, Hollis HC, Lawrence JH, Anafi RC, Dougherty JD, Fryer JD, Musiek ES. A glial circadian gene expression atlas reveals cell type and disease-specific reprogramming in response to amyloid pathology or aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596297. [PMID: 38853870 PMCID: PMC11160685 DOI: 10.1101/2024.05.28.596297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
While circadian rhythm disruption may promote neurodegenerative disease, how aging and neurodegenerative pathology impact circadian gene expression patterns in different brain cell types is unknown. Here, we used translating ribosome affinity purification methods to define the circadian translatomes of astrocytes, microglia, and bulk cerebral cortex, in healthy mouse brain and in the settings of amyloid-beta plaque pathology or aging. Our data reveal that glial circadian translatomes are highly cell type-specific and exhibit profound, context-dependent reprogramming of rhythmic transcripts in response to amyloid pathology or aging. Transcripts involved in glial activation, immunometabolism, and proteostasis, as well as nearly half of all Alzheimer Disease (AD)-associated risk genes, displayed circadian oscillations, many of which were altered by pathology. Amyloid-related differential gene expression was also dependent on time of day. Thus, circadian rhythms in gene expression are cell- and context dependent and provide important insights into glial gene regulation in health, AD, and aging.
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Affiliation(s)
- Patrick W. Sheehan
- Department of Neurology, Washington University School of Medicine, Saint Louis MO, USA
| | - Stuart Fass
- Department of Genetics, Washington University School of Medicine, Saint Louis MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis MO, USA
| | - Darshan Sapkota
- Department of Genetics, Washington University School of Medicine, Saint Louis MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis MO, USA
- Department of Biological Sciences and Department of Neuroscience, University of Texas at Dallas, Richardson, TX, USA
| | - Sylvia Kang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Henry C. Hollis
- School of Biomedical Engineering and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jennifer H. Lawrence
- Department of Neurology, Washington University School of Medicine, Saint Louis MO, USA
| | - Ron C. Anafi
- Department of Medicine, Chronobiology, and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph D. Dougherty
- Department of Genetics, Washington University School of Medicine, Saint Louis MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis MO, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Jon D. Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ, USA
| | - Erik S. Musiek
- Department of Neurology, Washington University School of Medicine, Saint Louis MO, USA
- Center on Biological Rhythms and Sleep, Washington University School of Medicine, St. Louis, MO, USA
- Lead contact
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4
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Buijink MR, van Weeghel M, Harms A, Murli DS, Meijer JH, Hankemeier T, Michel S, Kervezee L. Loss of temporal coherence in the circadian metabolome across multiple tissues during ageing in mice. Eur J Neurosci 2024. [PMID: 38802069 DOI: 10.1111/ejn.16428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Circadian clock function declines with ageing, which can aggravate ageing-related diseases such as type 2 diabetes and neurodegenerative disorders. Understanding age-related changes in the circadian system at a systemic level can contribute to the development of strategies to promote healthy ageing. The goal of this study was to investigate the impact of ageing on 24-h rhythms in amine metabolites across four tissues in young (2 months of age) and old (22-25 months of age) mice using a targeted metabolomics approach. Liver, plasma, the suprachiasmatic nucleus (SCN; the location of the central circadian clock in the hypothalamus) and the paraventricular nucleus (PVN; a downstream target of the SCN) were collected from young and old mice every 4 h during a 24-h period (n = 6-7 mice per group). Differential rhythmicity analysis revealed that ageing impacts 24-h rhythms in the amine metabolome in a tissue-specific manner. Most profound changes were observed in the liver, in which rhythmicity was lost in 60% of the metabolites in aged mice. Furthermore, we found strong correlations in metabolite levels between the liver and plasma and between the SCN and the PVN in young mice. These correlations were almost completely abolished in old mice. These results indicate that ageing is accompanied by a severe loss of the circadian coordination between tissues and by disturbed rhythmicity of metabolic processes. The tissue-specific impact of ageing may help to differentiate mechanisms of ageing-related disorders in the brain versus peripheral tissues and thereby contribute to the development of potential therapies for these disorders.
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Affiliation(s)
- M Renate Buijink
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel van Weeghel
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Amy Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Devika S Murli
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Johanna H Meijer
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Stephan Michel
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Laura Kervezee
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
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5
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Du K, Shi Q, Zhou X, Zhang L, Su H, Zhang C, Wei Z, Liu T, Wang L, Wang X, Cong B, Yun K. Melatonin attenuates fentanyl - induced behavioral sensitization and circadian rhythm disorders in mice. Physiol Behav 2024; 279:114523. [PMID: 38492912 DOI: 10.1016/j.physbeh.2024.114523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/01/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
Melatonin is a neurohormone synthesized by the pineal gland to regulate the circadian rhythms and has proven to be effective in treating drug addiction and dependence. However, the effects of melatonin to modulate the drug-seeking behavior of fentanyl and its underlying molecular mechanism is elusive. This study was designed to investigate the effects of melatonin on fentanyl - induced behavioral sensitization and circadian rhythm disorders in mice. The accompanying changes in the expression of Brain and Muscle Arnt-Like (BMAL1), tyrosine hydroxylase (TH), and monoamine oxidase A (MAO-A) in relevant brain regions including the suprachiasmatic nucleus (SCN), nucleus accumbens (NAc), prefrontal cortex (PFC), and hippocampus (Hip) were investigated by western blot assays to dissect the mechanism by which melatonin modulates fentanyl - induced behavioral sensitization and circadian rhythm disorders. The present study suggest that fentanyl (0.05, 0.1 and 0.2 mg/kg) could induce behavioral sensitization and melatonin (30.0 mg/kg) could attenuate the behavioral sensitization and circadian rhythm disorders in mice. Fentanyl treatment reduced the expression of BMAL1 and MAO-A and increased that of TH in relevant brain regions. Furthermore, melatonin treatment could reverse the expression levels of BMAL1, MAO-A, and TH. In conclusion, our study demonstrate for the first time that melatonin has therapeutic potential for fentanyl addiction.
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Affiliation(s)
- Kaili Du
- Department of Pathology, Shanxi Medical University, Taiyuan, 030001, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; School of Basic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Qianwen Shi
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Shanxi, 030600, China
| | - Xiuya Zhou
- Department of Pathology, Shanxi Medical University, Taiyuan, 030001, China; School of Basic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Lifei Zhang
- Department of Pathology, Shanxi Medical University, Taiyuan, 030001, China; School of Basic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Hongliang Su
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Shanxi, 030600, China
| | - Chao Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Shanxi, 030600, China
| | - Zhiwen Wei
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Shanxi, 030600, China
| | - Ting Liu
- Department of Pathology, Shanxi Medical University, Taiyuan, 030001, China; School of Basic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Li Wang
- Department of Pathology, Shanxi Medical University, Taiyuan, 030001, China; School of Basic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Xiaohui Wang
- Department of Pathology, Shanxi Medical University, Taiyuan, 030001, China; School of Basic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Bin Cong
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Shanxi, 030600, China; School of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Shanxi, 030600, China.
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6
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Jenkins AK, Ketchesin KD, Becker-Krail DD, McClung CA. Molecular Rhythmicity in Glia: Importance for Brain Health and Relevance to Psychiatric Disease. Biol Psychiatry 2024:S0006-3223(24)01298-8. [PMID: 38735357 DOI: 10.1016/j.biopsych.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/05/2024] [Accepted: 05/03/2024] [Indexed: 05/14/2024]
Abstract
Circadian rhythms are approximate 24-hour rhythms present in nearly all aspects of human physiology, including proper brain function. These rhythms are produced at the cellular level through a transcriptional-translational feedback loop known as the molecular clock. Diurnal variation in gene expression has been demonstrated in brain tissue from multiple species, including humans, in both cortical and subcortical regions. Interestingly, these rhythms in gene expression have been shown to be disrupted across psychiatric disorders and may be implicated in their underlying pathophysiology. However, little is known regarding molecular rhythms in specific cell types in the brain and how they might be involved in psychiatric disease. Although glial cells (e.g., astrocytes, microglia, and oligodendrocytes) have been historically understudied compared to neurons, evidence of the molecular clock is found within each of these cell subtypes. Here, we review the current literature, which suggests that molecular rhythmicity is essential to functional physiologic outputs from each glial subtype. Furthermore, disrupted molecular rhythms within these cells and the resultant functional deficits may be relevant to specific phenotypes across psychiatric illnesses. Given that circadian rhythm disruptions have been so integrally tied to psychiatric disease, the molecular mechanisms governing these associations could represent exciting new avenues for future research and potential novel pharmacologic targets for treatment.
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Affiliation(s)
- Aaron K Jenkins
- Translational Neuroscience Program, Department of Psychiatry, and Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kyle D Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, and Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Darius D Becker-Krail
- Translational Neuroscience Program, Department of Psychiatry, and Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Colleen A McClung
- Translational Neuroscience Program, Department of Psychiatry, and Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania.
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7
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Trujillo-Rangel WÁ, Acuña-Vaca S, Padilla-Ponce DJ, García-Mercado FG, Torres-Mendoza BM, Pacheco-Moises FP, Escoto-Delgadillo M, García-Benavides L, Delgado-Lara DLC. Modulation of the Circadian Rhythm and Oxidative Stress as Molecular Targets to Improve Vascular Dementia: A Pharmacological Perspective. Int J Mol Sci 2024; 25:4401. [PMID: 38673986 PMCID: PMC11050388 DOI: 10.3390/ijms25084401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The circadian rhythms generated by the master biological clock located in the brain's hypothalamus influence central physiological processes. At the molecular level, a core set of clock genes interact to form transcription-translation feedback loops that provide the molecular basis of the circadian rhythm. In animal models of disease, a desynchronization of clock genes in peripheral tissues with the central master clock has been detected. Interestingly, patients with vascular dementia have sleep disorders and irregular sleep patterns. These alterations in circadian rhythms impact hormonal levels, cardiovascular health (including blood pressure regulation and blood vessel function), and the pattern of expression and activity of antioxidant enzymes. Additionally, oxidative stress in vascular dementia can arise from ischemia-reperfusion injury, amyloid-beta production, the abnormal phosphorylation of tau protein, and alterations in neurotransmitters, among others. Several signaling pathways are involved in the pathogenesis of vascular dementia. While the precise mechanisms linking circadian rhythms and vascular dementia are still being studied, there is evidence to suggest that maintaining healthy sleep patterns and supporting proper circadian rhythm function may be important for reducing the risk of vascular dementia. Here, we reviewed the main mechanisms of action of molecular targets related to the circadian cycle and oxidative stress in vascular dementia.
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Affiliation(s)
- Walter Ángel Trujillo-Rangel
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Av. Nuevo Periférico No. 555, Ejido San José Tateposco, Tonalá 45425, Jalisco, Mexico; (W.Á.T.-R.); (D.J.P.-P.); (F.G.G.-M.); (L.G.-B.)
- Departamento de Formación Universitaria Ciencias de la Salud, Universidad Autónoma de Guadalajara, Av. Patria 1201, Lomas del Valle, Zapopan 45129, Jalisco, Mexico;
| | - Sofía Acuña-Vaca
- Departamento de Formación Universitaria Ciencias de la Salud, Universidad Autónoma de Guadalajara, Av. Patria 1201, Lomas del Valle, Zapopan 45129, Jalisco, Mexico;
| | - Danna Jocelyn Padilla-Ponce
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Av. Nuevo Periférico No. 555, Ejido San José Tateposco, Tonalá 45425, Jalisco, Mexico; (W.Á.T.-R.); (D.J.P.-P.); (F.G.G.-M.); (L.G.-B.)
| | - Florencia Guillermina García-Mercado
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Av. Nuevo Periférico No. 555, Ejido San José Tateposco, Tonalá 45425, Jalisco, Mexico; (W.Á.T.-R.); (D.J.P.-P.); (F.G.G.-M.); (L.G.-B.)
| | - Blanca Miriam Torres-Mendoza
- División de Neurociencias, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Sierra Mojada 800, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico; (B.M.T.-M.); (M.E.-D.)
- Departamento de Disciplinas Filosófico, Metodológicas e Instrumentales, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico
| | - Fermín P. Pacheco-Moises
- Departamento de Química, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd. Marcelino García Barragán No. 1421, Guadalajara 44430, Jalisco, Mexico;
| | - Martha Escoto-Delgadillo
- División de Neurociencias, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Sierra Mojada 800, Colonia Independencia, Guadalajara 44340, Jalisco, Mexico; (B.M.T.-M.); (M.E.-D.)
- Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez No. 2100, Zapopan 45200, Jalisco, Mexico
| | - Leonel García-Benavides
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Av. Nuevo Periférico No. 555, Ejido San José Tateposco, Tonalá 45425, Jalisco, Mexico; (W.Á.T.-R.); (D.J.P.-P.); (F.G.G.-M.); (L.G.-B.)
| | - Daniela L. C. Delgado-Lara
- Departamento de Formación Universitaria Ciencias de la Salud, Universidad Autónoma de Guadalajara, Av. Patria 1201, Lomas del Valle, Zapopan 45129, Jalisco, Mexico;
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8
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Zhu P, Peek CB. Circadian timing of satellite cell function and muscle regeneration. Curr Top Dev Biol 2024; 158:307-339. [PMID: 38670711 DOI: 10.1016/bs.ctdb.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Recent research has highlighted an important role for the molecular circadian machinery in the regulation of tissue-specific function and stress responses. Indeed, disruption of circadian function, which is pervasive in modern society, is linked to accelerated aging, obesity, and type 2 diabetes. Furthermore, evidence supporting the importance of the circadian clock within both the mature muscle tissue and satellite cells to regulate the maintenance of muscle mass and repair capacity in response injury has recently emerged. Here, we review the discovery of circadian clocks within the satellite cell (a.k.a. adult muscle stem cell) and how they act to regulate metabolism, epigenetics, and myogenesis during both healthy and diseased states.
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Affiliation(s)
- Pei Zhu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States; Department of Medicine-Endocrinology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States.
| | - Clara B Peek
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States; Department of Medicine-Endocrinology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States.
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9
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Petersen KA, Zong W, Depoy LM, Scott MR, Shankar VG, Burns JN, Cerwensky AJ, Kim SM, Ketchesin KD, Tseng GC, McClung CA. Comparative rhythmic transcriptome profiling of human and mouse striatal subregions. Neuropsychopharmacology 2024; 49:796-805. [PMID: 38182777 PMCID: PMC10948754 DOI: 10.1038/s41386-023-01788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024]
Abstract
The human striatum can be subdivided into the caudate, putamen, and nucleus accumbens (NAc). In mice, this roughly corresponds to the dorsal medial striatum (DMS), dorsal lateral striatum (DLS), and ventral striatum (NAc). Each of these structures have some overlapping and distinct functions related to motor control, cognitive processing, motivation, and reward. Previously, we used a "time-of-death" approach to identify diurnal rhythms in RNA transcripts in these three human striatal subregions. Here, we identify molecular rhythms across similar striatal subregions collected from C57BL/6J mice across 6 times of day and compare results to the human striatum. Pathway analysis indicates a large degree of overlap between species in rhythmic transcripts involved in processes like cellular stress, energy metabolism, and translation. Notably, a striking finding in humans is that small nucleolar RNAs (snoRNAs) and long non-coding RNAs (lncRNAs) are among the most highly rhythmic transcripts in the NAc and this is not conserved in mice, suggesting the rhythmicity of RNA processing in this region could be uniquely human. Furthermore, the peak timing of overlapping rhythmic genes is altered between species, but not consistently in one direction. Taken together, these studies reveal conserved as well as distinct transcriptome rhythms across the human and mouse striatum and are an important step in understanding the normal function of diurnal rhythms in humans and model organisms in these regions and how disruption could lead to pathology.
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Affiliation(s)
- Kaitlyn A Petersen
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Zong
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lauren M Depoy
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Madeline R Scott
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vaishnavi G Shankar
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jennifer N Burns
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Allison J Cerwensky
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sam-Moon Kim
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kyle D Ketchesin
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Colleen A McClung
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA.
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10
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Abstract
The brain is a complex organ, fundamentally changing across the day to perform basic functions like sleep, thought, and regulating whole-body physiology. This requires a complex symphony of nutrients, hormones, ions, neurotransmitters and more to be properly distributed across the brain to maintain homeostasis throughout 24 hours. These solutes are distributed both by the blood and by cerebrospinal fluid. Cerebrospinal fluid contents are distinct from the general circulation because of regulation at brain barriers including the choroid plexus, glymphatic system, and blood-brain barrier. In this review, we discuss the overlapping circadian (≈24-hour) rhythms in brain fluid biology and at the brain barriers. Our goal is for the reader to gain both a fundamental understanding of brain barriers alongside an understanding of the interactions between these fluids and the circadian timing system. Ultimately, this review will provide new insight into how alterations in these finely tuned clocks may lead to pathology.
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Affiliation(s)
- Velia S Vizcarra
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Ryann M Fame
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lauren M Hablitz
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
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11
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Naveed M, Chao OY, Hill JW, Yang YM, Huston JP, Cao R. Circadian neurogenetics and its implications in neurophysiology, behavior, and chronomedicine. Neurosci Biobehav Rev 2024; 157:105523. [PMID: 38142983 PMCID: PMC10872425 DOI: 10.1016/j.neubiorev.2023.105523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
The circadian rhythm affects multiple physiological processes, and disruption of the circadian system can be involved in a range of disease-related pathways. The genetic underpinnings of the circadian rhythm have been well-studied in model organisms. Significant progress has been made in understanding how clock genes affect the physiological functions of the nervous system. In addition, circadian timing is becoming a key factor in improving drug efficacy and reducing drug toxicity. The circadian biology of the target cell determines how the organ responds to the drug at a specific time of day, thus regulating pharmacodynamics. The current review brings together recent advances that have begun to unravel the molecular mechanisms of how the circadian clock affects neurophysiological and behavioral processes associated with human brain diseases. We start with a brief description of how the ubiquitous circadian rhythms are regulated at the genetic, cellular, and neural circuit levels, based on knowledge derived from extensive research on model organisms. We then summarize the latest findings from genetic studies of human brain disorders, focusing on the role of human clock gene variants in these diseases. Lastly, we discuss the impact of common dietary factors and medications on human circadian rhythms and advocate for a broader application of the concept of chronomedicine.
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Affiliation(s)
- Muhammad Naveed
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Department of Physiology and Pharmacology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Owen Y Chao
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Jennifer W Hill
- Department of Physiology and Pharmacology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Yi-Mei Yang
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Joseph P Huston
- Center for Behavioral Neuroscience, Institute of Experimental Psychology, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Ruifeng Cao
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA; Department of Neurology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA.
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12
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Ventresca C, Mohamed W, Russel WA, Ay A, Ingram KK. Machine learning analyses reveal circadian clock features predictive of anxiety among UK biobank participants. Sci Rep 2023; 13:22304. [PMID: 38102312 PMCID: PMC10724169 DOI: 10.1038/s41598-023-49644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Mood disorders, including depression and anxiety, affect almost one-fifth of the world's adult population and are becoming increasingly prevalent. Mutations in circadian clock genes have previously been associated with mood disorders both directly and indirectly through alterations in circadian phase, suggesting that the circadian clock influences multiple molecular pathways involved in mood. By targeting previously identified single nucleotide polymorphisms (SNPs) that have been implicated in anxiety and depressive disorders, we use a combination of statistical and machine learning techniques to investigate associations with the generalized anxiety disorder assessment (GAD-7) scores in a UK Biobank sample of 90,882 individuals. As in previous studies, we observed that females exhibited higher GAD-7 scores than males regardless of genotype. Interestingly, we found no significant effects on anxiety from individual circadian gene variants; only circadian genotypes with multiple SNP variants showed significant associations with anxiety. For both sexes, severe anxiety is associated with a 120-fold increase in odds for individuals with CRY2_AG(rs1083852)/ZBTB20_TT(rs1394593) genotypes and is associated with a near 40-fold reduction in odds for individuals with PER3-A_CG(rs228697)/ZBTB20_TT(rs1394593) genotypes. We also report several sex-specific associations with anxiety. In females, the CRY2/ZBTB20 genotype combination showed a > 200-fold increase in odds of anxiety and PER3/ZBTB20 and CRY1 /PER3-A genotype combinations also appeared as female risk factors. In males, CRY1/PER3-A and PER3-B/ZBTB20 genotype combinations were associated with anxiety risk. Mediation analysis revealed direct associations of CRY2/ZBTB20 variant genotypes with moderate anxiety in females and CRY1/PER3-A variant genotypes with severe anxiety in males. The association of CRY1/PER3-A variant genotypes with severe anxiety in females was partially mediated by extreme evening chronotype. Our results reinforce existing findings that females exhibit stronger anxiety outcomes than males, and provide evidence for circadian gene associations with anxiety, particularly in females. Our analyses only identified significant associations using two-gene combinations, underscoring the importance of combined gene effects on anxiety risk. We describe novel, robust associations between gene combinations involving the ZBTB20 SNP (rs1394593) and risk of anxiety symptoms in a large population sample. Our findings also support previous findings that the ZBTB20 SNP is an important factor in mood disorders, including seasonal affective disorder. Our results suggest that reduced expression of this gene significantly modulates the risk of anxiety symptoms through direct influences on mood-related pathways. Together, these observations provide novel links between the circadian clockwork and anxiety symptoms and identify potential molecular pathways through which clock genes may influence anxiety risk.
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Affiliation(s)
- Cole Ventresca
- Department of Mathematics, Colgate University, Hamilton, NY, USA
- Department of Computer Science, Colgate University, Hamilton, NY, USA
| | - Wael Mohamed
- Department of Computer Science, Colgate University, Hamilton, NY, USA
- Department of Psychological and Brain Sciences, Colgate University, Hamilton, NY, USA
| | | | - Ahmet Ay
- Department of Mathematics, Colgate University, Hamilton, NY, USA
- Department of Biology, Colgate University, Hamilton, NY, USA
| | - Krista K Ingram
- Department of Biology, Colgate University, Hamilton, NY, USA.
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13
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Wang Y, Du W, Hu X, Yu X, Guo C, Jin X, Wang W. Targeting the blood-brain barrier to delay aging-accompanied neurological diseases by modulating gut microbiota, circadian rhythms, and their interplays. Acta Pharm Sin B 2023; 13:4667-4687. [PMID: 38045038 PMCID: PMC10692395 DOI: 10.1016/j.apsb.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/05/2023] [Accepted: 08/02/2023] [Indexed: 12/05/2023] Open
Abstract
The blood-brain barrier (BBB) impairment plays a crucial role in the pathological processes of aging-accompanied neurological diseases (AAND). Meanwhile, circadian rhythms disruption and gut microbiota dysbiosis are associated with increased morbidity of neurological diseases in the accelerated aging population. Importantly, circadian rhythms disruption and gut microbiota dysbiosis are also known to induce the generation of toxic metabolites and pro-inflammatory cytokines, resulting in disruption of BBB integrity. Collectively, this provides a new perspective for exploring the relationship among circadian rhythms, gut microbes, and the BBB in aging-accompanied neurological diseases. In this review, we focus on recent advances in the interplay between circadian rhythm disturbances and gut microbiota dysbiosis, and their potential roles in the BBB disruption that occurs in AAND. Based on existing literature, we discuss and propose potential mechanisms underlying BBB damage induced by dysregulated circadian rhythms and gut microbiota, which would serve as the basis for developing potential interventions to protect the BBB in the aging population through targeting the BBB by exploiting its links with gut microbiota and circadian rhythms for treating AAND.
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Affiliation(s)
- Yanping Wang
- Department of Neurology, the Second Affiliated Hospital of Jiaxing City, Jiaxing 314000, China
| | - Weihong Du
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Histology and Embryology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Xiaoyan Hu
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Histology and Embryology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Xin Yu
- Bengbu Medical College (Department of Neurology, the Second Hospital of Jiaxing City), Jiaxing 233030, China
| | - Chun Guo
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Xinchun Jin
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Histology and Embryology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Wei Wang
- Department of Physiology and Pathophysiology, Capital Medical University, Beijing 100069, China
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14
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Chujan S, Cholpraipimolrat W, Satayavivad J. Integrated Transcriptomics and Network Analysis Identified Altered Neural Mechanisms in Frontal Aging Brain-Associated Alzheimer's Disease. Biochem Genet 2023:10.1007/s10528-023-10549-9. [PMID: 37934339 DOI: 10.1007/s10528-023-10549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease. The late stage of AD typically develops after 60 years of age and AD pathogenesis can be detected predominately in the frontal lobe, which is responsible for memory. Multiple alterations in cellular mechanisms have been associated with AD, but there is no clear information on AD pathogenesis during brain aging. This study aimed to explore the differentially expressed genes (DEGs) in the frontal lobe of aging brains and to identify shared crucial mechanisms in the aging brain linked to AD pathogenesis. Three datasets were downloaded from the Gene Expression Omnibus (GEO). Biological function analysis was performed by DAVID and KEGG databases. An AD patient's cohort (GSE150696) was collected for verification of the enriched pathway. The results demonstrated that multiple neurochemical synapsis and regulation of the cytoskeleton are linked to AD pathogenesis during aging. Taken together, this study contributes to our further understanding of neural alterations during aging in AD that could be used to develop therapeutics for early intervention to prevent or slow progression.
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Affiliation(s)
- Suthipong Chujan
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, 10400, Thailand
| | | | - Jutamaad Satayavivad
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, 10210, Thailand.
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, 10400, Thailand.
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15
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Chen R, Routh BN, Gaudet AD, Fonken LK. Circadian Regulation of the Neuroimmune Environment Across the Lifespan: From Brain Development to Aging. J Biol Rhythms 2023; 38:419-446. [PMID: 37357738 PMCID: PMC10475217 DOI: 10.1177/07487304231178950] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
Circadian clocks confer 24-h periodicity to biological systems, to ultimately maximize energy efficiency and promote survival in a world with regular environmental light cycles. In mammals, circadian rhythms regulate myriad physiological functions, including the immune, endocrine, and central nervous systems. Within the central nervous system, specialized glial cells such as astrocytes and microglia survey and maintain the neuroimmune environment. The contributions of these neuroimmune cells to both homeostatic and pathogenic demands vary greatly across the day. Moreover, the function of these cells changes across the lifespan. In this review, we discuss circadian regulation of the neuroimmune environment across the lifespan, with a focus on microglia and astrocytes. Circadian rhythms emerge in early life concurrent with neuroimmune sculpting of brain circuits and wane late in life alongside increasing immunosenescence and neurodegeneration. Importantly, circadian dysregulation can alter immune function, which may contribute to susceptibility to neurodevelopmental and neurodegenerative diseases. In this review, we highlight circadian neuroimmune interactions across the lifespan and share evidence that circadian dysregulation within the neuroimmune system may be a critical component in human neurodevelopmental and neurodegenerative diseases.
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Affiliation(s)
- Ruizhuo Chen
- Division of Pharmacology & Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas
| | - Brandy N. Routh
- Division of Pharmacology & Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas
- Institute for Neuroscience, The University of Texas at Austin, Austin, Texas
| | - Andrew D. Gaudet
- Institute for Neuroscience, The University of Texas at Austin, Austin, Texas
- Department of Psychology, The University of Texas at Austin, Austin, Texas
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Laura K. Fonken
- Division of Pharmacology & Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas
- Institute for Neuroscience, The University of Texas at Austin, Austin, Texas
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16
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Liu J, Si H, Huang D, Lu D, Zou S, Qi D, Pei X, Huang S, Li Z. Mechanisms of Extraorbital Lacrimal Gland Aging in Mice: An Integrative Analysis of the Temporal Transcriptome. Invest Ophthalmol Vis Sci 2023; 64:18. [PMID: 37695604 PMCID: PMC10501490 DOI: 10.1167/iovs.64.12.18] [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: 12/23/2022] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
Purpose This study used high-throughput RNA sequencing (RNA-Seq) and bioinformatics analysis to investigate the altered transcriptome profile of aging lacrimal glands in mice that occurs over the course of a 24-hour cycle. Methods Male C57BL/6J mice aged 12 weeks (young) and 20 months (aging) were housed in a pathogen-free setting with a 12-hour light/12-hour dark cycle. Throughout a 24-hour cycle, mouse extraorbital lacrimal glands (ELGs) were collected at eight time points at three-hour intervals. To prepare for the high-throughput RNA-Seq, whole mRNA was extracted. Differentially expressed genes (DEGs) in the young and aging groups were subjected to bioinformatic analysis based on diurnal patterns. Furthermore, the cell populations in which significant DEGs express and signaling pathways occur were validated at the single-cell RNA sequencing (scRNA-seq) level. Results The total transcriptome composition was significantly altered in aging ELGs compared with that in young mouse ELGs at eight time points during the 24-hour cycle, with 864 upregulated and 228 downregulated DEGs, which were primarily enriched in inflammatory pathways. Further comparative analysis of the point-to-point transcriptome revealed that aging ELGs underwent alterations in the temporal transcriptome profile in several pathways, including the inflammation-related, metabolism-related, mitochondrial bioenergetic function-associated, synaptome neural activity-associated, cell processes-associated, DNA processing-associated and fibrosis-associated pathways. Most of these pathways occurred separately in distinct cell populations. Conclusions Transcriptome profiles of aging lacrimal glands undergo considerable diurnal time-dependent changes; this finding offers a comprehensive source of information to better understand the pathophysiology of lacrimal gland aging and its underlying mechanisms.
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Affiliation(s)
- Jiangman Liu
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Hongli Si
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Duliurui Huang
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Dingli Lu
- Henan Eye Institute, Henan Eye Hospital, and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Sen Zou
- Henan Eye Institute, Henan Eye Hospital, and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Di Qi
- Henan Eye Institute, Henan Eye Hospital, and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Xiaoting Pei
- Henan Eye Institute, Henan Eye Hospital, and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Shenzhen Huang
- Henan Eye Institute, Henan Eye Hospital, and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Zhijie Li
- Henan Eye Institute, Henan Eye Hospital, and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
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17
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Larriba Y, Mason IC, Saxena R, Scheer FAJL, Rueda C. CIRCUST: A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans. PLoS Comput Biol 2023; 19:e1011510. [PMID: 37769026 PMCID: PMC10564179 DOI: 10.1371/journal.pcbi.1011510] [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: 02/12/2023] [Revised: 10/10/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023] Open
Abstract
The circadian system drives near-24-h oscillations in behaviors and biological processes. The underlying core molecular clock regulates the expression of other genes, and it has been shown that the expression of more than 50 percent of genes in mammals displays 24-h rhythmic patterns, with the specific genes that cycle varying from one tissue to another. Determining rhythmic gene expression patterns in human tissues sampled as single timepoints has several challenges, including the reconstruction of temporal order of highly noisy data. Previous methodologies have attempted to address these challenges in one or a small number of tissues for which rhythmic gene evolutionary conservation is assumed to be preserved. Here we introduce CIRCUST, a novel CIRCular-robUST methodology for analyzing molecular rhythms, that relies on circular statistics, is robust against noise, and requires fewer assumptions than existing methodologies. Next, we validated the method against four controlled experiments in which sampling times were known, and finally, CIRCUST was applied to 34 tissues from the Genotype-Tissue Expression (GTEx) dataset with the aim towards building a comprehensive daily rhythm gene expression atlas in humans. The validation and application shown here indicate that CIRCUST provides a flexible framework to formulate and solve the issues related to the analysis of molecular rhythms in human tissues. CIRCUST methodology is publicly available at https://github.com/yolandalago/CIRCUST/.
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Affiliation(s)
- Yolanda Larriba
- Department of Statistics and Operational Research, University of Valladolid, Valladolid, Spain
- Mathematics Research Institute of the University of Valladolid, University of Valladolid, Valladolid, Spain
| | - Ivy C. Mason
- Medical Chronobiology Program, Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richa Saxena
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Genomic Medicine and Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Division of Anesthesia, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Frank A. J. L. Scheer
- Medical Chronobiology Program, Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Cristina Rueda
- Department of Statistics and Operational Research, University of Valladolid, Valladolid, Spain
- Mathematics Research Institute of the University of Valladolid, University of Valladolid, Valladolid, Spain
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18
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Zong W, Seney ML, Ketchesin KD, Gorczyca MT, Liu AC, Esser KA, Tseng GC, McClung CA, Huo Z. Experimental design and power calculation in omics circadian rhythmicity detection using the cosinor model. Stat Med 2023; 42:3236-3258. [PMID: 37265194 PMCID: PMC10425922 DOI: 10.1002/sim.9803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/27/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Circadian clocks are 24-h endogenous oscillators in physiological and behavioral processes. Though recent transcriptomic studies have been successful in revealing the circadian rhythmicity in gene expression, the power calculation for omics circadian analysis have not been fully explored. In this paper, we develop a statistical method, namely CircaPower, to perform power calculation for circadian pattern detection. Our theoretical framework is determined by three key factors in circadian gene detection: sample size, intrinsic effect size and sampling design. Via simulations, we systematically investigate the impact of these key factors on circadian power calculation. We not only demonstrate that CircaPower is fast and accurate, but also show its underlying cosinor model is robust against variety of violations of model assumptions. In real applications, we demonstrate the performance of CircaPower using mouse pan-tissue data and human post-mortem brain data, and illustrate how to perform circadian power calculation using mouse skeleton muscle RNA-Seq pilot as case study. Our method CircaPower has been implemented in an R package, which is made publicly available on GitHub ( https://github.com/circaPower/circaPower).
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Affiliation(s)
- Wei Zong
- Department of Biostatistics, University of Pittsburgh, PA, USA
| | - Marianne L. Seney
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Kyle D. Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Michael T. Gorczyca
- Department of Computational and Systems Biology, University of Pittsburgh, PA, USA
| | - Andrew C. Liu
- Department of Physiology and Aging, University of Florida, FL, USA
| | - Karyn A. Esser
- Department of Physiology and Aging, University of Florida, FL, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, PA, USA
| | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, FL, USA
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19
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Ogholbake AA, Cheng Q. PENN: Phase Estimation Neural Network on Gene Expression Data. THE 4TH JOINT INTERNATIONAL CONFERENCE ON DEEP LEARNING, BIG DATA AND BLOCKCHAIN (DBB 2023). JOINT INTERNATIONAL CONFERENCE ON DEEP LEARNING, BIG DATA AND BLOCKCHAIN (4TH : 2023 : MARRAKECH, MOROCCO ; ONLINE) 2023; 768:59-67. [PMID: 37780416 PMCID: PMC10540272 DOI: 10.1007/978-3-031-42317-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
With the continuous expansion of available transcriptomic data like gene expression, deep learning techniques are becoming more and more valuable in analyzing and interpreting them. The National Center for Biotechnology Information Gene Expression Omnibus (GEO) encompasses approximately 5 million gene expression datasets from animal and human subjects. Unfortunately, the majority of them do not have a recorded timestamps, hindering the exploration of the behavior and patterns of circadian genes. Therefore, predicting the phases of these unordered gene expression measurements can help understand the behavior of the circadian genes, thus providing valuable insights into the physiology, behaviors, and diseases of humans and animals. In this paper, we propose a novel approach to predict the phases of the un-timed samples based on a deep neural network architecture. It incorporates the potential periodic oscillation information of the cyclic genes into the objective function to regulate the phase estimation. To validate our method, we use mouse heart, mouse liver and temporal cortex of human brain dataset. Through our experiments, we demonstrate the effectiveness of our proposed method in predicting phases and uncovering rhythmic pattern in circadian genes.
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Affiliation(s)
| | - Qiang Cheng
- University of Kentucky, Lexington KY 40526, USA
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20
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Xu K, Saaoud F, Shao Y, Lu Y, Wu S, Zhao H, Chen K, Vazquez-Padron R, Jiang X, Wang H, Yang X. Early hyperlipidemia triggers metabolomic reprogramming with increased SAH, increased acetyl-CoA-cholesterol synthesis, and decreased glycolysis. Redox Biol 2023; 64:102771. [PMID: 37364513 PMCID: PMC10310484 DOI: 10.1016/j.redox.2023.102771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
To identify metabolomic reprogramming in early hyperlipidemia, unbiased metabolome was screened in four tissues from ApoE-/- mice fed with high fat diet (HFD) for 3 weeks. 30, 122, 67, and 97 metabolites in the aorta, heart, liver, and plasma, respectively, were upregulated. 9 upregulated metabolites were uremic toxins, and 13 metabolites, including palmitate, promoted a trained immunity with increased syntheses of acetyl-CoA and cholesterol, increased S-adenosylhomocysteine (SAH) and hypomethylation and decreased glycolysis. The cross-omics analysis found upregulation of 11 metabolite synthetases in ApoE‾/‾ aorta, which promote ROS, cholesterol biosynthesis, and inflammation. Statistical correlation of 12 upregulated metabolites with 37 gene upregulations in ApoE‾/‾ aorta indicated 9 upregulated new metabolites to be proatherogenic. Antioxidant transcription factor NRF2-/- transcriptome analysis indicated that NRF2 suppresses trained immunity-metabolomic reprogramming. Our results have provided novel insights on metabolomic reprogramming in multiple tissues in early hyperlipidemia oriented toward three co-existed new types of trained immunity.
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Affiliation(s)
- Keman Xu
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Fatma Saaoud
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Ying Shao
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Yifan Lu
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Sheng Wu
- Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Huaqing Zhao
- Medical Education and Data Science, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Kaifu Chen
- Computational Biology Program, Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Vazquez-Padron
- DeWitt Daughtry Family Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, 33125, USA
| | - Xiaohua Jiang
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA; Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Hong Wang
- Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Xiaofeng Yang
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA; Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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Sun J, Peterson EA, Chen X, Wang J. hapln1a + cells guide coronary growth during heart morphogenesis and regeneration. Nat Commun 2023; 14:3505. [PMID: 37311876 PMCID: PMC10264374 DOI: 10.1038/s41467-023-39323-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/07/2023] [Indexed: 06/15/2023] Open
Abstract
Although several tissues and chemokines orchestrate coronary formation, the guidance cues for coronary growth remain unclear. Here, we profile the juvenile zebrafish epicardium during coronary vascularization and identify hapln1a+ cells enriched with vascular-regulating genes. hapln1a+ cells not only envelop vessels but also form linear structures ahead of coronary sprouts. Live-imaging demonstrates that coronary growth occurs along these pre-formed structures, with depletion of hapln1a+ cells blocking this growth. hapln1a+ cells also pre-lead coronary sprouts during regeneration and hapln1a+ cell loss inhibits revascularization. Further, we identify serpine1 expression in hapln1a+ cells adjacent to coronary sprouts, and serpine1 inhibition blocks vascularization and revascularization. Moreover, we observe the hapln1a substrate, hyaluronan, forming linear structures along and preceding coronary vessels. Depletion of hapln1a+ cells or serpine1 activity inhibition disrupts hyaluronan structure. Our studies reveal that hapln1a+ cells and serpine1 are required for coronary production by establishing a microenvironment to facilitate guided coronary growth.
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Affiliation(s)
- Jisheng Sun
- Cardiology Division, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Elizabeth A Peterson
- Cardiology Division, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Xin Chen
- Cardiology Division, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Jinhu Wang
- Cardiology Division, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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22
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Hammarlund JA, Li SY, Wu G, Lian JW, Howell SJ, Clarke R, Adamson A, Gonçalves CF, Hogenesch JB, Meng QJ, Anafi RC. Subtype-specific circadian clock dysregulation modulates breast cancer biology, invasiveness, and prognosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.540386. [PMID: 37293090 PMCID: PMC10245642 DOI: 10.1101/2023.05.17.540386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Studies in shift workers and model organisms link circadian disruption to breast cancer. However, molecular rhythms in non-cancerous and cancerous human breast tissues are largely unknown. We reconstructed rhythms informatically, integrating locally collected, time-stamped biopsies with public datasets. For non-cancerous tissue, the inferred order of core-circadian genes matches established physiology. Inflammatory, epithelial-mesenchymal transition (EMT), and estrogen responsiveness pathways show circadian modulation. Among tumors, clock correlation analysis demonstrates subtype-specific changes in circadian organization. Luminal A organoids and informatic ordering of Luminal A samples exhibit continued, albeit disrupted rhythms. However, CYCLOPS magnitude, a measure of global rhythm strength, varied widely among Luminal A samples. Cycling of EMT pathway genes was markedly increased in high-magnitude Luminal A tumors. Patients with high-magnitude tumors had reduced 5-year survival. Correspondingly, 3D Luminal A cultures show reduced invasion following molecular clock disruption. This study links subtype-specific circadian disruption in breast cancer to EMT, metastatic potential, and prognosis.
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Affiliation(s)
- Jan A Hammarlund
- School of Biomedical Engineering, Science and Health Systems. Drexel University, Philadelphia, PA, USA
| | - Shi-Yang Li
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gang Wu
- Divisions of Human Genetics and Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Jia-wen Lian
- School of Biomedical Engineering, Science and Health Systems. Drexel University, Philadelphia, PA, USA
| | - Sacha J Howell
- Breast Biology Group, Manchester Breast Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Rob Clarke
- Breast Biology Group, Manchester Breast Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Antony Adamson
- School of Biomedical Engineering, Science and Health Systems. Drexel University, Philadelphia, PA, USA
| | - Cátia F. Gonçalves
- School of Biomedical Engineering, Science and Health Systems. Drexel University, Philadelphia, PA, USA
| | - John B Hogenesch
- Divisions of Human Genetics and Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Qing-Jun Meng
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ron C Anafi
- Department of Medicine, Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
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23
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Bao H, Cao J, Chen M, Chen M, Chen W, Chen X, Chen Y, Chen Y, Chen Y, Chen Z, Chhetri JK, Ding Y, Feng J, Guo J, Guo M, He C, Jia Y, Jiang H, Jing Y, Li D, Li J, Li J, Liang Q, Liang R, Liu F, Liu X, Liu Z, Luo OJ, Lv J, Ma J, Mao K, Nie J, Qiao X, Sun X, Tang X, Wang J, Wang Q, Wang S, Wang X, Wang Y, Wang Y, Wu R, Xia K, Xiao FH, Xu L, Xu Y, Yan H, Yang L, Yang R, Yang Y, Ying Y, Zhang L, Zhang W, Zhang W, Zhang X, Zhang Z, Zhou M, Zhou R, Zhu Q, Zhu Z, Cao F, Cao Z, Chan P, Chen C, Chen G, Chen HZ, Chen J, Ci W, Ding BS, Ding Q, Gao F, Han JDJ, Huang K, Ju Z, Kong QP, Li J, Li J, Li X, Liu B, Liu F, Liu L, Liu Q, Liu Q, Liu X, Liu Y, Luo X, Ma S, Ma X, Mao Z, Nie J, Peng Y, Qu J, Ren J, Ren R, Song M, Songyang Z, Sun YE, Sun Y, Tian M, Wang S, Wang S, Wang X, Wang X, Wang YJ, Wang Y, Wong CCL, Xiang AP, Xiao Y, Xie Z, Xu D, Ye J, Yue R, Zhang C, Zhang H, Zhang L, Zhang W, Zhang Y, Zhang YW, Zhang Z, Zhao T, Zhao Y, Zhu D, Zou W, Pei G, Liu GH. Biomarkers of aging. SCIENCE CHINA. LIFE SCIENCES 2023; 66:893-1066. [PMID: 37076725 PMCID: PMC10115486 DOI: 10.1007/s11427-023-2305-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/27/2023] [Indexed: 04/21/2023]
Abstract
Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although a broad spectrum of aging biomarkers has been developed, their potential uses and limitations remain poorly characterized. An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research: How old are we? Why do we get old? And how can we age slower? This review aims to address this need. Here, we summarize our current knowledge of biomarkers developed for cellular, organ, and organismal levels of aging, comprising six pillars: physiological characteristics, medical imaging, histological features, cellular alterations, molecular changes, and secretory factors. To fulfill all these requisites, we propose that aging biomarkers should qualify for being specific, systemic, and clinically relevant.
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Affiliation(s)
- Hainan Bao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jiani Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengting Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Min Chen
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wei Chen
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Xiao Chen
- Department of Nuclear Medicine, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Yanhao Chen
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yutian Chen
- The Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zhiyang Chen
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Ageing and Regenerative Medicine, Jinan University, Guangzhou, 510632, China
| | - Jagadish K Chhetri
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Yingjie Ding
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junlin Feng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jun Guo
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China
| | - Mengmeng Guo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Chuting He
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Yujuan Jia
- Department of Neurology, First Affiliated Hospital, Shanxi Medical University, Taiyuan, 030001, China
| | - Haiping Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Ying Jing
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Dingfeng Li
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230036, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyi Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Qinhao Liang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Liang
- Research Institute of Transplant Medicine, Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, 300384, China
| | - Feng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Zuojun Liu
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Oscar Junhong Luo
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Jianwei Lv
- School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Jingyi Ma
- The State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Kehang Mao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China
| | - Jiawei Nie
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine (Shanghai), International Center for Aging and Cancer, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinpei Sun
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, 100101, China
| | - Xiaoqiang Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianfang Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siyuan Wang
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Xuan Wang
- Hepatobiliary and Pancreatic Center, Medical Research Center, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yuhan Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Rimo Wu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Kai Xia
- Center for Stem Cell Biologyand Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
- National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Fu-Hui Xiao
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yingying Xu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Haoteng Yan
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Liang Yang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Ruici Yang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuanxin Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yilin Ying
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital, Shanghai, 200025, China
| | - Le Zhang
- Gerontology Center of Hubei Province, Wuhan, 430000, China
- Institute of Gerontology, Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Weiwei Zhang
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, 100853, China
| | - Wenwan Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xing Zhang
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Min Zhou
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China
| | - Rui Zhou
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Qingchen Zhu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhengmao Zhu
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, 300071, China
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Feng Cao
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, 100853, China.
| | - Zhongwei Cao
- State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Piu Chan
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Guobing Chen
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China.
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou, 510000, China.
| | - Hou-Zao Chen
- Department of Biochemistryand Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
| | - Jun Chen
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China.
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
| | - Bi-Sen Ding
- State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Qiurong Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Feng Gao
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Kai Huang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Ageing and Regenerative Medicine, Jinan University, Guangzhou, 510632, China.
| | - Qing-Peng Kong
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Jian Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China.
| | - Xin Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Baohua Liu
- School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518060, China.
| | - Feng Liu
- Metabolic Syndrome Research Center, The Second Xiangya Hospital, Central South Unversity, Changsha, 410011, China.
| | - Lin Liu
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, 300071, China.
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Institute of Translational Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, 300000, China.
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, China.
| | - Qiang Liu
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230036, China.
| | - Qiang Liu
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
- Tianjin Institute of Immunology, Tianjin Medical University, Tianjin, 300070, China.
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
| | - Yong Liu
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.
| | - Xianghang Luo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China.
| | - Shuai Ma
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Jing Nie
- The State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Yaojin Peng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ruibao Ren
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine (Shanghai), International Center for Aging and Cancer, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- International Center for Aging and Cancer, Hainan Medical University, Haikou, 571199, China.
| | - Moshi Song
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, 510275, China.
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Yi Eve Sun
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
| | - Yu Sun
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA, 98195, USA.
| | - Mei Tian
- Human Phenome Institute, Fudan University, Shanghai, 201203, China.
| | - Shusen Wang
- Research Institute of Transplant Medicine, Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, 300384, China.
| | - Si Wang
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
| | - Xia Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| | - Xiaoning Wang
- Institute of Geriatrics, The second Medical Center, Beijing Key Laboratory of Aging and Geriatrics, National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Yan-Jiang Wang
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
| | - Yunfang Wang
- Hepatobiliary and Pancreatic Center, Medical Research Center, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China.
| | - Catherine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China.
| | - Andy Peng Xiang
- Center for Stem Cell Biologyand Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China.
- National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Yichuan Xiao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Zhengwei Xie
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, 100101, China.
- Beijing & Qingdao Langu Pharmaceutical R&D Platform, Beijing Gigaceuticals Tech. Co. Ltd., Beijing, 100101, China.
| | - Daichao Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Jing Ye
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital, Shanghai, 200025, China.
| | - Rui Yue
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Cuntai Zhang
- Gerontology Center of Hubei Province, Wuhan, 430000, China.
- Institute of Gerontology, Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Liang Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yong Zhang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Yun-Wu Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, China.
| | - Zhuohua Zhang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical Genetics, Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, 410078, China.
- Department of Neurosciences, Hengyang Medical School, University of South China, Hengyang, 421001, China.
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Dahai Zhu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Weiguo Zou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Gang Pei
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-Based Biomedicine, The Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, 200070, China.
| | - Guang-Hui Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
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24
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Schwarz JE, Mrčela A, Lahens NF, Li Y, Hsu CT, Grant G, Skarke C, Zhang SL, Sehgal A. Evidence for a role of human blood-borne factors in mediating age-associated changes in molecular circadian rhythms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537477. [PMID: 37808824 PMCID: PMC10557775 DOI: 10.1101/2023.04.19.537477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Aging is associated with a number of physiologic changes including perturbed circadian rhythms; however, mechanisms by which rhythms are altered remain unknown. To test the idea that circulating factors mediate age-dependent changes in peripheral rhythms, we compared the ability of human serum from young and old individuals to synchronize circadian rhythms in culture. We collected blood from apparently healthy young (age 25-30) and old (age 70-76) individuals and used the serum to synchronize cultured fibroblasts. We found that young and old sera are equally competent at driving robust ~24h oscillations of a luciferase reporter driven by clock gene promoter. However, cyclic gene expression is affected, such that young and old sera drive cycling of different genes. While genes involved in the cell cycle and transcription/translation remain rhythmic in both conditions, genes identified by STRING and IPA analyses as associated with oxidative phosphorylation and Alzheimer's Disease lose rhythmicity in the aged condition. Also, the expression of cycling genes associated with cholesterol biosynthesis increases in the cells entrained with old serum. We did not observe a global difference in the distribution of phase between groups, but find that peak expression of several clock controlled genes (PER3, NR1D1, NR1D2, CRY1, CRY2, and TEF) lags in the cells synchronized with old serum. Taken together, these findings demonstrate that age-dependent blood-borne factors affect peripheral circadian rhythms in cells and have the potential to impact health and disease via maintaining or disrupting rhythms respectively.
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Affiliation(s)
- Jessica E Schwarz
- Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics (ITMAT), Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics (ITMAT), Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Yongjun Li
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Cynthia T Hsu
- Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Gregory Grant
- Institute for Translational Medicine and Therapeutics (ITMAT), Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Carsten Skarke
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Institute for Translational Medicine and Therapeutics (ITMAT), Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
| | - Shirley L Zhang
- Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Current Institution: Department of Cell Biology, Emory University School of Medicine; Atlanta, GA 30323, United States
| | - Amita Sehgal
- Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, United States
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25
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Tran NQV, Le MK, Nguyen TA, Kondo T, Nakao A. Association of Circadian Clock Gene Expression with Pediatric/Adolescent Asthma and Its Comorbidities. Int J Mol Sci 2023; 24:ijms24087477. [PMID: 37108640 PMCID: PMC10138904 DOI: 10.3390/ijms24087477] [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: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
The pathology of asthma is characterized by marked day-night variation, which is likely controlled by circadian clock activity. This study aimed to clarify the association of core circadian clock gene expression with clinical features of asthma. For this purpose, we accessed the National Center for Biotechnology Information database and analyzed transcriptomes of peripheral blood mononuclear cells and clinical characteristics of 134 pediatric/adolescent patients with asthma. Based on the expression patterns of seven core circadian clock genes (CLOCK, BMAL1, PER1-3, CRY1-2), we identified three circadian clusters (CCs) with distinct comorbidities and transcriptomic expressions. In the three CC subtypes, allergic rhinitis, and atopic dermatitis, both asthma comorbidities occurred in different proportions: CC1 had a high proportion of allergic rhinitis and atopic dermatitis; CC2 had a high proportion of atopic dermatitis but a low proportion of allergic rhinitis; and CC3 had a high proportion of allergic rhinitis but a low proportion of atopic dermatitis. This might be associated with the low activity of the FcεRI signaling pathway in CC2 and the cytokine-cytokine receptor interaction pathways in CC3. This is the first report to consider circadian clock gene expression in subcategories of patients with asthma and to explore their contribution to pathophysiology and comorbidity.
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Affiliation(s)
- Nguyen Quoc Vuong Tran
- Department of Immunology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Minh-Khang Le
- Department of Human Pathology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Thuy-An Nguyen
- Department of Immunology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Tetsuo Kondo
- Department of Human Pathology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Atsuhito Nakao
- Department of Immunology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
- Atopy Research Center, Juntendo University, School of Medicine, Tokyo 113-8421, Japan
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26
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Kimura A, Ishida Y, Nosaka M, Ishigami A, Yamamoto H, Kuninaka Y, Hata S, Ozaki M, Kondo T. Application and limitation of a biological clock-based method for estimating time of death in forensic practices. Sci Rep 2023; 13:6093. [PMID: 37055510 PMCID: PMC10102023 DOI: 10.1038/s41598-023-33328-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/11/2023] [Indexed: 04/15/2023] Open
Abstract
Estimating time of death is one of the most important problems in forensics. Here, we evaluated the applicability, limitations and reliability of the developed biological clock-based method. We analyzed the expression of the clock genes, BMAL1 and NR1D1, in 318 dead hearts with defined time of death by real-time RT-PCR. For estimating the time of death, we chose two parameters, the NR1D1/BMAL1 ratio and BMAL1/NR1D1 ratio for morning and evening deaths, respectively. The NR1D1/BMAL1 ratio was significantly higher in morning deaths and the BMAL1/NR1D1 ratio was significantly higher in evening deaths. Sex, age, postmortem interval, and most causes of death had no significant effect on the two parameters, except for infants and the elderly, and severe brain injury. Although our method may not work in all cases, our method is useful for forensic practice in that it complements classical methods that are strongly influenced by the environment in which the corpse is placed. However, this method should be applied with caution in infants, the elderly, and patients with severe brain injury.
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Affiliation(s)
- Akihiko Kimura
- Department of Forensic Medicine, Wakayama Medical University, 811-1 Kimiidera, Wakayama, 641-8509, Japan
| | - Yuko Ishida
- Department of Forensic Medicine, Wakayama Medical University, 811-1 Kimiidera, Wakayama, 641-8509, Japan
| | - Mizuho Nosaka
- Department of Forensic Medicine, Wakayama Medical University, 811-1 Kimiidera, Wakayama, 641-8509, Japan
| | - Akiko Ishigami
- Department of Forensic Medicine, Wakayama Medical University, 811-1 Kimiidera, Wakayama, 641-8509, Japan
| | - Hiroki Yamamoto
- Department of Forensic Medicine, Wakayama Medical University, 811-1 Kimiidera, Wakayama, 641-8509, Japan
| | - Yumi Kuninaka
- Department of Forensic Medicine, Wakayama Medical University, 811-1 Kimiidera, Wakayama, 641-8509, Japan
| | - Satoshi Hata
- Department of Cardiovascular Medicine, Kinan Hospital, Wakayama, Japan
| | - Mitsunori Ozaki
- Department of Neurological Surgery, National Hospital Organization Minami Wakayama Medical Center, Wakayama, Japan
| | - Toshikazu Kondo
- Department of Forensic Medicine, Wakayama Medical University, 811-1 Kimiidera, Wakayama, 641-8509, Japan.
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27
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Salminen A. Aryl hydrocarbon receptor (AhR) impairs circadian regulation: impact on the aging process. Ageing Res Rev 2023; 87:101928. [PMID: 37031728 DOI: 10.1016/j.arr.2023.101928] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/23/2023] [Accepted: 04/06/2023] [Indexed: 04/11/2023]
Abstract
Circadian clocks control the internal sleep-wake rhythmicity of 24hours which is synchronized by the solar cycle. Circadian regulation of metabolism evolved about 2.5 billion years ago, i.e., the rhythmicity has been conserved from cyanobacteria and Archaea through to mammals although the mechanisms utilized have developed with evolution. While the aryl hydrocarbon receptor (AhR) is an evolutionarily conserved defence mechanism against environmental threats, it has gained many novel functions during evolution, such as the regulation of cell cycle, proteostasis, and many immune functions. There is robust evidence that AhR signaling impairs circadian rhythmicity, e.g., by interacting with the core BMAL1/CLOCK complex and disturbing the epigenetic regulation of clock genes. The maintenance of circadian rhythms is impaired with aging, disturbing metabolism and many important functions in aged organisms. Interestingly, it is known that AhR signaling promotes an age-related tissue degeneration, e.g., it is able to inhibit autophagy, enhance cellular senescence, and disrupt extracellular matrix. These alterations are rather similar to those induced by a long-term impairment of circadian rhythms. However, it is not known whether AhR signaling enhances the aging process by impairing circadian homeostasis. I will examine the experimental evidence indicating that AhR signaling is able to promote the age-related degeneration via a disruption of circadian rhythmicity.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
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28
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Morairty SR, Sun Y, Toll L, Bruchas MR, Kilduff TS. Activation of the nociceptin/orphanin-FQ receptor promotes NREM sleep and EEG slow wave activity. Proc Natl Acad Sci U S A 2023; 120:e2214171120. [PMID: 36947514 PMCID: PMC10068791 DOI: 10.1073/pnas.2214171120] [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: 08/23/2022] [Accepted: 02/13/2023] [Indexed: 03/23/2023] Open
Abstract
Sleep/wake control involves several neurotransmitter and neuromodulatory systems yet the coordination of the behavioral and physiological processes underlying sleep is incompletely understood. Previous studies have suggested that activation of the Nociceptin/orphanin FQ (N/OFQ) receptor (NOPR) reduces locomotor activity and produces a sedation-like effect in rodents. In the present study, we systematically evaluated the efficacy of two NOPR agonists, Ro64-6198 and SR16835, on sleep/wake in rats, mice, and Cynomolgus macaques. We found a profound, dose-related increase in non-Rapid Eye Movement (NREM) sleep and electroencephalogram (EEG) slow wave activity (SWA) and suppression of Rapid Eye Movement sleep (REM) sleep in all three species. At the highest dose tested in rats, the increase in NREM sleep and EEG SWA was accompanied by a prolonged inhibition of REM sleep, hypothermia, and reduced locomotor activity. However, even at the highest dose tested, rats were immediately arousable upon sensory stimulation, suggesting sleep rather than an anesthetic state. NOPR agonism also resulted in increased expression of c-Fos in the anterodorsal preoptic and parastrial nuclei, two GABAergic nuclei that are highly interconnected with brain regions involved in physiological regulation. These results suggest that the N/OFQ-NOPR system may have a previously unrecognized role in sleep/wake control and potential promise as a therapeutic target for the treatment of insomnia.
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Affiliation(s)
- Stephen R. Morairty
- Biosciences Division, Center for Neuroscience, SRI International, Menlo Park, CA94025
| | - Yu Sun
- Biosciences Division, Center for Neuroscience, SRI International, Menlo Park, CA94025
| | - Lawrence Toll
- Biosciences Division, Center for Neuroscience, SRI International, Menlo Park, CA94025
| | - Michael R. Bruchas
- Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA98195
- Department of Pharmacology, University of Washington, Seattle, WA98195
| | - Thomas S. Kilduff
- Biosciences Division, Center for Neuroscience, SRI International, Menlo Park, CA94025
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29
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Li Y, Fang Y, Chang HC, Gorczyca M, Liu P, Tseng GC. Adaptively Integrative Association between Multivariate Phenotypes and Transcriptomic Data for Complex Diseases. Genes (Basel) 2023; 14:genes14040798. [PMID: 37107556 PMCID: PMC10138055 DOI: 10.3390/genes14040798] [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: 01/14/2023] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Phenotype–gene association studies can uncover disease mechanisms for translational research. Association with multiple phenotypes or clinical variables in complex diseases has the advantage of increasing statistical power and offering a holistic view. Existing multi-variate association methods mostly focus on SNP-based genetic associations. In this paper, we extend and evaluate two adaptive Fisher’s methods, namely AFp and AFz, from the p-value combination perspective for phenotype–mRNA association analysis. The proposed method effectively aggregates heterogeneous phenotype–gene effects, allows association with different data types of phenotypes, and performs the selection of the associated phenotypes. Variability indices of the phenotype–gene effect selection are calculated by bootstrap analysis, and the resulting co-membership matrix identifies gene modules clustered by phenotype–gene effect. Extensive simulations demonstrate the superior performance of AFp compared to existing methods in terms of type I error control, statistical power and biological interpretation. Finally, the method is separately applied to three sets of transcriptomic and clinical datasets from lung disease, breast cancer, and brain aging and generates intriguing biological findings.
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Affiliation(s)
- Yujia Li
- Eli Lilly and Company, Indianapolis, IN 46225, USA
| | - Yusi Fang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hung-Ching Chang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Michael Gorczyca
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Peng Liu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Correspondence:
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30
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Crowdsourcing to predict RNA degradation and secondary structure. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-023-00615-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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31
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Talamanca L, Gobet C, Naef F. Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans. Science 2023; 379:478-483. [PMID: 36730411 DOI: 10.1126/science.add0846] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The circadian clock modulates human physiology. However, the organization of tissue-specific gene expression rhythms and how these depend on age and sex is not defined in humans. We combined data from the Genotype-Tissue Expression (GTEx) project with an algorithm that assigns circadian phases to 914 donors, by integrating temporal information from multiple tissues in each individual, to identify messenger RNA (mRNA) rhythms in 46 tissues. Clock transcripts showed conserved timing relationships and tight synchrony across the body. mRNA rhythms varied in breadth, covering global and tissue-specific functions, including metabolic pathways and systemic responses. The clock structure was conserved across sexes and age groups. However, overall gene expression rhythms were highly sex-dimorphic and more sustained in females. Rhythmic programs generally dampened with age across the body.
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Affiliation(s)
- Lorenzo Talamanca
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Cédric Gobet
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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32
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Sulukan E, Baran A, Şenol O, Kankaynar M, Yıldırım S, Bolat İ, Ceyhun HA, Toraman E, Ceyhun SB. Global warming and glyphosate toxicity (I): Adult zebrafish modelling with behavioural, immunohistochemical and metabolomic approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:160086. [PMID: 36356745 DOI: 10.1016/j.scitotenv.2022.160086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Global warming further increases the toxic threat of environmental pollutants on organisms. In order to reveal the dimensions of this threat more clearly, it is of great importance that the studies be carried out with temperature differences as close as possible to the temperature values that will represent the global climate projection. In our study, how the toxicity of glyphosate, which is widely used around the world, on zebrafish changes with temperature increases of 0.5° was investigated on behavioral and molecular basis. For this purpose, adult zebrafish were exposed to glyphosate at concentrations of 1 ppm and 5 ppm for 96 h in four environments with a temperature difference of 0.5° (28.5; 29.0; 29.5; 30.0 °C). At the end of the exposure, half of the zebrafish were sampled and remaining half were left for a 10-day recovery process. At the end of the trials, zebrafish were subjected to circadian rhythm and anxiety tests. In addition, histopathological, immunohistochemical and metabolome analyses were performed on brain tissues. As a result, it has been detected that anxiety and circadian rhythm were disrupted in parallel with the increased temperature and glyphosate concentration, and increased histopathological findings and 5-HT4R and GNAT2 immunopositivity in the brain. As a result of metabolome analysis, more than thirty annotated metabolites have been determined due to the synergistic effect of temperature increase and glyphosate exposure. As a conclusion, it was concluded that even a temperature increase of 0.5° caused an increasing effect of glyphosate toxicity in the zebrafish model.
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Affiliation(s)
- Ekrem Sulukan
- Aquatic Biotechnology Laboratory, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Aquaculture Department, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Department of Aquaculture Engineering, Graduate School of Natural and Applied Science, Atatürk University, Erzurum, Turkey
| | - Alper Baran
- Aquatic Biotechnology Laboratory, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Department of Food Quality Control and Analysis, Technical Vocational School, Atatürk University, Erzurum, Turkey
| | - Onur Şenol
- Department of Analytical Chemistry, Faculty of Pharmacy, Atatürk University, Erzurum, Turkey
| | - Meryem Kankaynar
- Aquatic Biotechnology Laboratory, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Department of Nanoscience and Nanoengineering, Graduate School of Natural and Applied Science, Atatürk University, Erzurum, Turkey
| | - Serkan Yıldırım
- Department of Pathology, Faculty of Veterinary, Atatürk University, Erzurum, Turkey
| | - İsmail Bolat
- Department of Pathology, Faculty of Veterinary, Atatürk University, Erzurum, Turkey
| | - Hacer Akgül Ceyhun
- Department of Psychiatry, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Emine Toraman
- Department of Molecular Biology and Genetics, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Saltuk Buğrahan Ceyhun
- Aquatic Biotechnology Laboratory, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Aquaculture Department, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Department of Aquaculture Engineering, Graduate School of Natural and Applied Science, Atatürk University, Erzurum, Turkey; Department of Nanoscience and Nanoengineering, Graduate School of Natural and Applied Science, Atatürk University, Erzurum, Turkey.
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33
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Obodo D, Outland EH, Hughey JJ. Sex Inclusion in Transcriptome Studies of Daily Rhythms. J Biol Rhythms 2023; 38:3-14. [PMID: 36419398 PMCID: PMC9903005 DOI: 10.1177/07487304221134160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Biomedical research on mammals has traditionally neglected females, raising the concern that some scientific findings may generalize poorly to half the population. Although this lack of sex inclusion has been broadly documented, its extent within circadian genomics remains undescribed. To address this gap, we examined sex inclusion practices in a comprehensive collection of publicly available transcriptome studies on daily rhythms. Among 148 studies having samples from mammals in vivo, we found strong underrepresentation of females across organisms and tissues. Overall, only 23 of 123 studies in mice, 0 of 10 studies in rats, and 9 of 15 studies in humans included samples from females. In addition, studies having samples from both sexes tended to have more samples from males than from females. These trends appear to have changed little over time, including since 2016, when the US National Institutes of Health began requiring investigators to consider sex as a biological variable. Our findings highlight an opportunity to dramatically improve representation of females in circadian research and to explore sex differences in daily rhythms at the genome level.
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Affiliation(s)
- Dora Obodo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Elliot H. Outland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jacob J. Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee,Jacob J. Hughey, Department of Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End Ave., Suite 1475, Nashville, TN 37232, USA; e-mail:
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34
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Verma AK, Singh S, Rizvi SI. Aging, circadian disruption and neurodegeneration: Interesting interplay. Exp Gerontol 2023; 172:112076. [PMID: 36574855 DOI: 10.1016/j.exger.2022.112076] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/26/2022] [Accepted: 12/22/2022] [Indexed: 12/26/2022]
Abstract
The circadian system is an intricate molecular network of coordinating circadian clocks that organize the internal synchrony of the organism in response to the environment. These rhythms are maintained by genetically programmed positive and negative auto-regulated transcriptional and translational feedback loops that sustain 24-hour oscillations in mRNA and protein components of the endogenous circadian clock. Since inter and intracellular activity of the central pacemaker appears to reduce with aging, the interaction between the circadian clock and aging continues to elude our understanding. In this review article, we discuss circadian clock components at the molecular level and how aging adversely affects circadian clock functioning in rodents and humans. The natural decline in melatonin levels with aging strongly contributes to circadian dysregulation resulting in the development of neurological anomalies. Additionally, inappropriate environmental conditions such as Artificial Light at Night (ALAN) can cause circadian disruption or chronodisruption (CD) which can result in a variety of pathological diseases, including premature aging. Furthermore, we summarize recent evidence suggesting that CD may also be a predisposing factor for the development of age-related neurodegenerative diseases (NDDs) such as Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD), although more investigation is required to prove this link. Finally, certain chrono-enhancement approaches have been offered as intervention strategies to prevent, alleviate, or mitigate the impacts of CD. This review thus aims to bring together recent advancements in the chronobiology of the aging process, as well as its role in NDDs.
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Affiliation(s)
- Avnish Kumar Verma
- Department of Biochemistry, University of Allahabad, Allahabad 211002, India
| | - Sandeep Singh
- Department of Biochemistry, University of Allahabad, Allahabad 211002, India; Psychedelics Research Group, Biological Psychiatry Laboratory and Hadassah BrainLabs, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Syed Ibrahim Rizvi
- Department of Biochemistry, University of Allahabad, Allahabad 211002, India.
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35
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Wolff CA, Gutierrez-Monreal MA, Meng L, Zhang X, Douma LG, Costello HM, Douglas CM, Ebrahimi E, Pham A, Oliveira AC, Fu C, Nguyen A, Alava BR, Hesketh SJ, Morris AR, Endale MM, Crislip GR, Cheng KY, Schroder EA, Delisle BP, Bryant AJ, Gumz ML, Huo Z, Liu AC, Esser KA. Defining the age-dependent and tissue-specific circadian transcriptome in male mice. Cell Rep 2023; 42:111982. [PMID: 36640301 PMCID: PMC9929559 DOI: 10.1016/j.celrep.2022.111982] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/01/2022] [Accepted: 12/23/2022] [Indexed: 01/10/2023] Open
Abstract
Cellular circadian clocks direct a daily transcriptional program that supports homeostasis and resilience. Emerging evidence has demonstrated age-associated changes in circadian functions. To define age-dependent changes at the systems level, we profile the circadian transcriptome in the hypothalamus, lung, heart, kidney, skeletal muscle, and adrenal gland in three age groups. We find age-dependent and tissue-specific clock output changes. Aging reduces the number of rhythmically expressed genes (REGs), indicative of weakened circadian control. REGs are enriched for the hallmarks of aging, adding another dimension to our understanding of aging. Analyzing differential gene expression within a tissue at four different times of day identifies distinct clusters of differentially expressed genes (DEGs). Increased variability of gene expression across the day is a common feature of aged tissues. This analysis extends the landscape for understanding aging and highlights the impact of aging on circadian clock function and temporal changes in gene expression.
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Affiliation(s)
- Christopher A Wolff
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Miguel A Gutierrez-Monreal
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA; Claude D. Pepper Older Americans Independence Center, University of Florida, Gainesville, FL 32610, USA
| | - Lingsong Meng
- Department of Biostatistics, University of Florida, Gainesville, FL 32610, USA
| | - Xiping Zhang
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lauren G Douma
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Hannah M Costello
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Collin M Douglas
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Elnaz Ebrahimi
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ann Pham
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Aline C Oliveira
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Chunhua Fu
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Amy Nguyen
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Bryan R Alava
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Stuart J Hesketh
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Andrew R Morris
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mehari M Endale
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - G Ryan Crislip
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Kit-Yan Cheng
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Elizabeth A Schroder
- Internal Medicine, Pulmonary, University of Kentucky, Lexington, KY 40506, USA; Department of Physiology, University of Kentucky, Lexington, KY 40506, USA
| | - Brian P Delisle
- Department of Physiology, University of Kentucky, Lexington, KY 40506, USA
| | - Andrew J Bryant
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Michelle L Gumz
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; Center for Integrative Cardiovascular and Metabolic Disease, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, FL 32610, USA.
| | - Andrew C Liu
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
| | - Karyn A Esser
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA; Claude D. Pepper Older Americans Independence Center, University of Florida, Gainesville, FL 32610, USA.
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36
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Qu M. Molecular crosstalk between circadian clock and cancer and therapeutic implications. Front Nutr 2023; 10:1143001. [PMID: 36937362 PMCID: PMC10017454 DOI: 10.3389/fnut.2023.1143001] [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: 01/12/2023] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
The circadian clock governs activity of many physiological processes, thereby playing a pivotal role in human health. Circadian disruption is closely associated with cancer development; in particular, recent discoveries have provided strong evidence supporting specific functions of different molecular clock components in either promoting or inhibiting tumorigenesis. This narrative review aims to summarize the existing data on molecular connections between the clock and cancer. These results along with future efforts pave the road to targeting the circadian clock as a novel pathway for therapeutic intervention. Given the implications of chrono-nutrition interventions such as time-restricted feeding in extending lifespan, chrono-nutrition may have preventive and therapeutic applications for individuals with and at-risk of age-related diseases including cancer.
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37
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He Y, B'nai Taub A, Yu L, Yao Y, Zhang R, Zahr T, Aaron N, LeSauter J, Fan L, Liu L, Tazebay R, Que J, Pajvani U, Wang L, Silver R, Qiang L. PPARγ Acetylation Orchestrates Adipose Plasticity and Metabolic Rhythms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204190. [PMID: 36394167 PMCID: PMC9839851 DOI: 10.1002/advs.202204190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/13/2022] [Indexed: 05/28/2023]
Abstract
Systemic glucose metabolism and insulin activity oscillate in response to diurnal rhythms and nutrient availability with the necessary involvement of adipose tissue to maintain metabolic homeostasis. However, the adipose-intrinsic regulatory mechanism remains elusive. Here, the dynamics of PPARγ acetylation in adipose tissue are shown to orchestrate metabolic oscillation in daily rhythms. Acetylation of PPARγ displays a diurnal rhythm in young healthy mice, with the peak at zeitgeber time 0 (ZT0) and the trough at ZT18. This rhythmic pattern is deranged in pathological conditions such as obesity, aging, and circadian disruption. The adipocyte-specific acetylation-mimetic mutation of PPARγ K293Q (aKQ) restrains adipose plasticity during calorie restriction and diet-induced obesity, associated with proteolysis of a core circadian component BMAL1. Consistently, the rhythmicity in glucose tolerance and insulin sensitivity is altered in aKQ and the complementary PPARγ deacetylation-mimetic K268R/K293R (2KR) mouse models. Furthermore, the PPARγ acetylation-sensitive downstream target adipsin is revealed as a novel diurnal factor that destabilizes BMAL1 and mediates metabolic rhythms. These findings collectively signify that PPARγ acetylation is a hinge connecting adipose plasticity and metabolic rhythms, the two determinants of metabolic health.
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Affiliation(s)
- Ying He
- Naomi Berrie Diabetes Center, Columbia UniversityNew YorkNY10032USA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNY10032USA
| | | | - Lexiang Yu
- Naomi Berrie Diabetes Center, Columbia UniversityNew YorkNY10032USA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNY10032USA
| | - Yifan Yao
- Department of NeuroscienceBarnard CollegeNew YorkNY10027USA
| | - Ruotong Zhang
- Naomi Berrie Diabetes Center, Columbia UniversityNew YorkNY10032USA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNY10032USA
| | - Tarik Zahr
- Naomi Berrie Diabetes Center, Columbia UniversityNew YorkNY10032USA
- Department of Molecular Pharmacology and TherapeuticsColumbia UniversityNew YorkNY10032USA
| | - Nicole Aaron
- Naomi Berrie Diabetes Center, Columbia UniversityNew YorkNY10032USA
- Department of Molecular Pharmacology and TherapeuticsColumbia UniversityNew YorkNY10032USA
| | | | - Lihong Fan
- Naomi Berrie Diabetes Center, Columbia UniversityNew YorkNY10032USA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNY10032USA
| | - Longhua Liu
- Naomi Berrie Diabetes Center, Columbia UniversityNew YorkNY10032USA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNY10032USA
| | - Ruya Tazebay
- Department of NeuroscienceBarnard CollegeNew YorkNY10027USA
| | - Jianwen Que
- Department of MedicineColumbia UniversityNew YorkNY10032USA
| | - Utpal Pajvani
- Naomi Berrie Diabetes Center, Columbia UniversityNew YorkNY10032USA
- Department of MedicineColumbia UniversityNew YorkNY10032USA
| | - Liheng Wang
- The DiabetesObesity and Metabolism InstituteThe Icahn School of Medicine at Mount SinaiNew YorkNY10029USA
| | - Rae Silver
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNY10032USA
- Department of PsychologyColumbia UniversityNew YorkNY10027USA
- Department of NeuroscienceBarnard CollegeNew YorkNY10027USA
| | - Li Qiang
- Naomi Berrie Diabetes Center, Columbia UniversityNew YorkNY10032USA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNY10032USA
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38
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Scott MR, Zong W, Ketchesin KD, Seney ML, Tseng GC, Zhu B, McClung CA. Twelve-hour rhythms in transcript expression within the human dorsolateral prefrontal cortex are altered in schizophrenia. PLoS Biol 2023; 21:e3001688. [PMID: 36693045 PMCID: PMC9873190 DOI: 10.1371/journal.pbio.3001688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 12/01/2022] [Indexed: 01/25/2023] Open
Abstract
Twelve-hour (12 h) ultradian rhythms are a well-known phenomenon in coastal marine organisms. While 12 h cycles are observed in human behavior and physiology, no study has measured 12 h rhythms in the human brain. Here, we identify 12 h rhythms in transcripts that either peak at sleep/wake transitions (approximately 9 AM/PM) or static times (approximately 3 PM/AM) in the dorsolateral prefrontal cortex, a region involved in cognition. Subjects with schizophrenia (SZ) lose 12 h rhythms in genes associated with the unfolded protein response and neuronal structural maintenance. Moreover, genes involved in mitochondrial function and protein translation, which normally peak at sleep/wake transitions, peak instead at static times in SZ, suggesting suboptimal timing of these essential processes.
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Affiliation(s)
- Madeline R. Scott
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Wei Zong
- Department of Bioinformatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kyle D. Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Marianne L. Seney
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - George C. Tseng
- Department of Bioinformatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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39
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Xue X, Zong W, Huo Z, Ketchesin KD, Scott MR, Petersen KA, Logan RW, Seney ML, McClung C, Tseng G. DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity. Bioinformatics 2023; 39:btad039. [PMID: 36655766 PMCID: PMC9889843 DOI: 10.1093/bioinformatics/btad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
SUMMARY Circadian oscillations of gene expression regulate daily physiological processes, and their disruption is linked to many diseases. Circadian rhythms can be disrupted in a variety of ways, including differential phase, amplitude and rhythm fitness. Although many differential circadian biomarker detection methods have been proposed, a workflow for systematic detection of multifaceted differential circadian characteristics with accurate false positive control is not currently available. We propose a comprehensive and interactive pipeline to capture the multifaceted characteristics of differentially rhythmic biomarkers. Analysis outputs are accompanied by informative visualization and interactive exploration. The workflow is demonstrated in multiple case studies and is extensible to general omics applications. AVAILABILITY AND IMPLEMENTATION R package, Shiny app and source code are available in GitHub (https://github.com/DiffCircaPipeline) and Zenodo (https://doi.org/10.5281/zenodo.7507989). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiangning Xue
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wei Zong
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, USA
| | - Kyle D Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Madeline R Scott
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Kaitlyn A Petersen
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Ryan W Logan
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marianne L Seney
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Colleen McClung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - George Tseng
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA 15213, USA
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40
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Lower morning levels of cortisol and neuropeptides in blood samples from patients with bipolar disorder. JOURNAL OF AFFECTIVE DISORDERS REPORTS 2022. [DOI: 10.1016/j.jadr.2022.100406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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41
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Srinivasan M, Walker C. Circadian Clock, Glucocorticoids and NF-κB Signaling in Neuroinflammation- Implicating Glucocorticoid Induced Leucine Zipper as a Molecular Link. ASN Neuro 2022; 14:17590914221120190. [PMID: 36317290 PMCID: PMC9629546 DOI: 10.1177/17590914221120190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Inflammation including neuroinflammation is considered a protective response and is directed to repair, regenerate, and restore damaged tissues in the central nervous system. Persistent inflammation due to chronic stress, age related accrual of free radicals, subclinical infections or other factors lead to reduced survival and increased neuronal death. Circadian abnormalities secondary to altered sleep/wake cycles is one of the earliest signs of neurodegenerative diseases. Brain specific or global deficiency of core circadian trans-activator brain and muscle ARNT (Arylhydrocarbon Receptor Nuclear Translocator)-like protein 1 (BMAL1) or that of the transrepressor REV-ERBα, impaired neural function and cognitive performance in rodents. Consistently, transcripts of inflammatory cytokines and host immune responses have been shown to exhibit diurnal variation, in parallel with the disruption of the circadian rhythm. Glucocorticoids that exhibit both a circadian rhythm similar to that of the core clock transactivator BMAL1 and tissue specific ultradian rhythm are critical in the control of neuroinflammation and re-establishment of homeostasis. It is widely accepted that the glucocorticoids suppress nuclear factor-kappa B (NF-κB) mediated transactivation and suppress inflammation. Recent mechanistic elucidations suggest that the core clock components also modulate NF-κB mediated transactivation in the brain and peripheral tissues. In this review we discuss evidence for interactions between the circadian clock components, glucocorticoids and NF-κB signaling responses in the brain and propose glucocorticoid induced leucine zipper (GILZ) encoded by Tsc22d3, as a molecular link that connect all three pathways in the maintenance of CNS homeostasis as well as in the pathogenesis of neuroinflammation-neurodegeneration.
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Affiliation(s)
- Mythily Srinivasan
- Department of Oral Pathology, Medicine and Radiology, Indiana University School of Dentistry, Indiana University Purdue University at Indianapolis, Indiana, USA,Provaidya LLC, Indiana Center for Biomedical Innovation, Indianapolis, Indiana, USA,Mythily Srinivasan, Oral Pathology, Radiology and Medicine, Indiana University School of Dentistry, Indianapolis, Indiana, United States; Provaidya LLC, Indiana Center for Biomedical Innovation, 1800 North Capitol Av, Indianapolis, IN 46202, United States.
;
| | - Chandler Walker
- Department of Oral Pathology, Medicine and Radiology, Indiana University School of Dentistry, Indiana University Purdue University at Indianapolis, Indiana, USA,Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indiana University Purdue University at Indianapolis, Indiana, USA
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42
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Loss of thyroid gland circadian PER2 rhythmicity in aged mice and its potential association with thyroid cancer development. Cell Death Dis 2022; 13:898. [PMID: 36284088 PMCID: PMC9596494 DOI: 10.1038/s41419-022-05342-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/28/2022]
Abstract
Molecular clocks operate in peripheral tissues, including endocrine glands, and play important regulatory roles in this context. However, potential age-related changes in the expression rhythmicity of clock genes and the effects of these changes on the thyroid gland remain unknown. In the present study, we evaluated the expression rhythmicity of peripheral thyroid clock genes in aged mice using RNA-seq transcriptomic analysis in young (3.5-month) versus aged (20-month) mice. In addition, we determined the cellular effects of silencing of PER2, a major clock gene regulator, in human thyroid cell lines. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that differentially expressed genes (DEGs) in the thyroid glands of aged mice were involved in mitogen-activated protein kinase (MAPK) signaling, chemokine signaling, circadian entrainment, PI3K/AKT signaling, and Apelin signaling. The expression of circadian clock genes Arntl/Bmal1 was significantly downregulated in thyroid glands of aged mice, whereas the expression of genes involved in regulation of cell proliferation, migration, and tumorigenesis was upregulated. Peripheral thyroid clock genes, particularly Per mRNA and PER2 protein, were downregulated in the thyroid glands of aged mice, and circadian oscillation of these genes was declined. Knockdown of the circadian clock gene PER2 in human thyroid follicular cells induced AP-1 activity via JNK MAPK signaling activation, which increased cell proliferation. Furthermore, the aging-related loss of PER2 circadian oscillation activated the AP-1 transcription factor via the JNK MAPK pathway, which could contribute to thyroid hyperplasia, a common age-related condition.
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43
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Valeri J, O’Donovan SM, Wang W, Sinclair D, Bollavarapu R, Gisabella B, Platt D, Stockmeier C, Pantazopoulos H. Altered expression of somatostatin signaling molecules and clock genes in the hippocampus of subjects with substance use disorder. Front Neurosci 2022; 16:903941. [PMID: 36161151 PMCID: PMC9489843 DOI: 10.3389/fnins.2022.903941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Substance use disorders are a debilitating group of psychiatric disorders with a high degree of comorbidity with major depressive disorder. Sleep and circadian rhythm disturbances are commonly reported in people with substance use disorder and major depression and associated with increased risk of relapse. Hippocampal somatostatin signaling is involved in encoding and consolidation of contextual memories which contribute to relapse in substance use disorder. Somatostatin and clock genes also have been implicated in depression, suggesting that these molecules may represent key converging pathways involved in contextual memory processing in substance use and major depression. We used hippocampal tissue from a cohort of subjects with substance use disorder (n = 20), subjects with major depression (n = 20), subjects with comorbid substance use disorder and major depression (n = 24) and psychiatrically normal control subjects (n = 20) to test the hypothesis that expression of genes involved in somatostatin signaling and clock genes is altered in subjects with substance use disorder. We identified decreased expression of somatostatin in subjects with substance use disorder and in subjects with major depression. We also observed increased somatostatin receptor 2 expression in subjects with substance use disorder with alcohol in the blood at death and decreased expression in subjects with major depression. Expression of the clock genes Arntl, Nr1d1, Per2 and Cry2 was increased in subjects with substance use disorder. Arntl and Nr1d1 expression in comparison was decreased in subjects with major depression. We observed decreased expression of Gsk3β in subjects with substance use disorder. Subjects with comorbid substance use disorder and major depression displayed minimal changes across all outcome measures. Furthermore, we observed a significant increase in history of sleep disturbances in subjects with substance use disorder. Our findings represent the first evidence for altered somatostatin and clock gene expression in the hippocampus of subjects with substance use disorder and subjects with major depression. Altered expression of these molecules may impact memory consolidation and contribute to relapse risk.
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Affiliation(s)
- Jake Valeri
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, MS, United States
| | - Sinead M. O’Donovan
- Department of Neuroscience, University of Toledo Medical Center, Toledo, OH, United States
| | - Wei Wang
- Department of Medicine and Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - David Sinclair
- Department of Neuroscience, University of Toledo Medical Center, Toledo, OH, United States
| | - Ratna Bollavarapu
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
| | - Barbara Gisabella
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, MS, United States
| | - Donna Platt
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, MS, United States
| | - Craig Stockmeier
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, MS, United States
| | - Harry Pantazopoulos
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, MS, United States
- *Correspondence: Harry Pantazopoulos,
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Common Ground between Biological Rhythms and Forensics. BIOLOGY 2022; 11:biology11071071. [PMID: 36101448 PMCID: PMC9312156 DOI: 10.3390/biology11071071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Biological clocks regulate the timing of numerous body functions in adaption to daily repeating cycles in the environment, such as the sleep–wake phases that are trained by the cycling changes of night and day light. The identification of a deceased victim is a critical component in a forensic investigation, but it can be significantly hampered by the condition of the dead body and the lack of personal records and documents. This review links current knowledge on the molecular mechanisms of biological rhythms to forensically relevant aspects, including the time period since death, cause of death, the use of insects for forensics, sex and age of a person, ethnic background and development. Putting these findings in context demonstrates how the analysis of molecular clock analysis could be used as tool for future personal identification in forensic investigations. Abstract Biological clocks set the timing for a large number of essential processes in the living human organism. After death, scientific evidence is required in forensic investigations in order to collect as much information as possible on the death circumstances and personal identifiers of the deceased victim. We summarize the associations between the molecular mechanisms of biological rhythms and forensically relevant aspects, including post-mortem interval and cause of death, entomological findings, sex, age, ethnicity and development. Given their importance during lifetime, biological rhythms could be potential tools to draw conclusions on the death circumstances and the identity of a deceased person by mechanistic investigations of the different biological clocks in a forensic context. This review puts the known effects of biological rhythms on the functions of the human organism in context with potential applications in forensic fields of interest, such as personal identification, entomology as well as the determination of the post-mortem interval and cause of death.
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Real age prediction from the transcriptome with RAPToR. Nat Methods 2022; 19:969-975. [PMID: 35817937 DOI: 10.1038/s41592-022-01540-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/25/2022] [Indexed: 11/08/2022]
Abstract
Transcriptomic data is often affected by uncontrolled variation among samples that can obscure and confound the effects of interest. This variation is frequently due to unintended differences in developmental stages between samples. The transcriptome itself can be used to estimate developmental progression, but existing methods require many samples and do not estimate a specimen's real age. Here we present real-age prediction from transcriptome staging on reference (RAPToR), a computational method that precisely estimates the real age of a sample from its transcriptome, exploiting existing time-series data as reference. RAPToR works with whole animal, dissected tissue and single-cell data for the most common animal models, humans and even for non-model organisms lacking reference data. We show that RAPToR can be used to remove age as a confounding factor and allow recovery of a signal of interest in differential expression analysis. RAPToR will be especially useful in large-scale single-organism profiling because it eliminates the need for accurate staging or synchronisation before profiling.
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Fernández-Ortiz M, Sayed RKA, Román-Montoya Y, de Lama MÁR, Fernández-Martínez J, Ramírez-Casas Y, Florido-Ruiz J, Rusanova I, Escames G, Acuña-Castroviejo D. Age and Chronodisruption in Mouse Heart: Effect of the NLRP3 Inflammasome and Melatonin Therapy. Int J Mol Sci 2022; 23:ijms23126846. [PMID: 35743288 PMCID: PMC9224376 DOI: 10.3390/ijms23126846] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/13/2022] [Accepted: 06/18/2022] [Indexed: 02/04/2023] Open
Abstract
Age and age-dependent inflammation are two main risk factors for cardiovascular diseases. Aging can also affect clock gene-related impairments such as chronodisruption and has been linked to a decline in melatonin synthesis and aggravation of the NF-κB/NLRP3 innate immune response known as inflammaging. The molecular drivers of these mechanisms remain unknown. This study investigated the impact of aging and NLRP3 expression on the cardiac circadian system, and the actions of melatonin as a potential therapy to restore daily rhythms by mitigating inflammaging. We analyzed the circadian expression and rhythmicity of clock genes in heart tissue of wild-type and NLRP3-knockout mice at 3, 12, and 24 months of age, with and without melatonin treatment. Our results support that aging, NLRP3 inflammasome, and melatonin affected the cardiac clock genes expression, except for Rev-erbα, which was not influenced by genotype. Aging caused small phase changes in Clock, loss of rhythmicity in Per2 and Rorα, and mesor dampening of Clock, Bmal1, and Per2. NLRP3 inflammasome influenced the acrophase of Clock, Per2, and Rorα. Melatonin restored the acrophase and the rhythm of clock genes affected by age or NLRP3 activation. The administration of melatonin re-established murine cardiac homeostasis by reversing age-associated chronodisruption. Altogether, these results highlight new findings about the effects aging and NLRP3 inflammasome have on clock genes in cardiac tissue, pointing to continuous melatonin as a promising therapy to placate inflammaging and restore circadian rhythm in heart muscle. Additionally, light microscopy analysis showed age-related morphological impairments in cardiomyocytes, which were less severe in mice lacking NLRP3. Melatonin supplementation preserved the structure of cardiac muscle fibers in all experimental groups.
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Affiliation(s)
- Marisol Fernández-Ortiz
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain; (M.F.-O.); (R.K.A.S.); (J.F.-M.); (Y.R.-C.); (J.F.-R.); (I.R.); (G.E.)
- Department of Pediatrics, Division of Hematology-Oncology, Greehey Children’s Cancer Research Institute, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
- Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Investigación Biosanitaria de Granada (Ibs), 18012 Granada, Spain
| | - Ramy K. A. Sayed
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain; (M.F.-O.); (R.K.A.S.); (J.F.-M.); (Y.R.-C.); (J.F.-R.); (I.R.); (G.E.)
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Sohag University, Sohag 82524, Egypt
| | - Yolanda Román-Montoya
- Departamento de Estadística e Investigación Operativa, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - María Ángeles Rol de Lama
- Chronobiology Lab, Department of Physiology, College of Biology, University of Murcia, Mare Nostrum Campus, IUIE, IMIB–Arrixaca, 30100 Murcia, Spain;
| | - José Fernández-Martínez
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain; (M.F.-O.); (R.K.A.S.); (J.F.-M.); (Y.R.-C.); (J.F.-R.); (I.R.); (G.E.)
| | - Yolanda Ramírez-Casas
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain; (M.F.-O.); (R.K.A.S.); (J.F.-M.); (Y.R.-C.); (J.F.-R.); (I.R.); (G.E.)
| | - Javier Florido-Ruiz
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain; (M.F.-O.); (R.K.A.S.); (J.F.-M.); (Y.R.-C.); (J.F.-R.); (I.R.); (G.E.)
| | - Iryna Rusanova
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain; (M.F.-O.); (R.K.A.S.); (J.F.-M.); (Y.R.-C.); (J.F.-R.); (I.R.); (G.E.)
- Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Investigación Biosanitaria de Granada (Ibs), 18012 Granada, Spain
| | - Germaine Escames
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain; (M.F.-O.); (R.K.A.S.); (J.F.-M.); (Y.R.-C.); (J.F.-R.); (I.R.); (G.E.)
- Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Investigación Biosanitaria de Granada (Ibs), 18012 Granada, Spain
| | - Darío Acuña-Castroviejo
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain; (M.F.-O.); (R.K.A.S.); (J.F.-M.); (Y.R.-C.); (J.F.-R.); (I.R.); (G.E.)
- Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Investigación Biosanitaria de Granada (Ibs), 18012 Granada, Spain
- UGC de Laboratorios Clínicos, Hospital Universitario San Cecilio, 18016 Granada, Spain
- Correspondence: ; Tel.: +34-958241000 (ext. 20196)
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McCarthy MJ, Gottlieb JF, Gonzalez R, McClung CA, Alloy LB, Cain S, Dulcis D, Etain B, Frey BN, Garbazza C, Ketchesin KD, Landgraf D, Lee H, Marie‐Claire C, Nusslock R, Porcu A, Porter R, Ritter P, Scott J, Smith D, Swartz HA, Murray G. Neurobiological and behavioral mechanisms of circadian rhythm disruption in bipolar disorder: A critical multi-disciplinary literature review and agenda for future research from the ISBD task force on chronobiology. Bipolar Disord 2022; 24:232-263. [PMID: 34850507 PMCID: PMC9149148 DOI: 10.1111/bdi.13165] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AIM Symptoms of bipolar disorder (BD) include changes in mood, activity, energy, sleep, and appetite. Since many of these processes are regulated by circadian function, circadian rhythm disturbance has been examined as a biological feature underlying BD. The International Society for Bipolar Disorders Chronobiology Task Force (CTF) was commissioned to review evidence for neurobiological and behavioral mechanisms pertinent to BD. METHOD Drawing upon expertise in animal models, biomarkers, physiology, and behavior, CTF analyzed the relevant cross-disciplinary literature to precisely frame the discussion around circadian rhythm disruption in BD, highlight key findings, and for the first time integrate findings across levels of analysis to develop an internally consistent, coherent theoretical framework. RESULTS Evidence from multiple sources implicates the circadian system in mood regulation, with corresponding associations with BD diagnoses and mood-related traits reported across genetic, cellular, physiological, and behavioral domains. However, circadian disruption does not appear to be specific to BD and is present across a variety of high-risk, prodromal, and syndromic psychiatric disorders. Substantial variability and ambiguity among the definitions, concepts and assumptions underlying the research have limited replication and the emergence of consensus findings. CONCLUSIONS Future research in circadian rhythms and its role in BD is warranted. Well-powered studies that carefully define associations between BD-related and chronobiologically-related constructs, and integrate across levels of analysis will be most illuminating.
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Affiliation(s)
- Michael J. McCarthy
- UC San Diego Department of Psychiatry & Center for Circadian BiologyLa JollaCaliforniaUSA
- VA San Diego Healthcare SystemSan DiegoCaliforniaUSA
| | - John F. Gottlieb
- Department of PsychiatryFeinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Robert Gonzalez
- Department of Psychiatry and Behavioral HealthPennsylvania State UniversityHersheyPennsylvaniaUSA
| | - Colleen A. McClung
- Department of PsychiatryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Lauren B. Alloy
- Department of PsychologyTemple UniversityPhiladelphiaPennsylvaniaUSA
| | - Sean Cain
- School of Psychological Sciences and Turner Institute for Brain and Mental HealthMonash UniversityMelbourneVictoriaAustralia
| | - Davide Dulcis
- UC San Diego Department of Psychiatry & Center for Circadian BiologyLa JollaCaliforniaUSA
| | - Bruno Etain
- Université de ParisINSERM UMR‐S 1144ParisFrance
| | - Benicio N. Frey
- Department Psychiatry and Behavioral NeuroscienceMcMaster UniversityHamiltonOntarioCanada
| | - Corrado Garbazza
- Centre for ChronobiologyPsychiatric Hospital of the University of Basel and Transfaculty Research Platform Molecular and Cognitive NeurosciencesUniversity of BaselBaselSwitzerland
| | - Kyle D. Ketchesin
- Department of PsychiatryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Dominic Landgraf
- Circadian Biology GroupDepartment of Molecular NeurobiologyClinic of Psychiatry and PsychotherapyUniversity HospitalLudwig Maximilian UniversityMunichGermany
| | - Heon‐Jeong Lee
- Department of Psychiatry and Chronobiology InstituteKorea UniversitySeoulSouth Korea
| | | | - Robin Nusslock
- Department of Psychology and Institute for Policy ResearchNorthwestern UniversityChicagoIllinoisUSA
| | - Alessandra Porcu
- UC San Diego Department of Psychiatry & Center for Circadian BiologyLa JollaCaliforniaUSA
| | | | - Philipp Ritter
- Clinic for Psychiatry and PsychotherapyCarl Gustav Carus University Hospital and Technical University of DresdenDresdenGermany
| | - Jan Scott
- Institute of NeuroscienceNewcastle UniversityNewcastleUK
| | - Daniel Smith
- Division of PsychiatryUniversity of EdinburghEdinburghUK
| | - Holly A. Swartz
- Department of PsychiatryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Greg Murray
- Centre for Mental HealthSwinburne University of TechnologyMelbourneVictoriaAustralia
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Clavere NG, Alqallaf A, Rostron KA, Parnell A, Mitchell R, Patel K, Boateng SY. Inhibition of activin A receptor signalling attenuates age-related pathological cardiac remodelling. Dis Model Mech 2022; 15:275323. [PMID: 35380160 PMCID: PMC9118092 DOI: 10.1242/dmm.049424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/16/2022] [Indexed: 11/20/2022] Open
Abstract
In the heart, ageing is associated with DNA damage, oxidative stress, fibrosis and activation of the activin signalling pathway, leading to cardiac dysfunction. The cardiac effects of activin signalling blockade in progeria are unknown. This study investigated the cardiac effects of progeria induced by attenuated levels of Ercc1, which is required for DNA excision and repair, and the impact of activin signalling blockade using a soluble activin receptor type IIB (sActRIIB). DNA damage and oxidative stress were significantly increased in Ercc1Δ/− hearts, but were reduced by sActRIIB treatment. sActRIIB treatment improved cardiac systolic function and induced cardiomyocyte hypertrophy in Ercc1Δ/− hearts. RNA-sequencing analysis showed that in Ercc1Δ/− hearts, there was an increase in pro-oxidant and a decrease in antioxidant gene expression, whereas sActRIIB treatment reversed this effect. Ercc1Δ/− hearts also expressed higher levels of anti-hypertrophic genes and decreased levels of pro-hypertrophic ones, which were also reversed by sActRIIB treatment. These results show for the first time that inhibition of activin A receptor signalling attenuates cardiac dysfunction, pathological tissue remodelling and gene expression in Ercc1-deficient mice and presents a potentially novel therapeutic target for heart diseases. Summary: Attenuated DNA repair is associated with pathological cardiac remodelling and gene expression. Much of this phenotype is attenuated by inhibition of the activin signalling pathway using soluble activin receptor treatment.
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Affiliation(s)
- Nicolas G Clavere
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Ali Alqallaf
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Kerry A Rostron
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Commonwealth Building, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Andrew Parnell
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Robert Mitchell
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Ketan Patel
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Samuel Y Boateng
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
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Xue X, Zong W, Glausier JR, Kim SM, Shelton MA, Phan BN, Srinivasan C, Pfenning AR, Tseng GC, Lewis DA, Seney ML, Logan RW. Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder. Transl Psychiatry 2022; 12:123. [PMID: 35347109 PMCID: PMC8960783 DOI: 10.1038/s41398-022-01894-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 11/21/2022] Open
Abstract
Severe and persistent disruptions to sleep and circadian rhythms are common in people with opioid use disorder (OUD). Preclinical evidence suggests altered molecular rhythms in the brain modulate opioid reward and relapse. However, whether molecular rhythms are disrupted in the brains of people with OUD remained an open question, critical to understanding the role of circadian rhythms in opioid addiction. Using subjects' times of death as a marker of time of day, we investigated transcriptional rhythms in the brains of subjects with OUD compared to unaffected comparison subjects. We discovered rhythmic transcripts in both the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc), key brain areas involved in OUD, that were largely distinct between OUD and unaffected subjects. Fewer rhythmic transcripts were identified in DLPFC of subjects with OUD compared to unaffected subjects, whereas in the NAc, nearly double the number of rhythmic transcripts was identified in subjects with OUD. In NAc of subjects with OUD, rhythmic transcripts peaked either in the evening or near sunrise, and were associated with an opioid, dopamine, and GABAergic neurotransmission. Associations with altered neurotransmission in NAc were further supported by co-expression network analysis which identified OUD-specific modules enriched for transcripts involved in dopamine, GABA, and glutamatergic synaptic functions. Additionally, rhythmic transcripts in DLPFC and NAc of subjects with OUD were enriched for genomic loci associated with sleep-related GWAS traits, including sleep duration and insomnia. Collectively, our findings connect transcriptional rhythm changes in opioidergic, dopaminergic, GABAergic signaling in the human brain to sleep-related traits in opioid addiction.
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Affiliation(s)
- Xiangning Xue
- grid.21925.3d0000 0004 1936 9000Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Wei Zong
- grid.21925.3d0000 0004 1936 9000Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Jill R. Glausier
- grid.21925.3d0000 0004 1936 9000Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219 USA
| | - Sam-Moon Kim
- grid.21925.3d0000 0004 1936 9000Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219 USA ,grid.21925.3d0000 0004 1936 9000Center for Adolescent Reward, Rhythms, and Sleep, University of Pittsburgh, Pittsburgh, PA 15219 USA
| | - Micah A. Shelton
- grid.21925.3d0000 0004 1936 9000Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219 USA
| | - BaDoi N. Phan
- grid.147455.60000 0001 2097 0344Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213 USA
| | - Chaitanya Srinivasan
- grid.147455.60000 0001 2097 0344Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213 USA
| | - Andreas R. Pfenning
- grid.147455.60000 0001 2097 0344Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213 USA ,grid.147455.60000 0001 2097 0344Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213 USA
| | - George C. Tseng
- grid.21925.3d0000 0004 1936 9000Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - David A. Lewis
- grid.21925.3d0000 0004 1936 9000Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219 USA
| | - Marianne L. Seney
- grid.21925.3d0000 0004 1936 9000Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219 USA ,grid.21925.3d0000 0004 1936 9000Center for Adolescent Reward, Rhythms, and Sleep, University of Pittsburgh, Pittsburgh, PA 15219 USA
| | - Ryan W. Logan
- grid.189504.10000 0004 1936 7558Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558Center for Systems Neuroscience, Boston University, Boston, MA 02118 USA
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Govoni S, Fagiani F, Lanni C, Allegri N. The Frailty Puzzle: Searching for Immortality or for Knowledge Survival? Front Cell Neurosci 2022; 16:838447. [PMID: 35250489 PMCID: PMC8891148 DOI: 10.3389/fncel.2022.838447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/25/2022] [Indexed: 12/18/2022] Open
Abstract
What is the value of assessing the biological age and frailty and predicting residual lifespan and health status? The benefit is obvious if we have means to alter the pace of aging and the development of frailty. So far, limited but increasing examples of interventions altering the predicted status indicate that, at least in some cases, this is possible through interventions spanning from the economic-social through drug treatments. Thus, why searching for biological markers, when some clinical and socio-economic indicators do already provide sufficiently accurate predictions? Indeed, the search of frailty biomarkers and of their biological clocks helps to build up a mechanistic frame that may orientate the design of interventions and the time window of their efficacy. Among the candidate biomarkers identified, several studies converge to indicate epigenetic clocks as a promising sensitive biomarker of the aging process. Moreover, it will help to establish the relationship between personal aging and health trajectories and to individuate the check points beyond which biological changes are irreversible.
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Affiliation(s)
- Stefano Govoni
- Department of Drug Sciences (Pharmacology Section), University of Pavia, Pavia, Italy
- CEFAT (Center of Pharmaceuticals Economics and Medical Technologies Evaluation), University of Pavia, Pavia, Italy
| | - Francesca Fagiani
- Department of Drug Sciences (Pharmacology Section), University of Pavia, Pavia, Italy
| | - Cristina Lanni
- Department of Drug Sciences (Pharmacology Section), University of Pavia, Pavia, Italy
| | - Nicola Allegri
- CEFAT (Center of Pharmaceuticals Economics and Medical Technologies Evaluation), University of Pavia, Pavia, Italy
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