101
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Di Paolo A, Garat J, Eastman G, Farias J, Dajas-Bailador F, Smircich P, Sotelo-Silveira JR. Functional Genomics of Axons and Synapses to Understand Neurodegenerative Diseases. Front Cell Neurosci 2021; 15:686722. [PMID: 34248504 PMCID: PMC8267896 DOI: 10.3389/fncel.2021.686722] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 01/02/2023] Open
Abstract
Functional genomics studies through transcriptomics, translatomics and proteomics have become increasingly important tools to understand the molecular basis of biological systems in the last decade. In most cases, when these approaches are applied to the nervous system, they are centered in cell bodies or somatodendritic compartments, as these are easier to isolate and, at least in vitro, contain most of the mRNA and proteins present in all neuronal compartments. However, key functional processes and many neuronal disorders are initiated by changes occurring far away from cell bodies, particularly in axons (axopathologies) and synapses (synaptopathies). Both neuronal compartments contain specific RNAs and proteins, which are known to vary depending on their anatomical distribution, developmental stage and function, and thus form the complex network of molecular pathways required for neuron connectivity. Modifications in these components due to metabolic, environmental, and/or genetic issues could trigger or exacerbate a neuronal disease. For this reason, detailed profiling and functional understanding of the precise changes in these compartments may thus yield new insights into the still intractable molecular basis of most neuronal disorders. In the case of synaptic dysfunctions or synaptopathies, they contribute to dozens of diseases in the human brain including neurodevelopmental (i.e., autism, Down syndrome, and epilepsy) as well as neurodegenerative disorders (i.e., Alzheimer's and Parkinson's diseases). Histological, biochemical, cellular, and general molecular biology techniques have been key in understanding these pathologies. Now, the growing number of omics approaches can add significant extra information at a high and wide resolution level and, used effectively, can lead to novel and insightful interpretations of the biological processes at play. This review describes current approaches that use transcriptomics, translatomics and proteomic related methods to analyze the axon and presynaptic elements, focusing on the relationship that axon and synapses have with neurodegenerative diseases.
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Affiliation(s)
- Andres Di Paolo
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Proteínas y Ácidos Nucleicos, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquin Garat
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Guillermo Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Polo de Desarrollo Universitario “Espacio de Biología Vegetal del Noreste”, Centro Universitario Regional Noreste, Universidad de la República (UdelaR), Tacuarembó, Uruguay
| | - Federico Dajas-Bailador
- School of Life Sciences, Medical School Building, University of Nottingham, Nottingham, United Kingdom
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - José Roberto Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
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102
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Puentes-Mestril C, Delorme J, Wang L, Donnelly M, Popke D, Jiang S, Aton SJ. Sleep Loss Drives Brain Region-Specific and Cell Type-Specific Alterations in Ribosome-Associated Transcripts Involved in Synaptic Plasticity and Cellular Timekeeping. J Neurosci 2021; 41:5386-5398. [PMID: 34001629 PMCID: PMC8221591 DOI: 10.1523/jneurosci.1883-20.2021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 03/07/2021] [Accepted: 03/24/2021] [Indexed: 12/22/2022] Open
Abstract
Sleep and sleep loss are thought to impact synaptic plasticity, and recent studies have shown that sleep and sleep deprivation (SD) differentially affect gene transcription and protein translation in the mammalian forebrain. However, much less is known regarding how sleep and SD affect these processes in different microcircuit elements within the hippocampus and neocortex, for example, in inhibitory versus excitatory neurons. Here, we use translating ribosome affinity purification (TRAP) and in situ hybridization to characterize the effects of sleep versus SD on abundance of ribosome-associated transcripts in Camk2a-expressing (Camk2a+) pyramidal neurons and parvalbumin-expressing (PV+) interneurons in the hippocampus and neocortex of male mice. We find that while both Camk2a+ neurons and PV+ interneurons in neocortex show concurrent SD-driven increases in ribosome-associated transcripts for activity-regulated effectors of plasticity and transcriptional regulation, these transcripts are minimally affected by SD in hippocampus. Similarly, we find that while SD alters several ribosome-associated transcripts involved in cellular timekeeping in neocortical Camk2a+ and PV+ neurons, effects on circadian clock transcripts in hippocampus are minimal, and restricted to Camk2a+ neurons. Taken together, our results indicate that SD effects on transcripts associated with translating ribosomes are both cell type-specific and brain region-specific, and that these effects are substantially more pronounced in the neocortex than the hippocampus. We conclude that SD-driven alterations in the strength of synapses, excitatory-inhibitory (E-I) balance, and cellular timekeeping are likely more heterogeneous than previously appreciated.SIGNIFICANCE STATEMENT Sleep loss-driven changes in transcript and protein abundance have been used as a means to better understand the function of sleep for the brain. Here, we use translating ribosome affinity purification (TRAP) to characterize changes in abundance of ribosome-associated transcripts in excitatory and inhibitory neurons in mouse hippocampus and neocortex after a brief period of sleep or sleep loss. We show that these changes are not uniform, but are generally more pronounced in excitatory neurons than inhibitory neurons, and more pronounced in neocortex than in hippocampus.
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Affiliation(s)
- Carlos Puentes-Mestril
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48019
| | - James Delorme
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48019
| | - Lijing Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48019
| | - Marcus Donnelly
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48019
| | - Donald Popke
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48019
| | - Sha Jiang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48019
| | - Sara J Aton
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48019
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103
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Joye DAM, Evans JA. Sex differences in daily timekeeping and circadian clock circuits. Semin Cell Dev Biol 2021; 126:45-55. [PMID: 33994299 DOI: 10.1016/j.semcdb.2021.04.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/24/2021] [Accepted: 04/29/2021] [Indexed: 11/19/2022]
Abstract
The circadian system regulates behavior and physiology in many ways important for health. Circadian rhythms are expressed by nearly every cell in the body, and this large system is coordinated by a central clock in the suprachiasmatic nucleus (SCN). Sex differences in daily rhythms are evident in humans and understanding how circadian function is modulated by biological sex is an important goal. This review highlights work examining effects of sex and gonadal hormones on daily rhythms, with a focus on behavior and SCN circuitry in animal models commonly used in pre-clinical studies. Many questions remain in this area of the field, which would benefit from further work investigating this topic.
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Affiliation(s)
- Deborah A M Joye
- Marquette University, Department of Biomedical Sciences, Milwaukee, WI, USA
| | - Jennifer A Evans
- Marquette University, Department of Biomedical Sciences, Milwaukee, WI, USA.
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104
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Karoly PJ, Rao VR, Gregg NM, Worrell GA, Bernard C, Cook MJ, Baud MO. Cycles in epilepsy. Nat Rev Neurol 2021; 17:267-284. [PMID: 33723459 DOI: 10.1038/s41582-021-00464-1] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 01/31/2023]
Abstract
Epilepsy is among the most dynamic disorders in neurology. A canonical view holds that seizures, the characteristic sign of epilepsy, occur at random, but, for centuries, humans have looked for patterns of temporal organization in seizure occurrence. Observations that seizures are cyclical date back to antiquity, but recent technological advances have, for the first time, enabled cycles of seizure occurrence to be quantitatively characterized with direct brain recordings. Chronic recordings of brain activity in humans and in animals have yielded converging evidence for the existence of cycles of epileptic brain activity that operate over diverse timescales: daily (circadian), multi-day (multidien) and yearly (circannual). Here, we review this evidence, synthesizing data from historical observational studies, modern implanted devices, electronic seizure diaries and laboratory-based animal neurophysiology. We discuss advances in our understanding of the mechanistic underpinnings of these cycles and highlight the knowledge gaps that remain. The potential clinical applications of a knowledge of cycles in epilepsy, including seizure forecasting and chronotherapy, are discussed in the context of the emerging concept of seizure risk. In essence, this Review addresses the broad question of why seizures occur when they occur.
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Affiliation(s)
- Philippa J Karoly
- Graeme Clark Institute, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Vikram R Rao
- Department of Neurology, University of California, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Nicholas M Gregg
- Bioelectronics, Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Gregory A Worrell
- Bioelectronics, Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Christophe Bernard
- Aix Marseille University, Inserm, Institut de Neurosciences des Systèmes, Marseille, France
| | - Mark J Cook
- Graeme Clark Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Maxime O Baud
- Sleep-Wake-Epilepsy Center, Department of Neurology, Inselspital Bern, University Hospital, University of Bern, Bern, Switzerland. .,Center for Experimental Neurology, Department of Neurology, Inselspital Bern, University Hospital, University of Bern, Bern, Switzerland.
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105
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van Gelder CAGH, Altelaar M. Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics. Mol Cell Proteomics 2021; 20:100087. [PMID: 33933679 PMCID: PMC8167277 DOI: 10.1016/j.mcpro.2021.100087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/21/2023] Open
Abstract
One of the most fascinating features of the brain is its ability to adapt to its surroundings. Synaptic plasticity, the dynamic mechanism of functional and structural alterations in synaptic strength, is essential for brain functioning and underlies a variety of processes such as learning and memory. Although the molecular mechanisms underlying such rapid plasticity are not fully understood, a consensus exists on the important role of proteins. The study of these neuronal proteins using neuroproteomics has increased rapidly in the last decades, and advancements in MS-based proteomics have broadened our understanding of neuroplasticity exponentially. In this review, we discuss the trends in MS-based neuroproteomics for the study of synaptic protein-protein interactions and protein signaling dynamics, with a focus on sample types, different labeling and enrichment approaches, and data analysis and interpretation. We highlight studies from the last 5 years, with a focus on synapse structure, composition, functioning, or signaling and finally discuss some recent developments that could further advance the field of neuroproteomics.
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Affiliation(s)
- Charlotte A G H van Gelder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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106
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Ruggiero A, Katsenelson M, Slutsky I. Mitochondria: new players in homeostatic regulation of firing rate set points. Trends Neurosci 2021; 44:605-618. [PMID: 33865626 DOI: 10.1016/j.tins.2021.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/10/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
Neural circuit functions are stabilized by homeostatic processes at long timescales in response to changes in behavioral states, experience, and learning. However, it remains unclear which specific physiological variables are being stabilized and which cellular or neural network components compose the homeostatic machinery. At this point, most evidence suggests that the distribution of firing rates among neurons in a neuronal circuit is the key variable that is maintained around a set-point value in a process called 'firing rate homeostasis.' Here, we review recent findings that implicate mitochondria as central players in mediating firing rate homeostasis. While mitochondria are known to regulate neuronal variables such as synaptic vesicle release or intracellular calcium concentration, the mitochondrial signaling pathways that are essential for firing rate homeostasis remain largely unknown. We used basic concepts of control theory to build a framework for classifying possible components of the homeostatic machinery that stabilizes firing rate, and we particularly emphasize the potential role of sleep and wakefulness in this homeostatic process. This framework may facilitate the identification of new homeostatic pathways whose malfunctions drive instability of neural circuits in distinct brain disorders.
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Affiliation(s)
- Antonella Ruggiero
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Maxim Katsenelson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Inna Slutsky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel.
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107
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Parnell AA, De Nobrega AK, Lyons LC. Translating around the clock: Multi-level regulation of post-transcriptional processes by the circadian clock. Cell Signal 2021; 80:109904. [PMID: 33370580 PMCID: PMC8054296 DOI: 10.1016/j.cellsig.2020.109904] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022]
Abstract
The endogenous circadian clock functions to maintain optimal physiological health through the tissue specific coordination of gene expression and synchronization between tissues of metabolic processes throughout the 24 hour day. Individuals face numerous challenges to circadian function on a daily basis resulting in significant incidences of circadian disorders in the United States and worldwide. Dysfunction of the circadian clock has been implicated in numerous diseases including cancer, diabetes, obesity, cardiovascular and hepatic abnormalities, mood disorders and neurodegenerative diseases. The circadian clock regulates molecular, metabolic and physiological processes through rhythmic gene expression via transcriptional and post-transcriptional processes. Mounting evidence indicates that post-transcriptional regulation by the circadian clock plays a crucial role in maintaining tissue specific biological rhythms. Circadian regulation affecting RNA stability and localization through RNA processing, mRNA degradation, and RNA availability for translation can result in rhythmic protein synthesis, even when the mRNA transcripts themselves do not exhibit rhythms in abundance. The circadian clock also targets the initiation and elongation steps of translation through multiple pathways. In this review, the influence of the circadian clock across the levels of post-transcriptional, translation, and post-translational modifications are examined using examples from humans to cyanobacteria demonstrating the phylogenetic conservation of circadian regulation. Lastly, we briefly discuss chronotherapies and pharmacological treatments that target circadian function. Understanding the complexity and levels through which the circadian clock regulates molecular and physiological processes is important for future advancement of therapeutic outcomes.
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Affiliation(s)
- Amber A Parnell
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Aliza K De Nobrega
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Lisa C Lyons
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA.
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108
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Changes in sleep EEG with aging in humans and rodents. Pflugers Arch 2021; 473:841-851. [PMID: 33791849 PMCID: PMC8076123 DOI: 10.1007/s00424-021-02545-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/18/2022]
Abstract
Sleep is one of the most ubiquitous but also complex animal behaviors. It is regulated at the global, systems level scale by circadian and homeostatic processes. Across the 24-h day, distribution of sleep/wake activity differs between species, with global sleep states characterized by defined patterns of brain electric activity and electromyography. Sleep patterns have been most intensely investigated in mammalian species. The present review begins with a brief overview on current understandings on the regulation of sleep, and its interaction with aging. An overview on age-related variations in the sleep states and associated electrophysiology and oscillatory events in humans as well as in the most common laboratory rodents follows. We present findings observed in different studies and meta-analyses, indicating links to putative physiological changes in the aged brain. Concepts requiring a more integrative view on the role of circadian and homeostatic sleep regulatory mechanisms to explain aging in sleep are emerging.
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109
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Koronowski KB, Sassone-Corsi P. Communicating clocks shape circadian homeostasis. Science 2021; 371:371/6530/eabd0951. [PMID: 33574181 DOI: 10.1126/science.abd0951] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Circadian clocks temporally coordinate physiology and align it with geophysical time, which enables diverse life-forms to anticipate daily environmental cycles. In complex organisms, clock function originates from the molecular oscillator within each cell and builds upward anatomically into an organism-wide system. Recent advances have transformed our understanding of how clocks are connected to achieve coherence across tissues. Circadian misalignment, often imposed in modern society, disrupts coordination among clocks and has been linked to diseases ranging from metabolic syndrome to cancer. Thus, uncovering the physiological circuits whereby biological clocks achieve coherence will inform on both challenges and opportunities in human health.
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Affiliation(s)
- Kevin B Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
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110
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Sanchez RE, de la Iglesia HO. Sleep and the circadian system: The latest gossip on a tumultuous long-term relationship. Neurobiol Sleep Circadian Rhythms 2021; 10:100061. [PMID: 33665478 PMCID: PMC7906888 DOI: 10.1016/j.nbscr.2021.100061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 12/02/2022] Open
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111
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Jha PK, Bouâouda H, Kalsbeek A, Challet E. Distinct feedback actions of behavioural arousal to the master circadian clock in nocturnal and diurnal mammals. Neurosci Biobehav Rev 2021; 123:48-60. [PMID: 33440199 DOI: 10.1016/j.neubiorev.2020.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/16/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022]
Abstract
The master clock in the suprachiasmatic nucleus (SCN) of the hypothalamus provides a temporal pattern of sleep and wake that - like many other behavioural and physiological rhythms - is oppositely phased in nocturnal and diurnal animals. The SCN primarily uses environmental light, perceived through the retina, to synchronize its endogenous circadian rhythms with the exact 24 h light/dark cycle of the outside world. The light responsiveness of the SCN is maximal during the night in both nocturnal and diurnal species. Behavioural arousal during the resting period not only perturbs sleep homeostasis, but also acts as a potent non-photic synchronizing cue. The feedback action of arousal on the SCN is mediated by processes involving several brain nuclei and neurotransmitters, which ultimately change the molecular functions of SCN pacemaker cells. Arousing stimuli during the sleeping period differentially affect the circadian system of nocturnal and diurnal species, as evidenced by the different circadian windows of sensitivity to behavioural arousal. In addition, arousing stimuli reduce and increase light resetting in nocturnal and diurnal species, respectively. It is important to address further question of circadian impairments associated with shift work and trans-meridian travel not only in the standard nocturnal laboratory animals but also in diurnal animal models.
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Affiliation(s)
- Pawan Kumar Jha
- Circadian Clocks and Metabolism Team, Institute of Cellular and Integrative Neurosciences, Centre National de la Recherche Scientifique (CNRS), University of Strasbourg, France; Department of Endocrinology and Metabolism, Amsterdam University Medical Center (AUMC), University of Amsterdam, the Netherlands; Hypothalamic Integration Mechanisms, Netherlands Institute for Neuroscience, Amsterdam, the Netherlands.
| | - Hanan Bouâouda
- Circadian Clocks and Metabolism Team, Institute of Cellular and Integrative Neurosciences, Centre National de la Recherche Scientifique (CNRS), University of Strasbourg, France
| | - Andries Kalsbeek
- Department of Endocrinology and Metabolism, Amsterdam University Medical Center (AUMC), University of Amsterdam, the Netherlands; Hypothalamic Integration Mechanisms, Netherlands Institute for Neuroscience, Amsterdam, the Netherlands
| | - Etienne Challet
- Circadian Clocks and Metabolism Team, Institute of Cellular and Integrative Neurosciences, Centre National de la Recherche Scientifique (CNRS), University of Strasbourg, France
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112
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Brüning F, Humphrey SJ, Robles MS. Phosphoproteome and Proteome Sample Preparation from Mouse Tissues for Circadian Analysis. Methods Mol Biol 2021; 2130:185-193. [PMID: 33284445 DOI: 10.1007/978-1-0716-0381-9_14] [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: 06/12/2023]
Abstract
Recent advances in mass spectrometry (MS)-based quantitative proteomics now allow the identification and quantification of deep proteomes and post-translational modifications (PTMs) in relatively short times. Therefore, in the last few years, this technology has proven successful in the circadian field to characterize temporal oscillations of the proteome and more recently PTMs in cellular systems and in tissues. In this chapter, we describe a robust and simple protocol, based on the EasyPhos workflow, to enable preparation of large number of proteomes and phosphoproteomes from mouse tissues for MS-based quantitative analysis. We additionally discuss computational methods to analyze proteome and phosphoproteome time series to determine circadian oscillations.
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Affiliation(s)
- Franziska Brüning
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Medical Psychology, Faculty of Medicine, LMU, Munich, Germany
| | - Sean J Humphrey
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Maria S Robles
- Institute of Medical Psychology, Faculty of Medicine, LMU, Munich, Germany.
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113
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Lim ASP. Diurnal and seasonal molecular rhythms in the human brain and their relation to Alzheimer disease. HANDBOOK OF CLINICAL NEUROLOGY 2021; 179:271-284. [PMID: 34225968 DOI: 10.1016/b978-0-12-819975-6.00017-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Diurnal and seasonal rhythms influence many aspects of human physiology including brain function. Moreover, altered diurnal and seasonal behavioral and physiological rhythms have been linked to Alzheimer's disease and related dementias (ADRD). Understanding the molecular basis for these links may lead to identification of novel targets to mitigate the negative impact of normal and abnormal diurnal and seasonal rhythms on ADRD or to alleviate the adverse consequences of ADRD on normal diurnal and seasonal rhythms. Diurnally and seasonally rhythmic gene expression and epigenetic modification in the human neocortex may be a key mechanism underlying these links. This chapter will first review the observed epidemiological links between normal and abnormal diurnal and seasonal rhythmicity, cognitive impairment, and ADRD. Then it will review normal diurnal and seasonal rhythms of brain epigenetic modification and gene expression in model organisms. Finally, it will review evidence for diurnal and seasonal rhythms of epigenetic modification and gene expression the human brain in aging, Alzheimer's disease, and other brain disorders.
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Affiliation(s)
- Andrew S P Lim
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada.
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114
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Mills WT, Nassar NN, Ravindra D, Li X, Meffert MK. Multi-Level Regulatory Interactions between NF-κB and the Pluripotency Factor Lin28. Cells 2020; 9:E2710. [PMID: 33348917 PMCID: PMC7767241 DOI: 10.3390/cells9122710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/22/2022] Open
Abstract
An appreciation for the complex interactions between the NF-κB transcription factor and the Lin28 RNA binding protein/let-7 microRNA pathways has grown substantially over the past decade. Both the NF-κB and Lin28/let-7 pathways are master regulators impacting cell survival, growth and proliferation, and an understanding of how interfaces between these pathways participate in governing pluripotency, progenitor differentiation, and neuroplastic responses remains an emerging area of research. In this review, we provide a concise summary of the respective pathways and focus on the function of signaling interactions at both the transcriptional and post-transcriptional levels. Regulatory loops capable of providing both reinforcing and extinguishing feedback have been described. We highlight convergent findings in disparate biological systems and indicate future directions for investigation.
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Affiliation(s)
- William T. Mills
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (W.T.M.IV); (N.N.N.); (D.R.); (X.L.)
| | - Noor N. Nassar
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (W.T.M.IV); (N.N.N.); (D.R.); (X.L.)
| | - Deepa Ravindra
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (W.T.M.IV); (N.N.N.); (D.R.); (X.L.)
| | - Xinbei Li
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (W.T.M.IV); (N.N.N.); (D.R.); (X.L.)
| | - Mollie K. Meffert
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (W.T.M.IV); (N.N.N.); (D.R.); (X.L.)
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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115
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The mRNA-Binding Protein RBM3 Regulates Activity Patterns and Local Synaptic Translation in Cultured Hippocampal Neurons. J Neurosci 2020; 41:1157-1173. [PMID: 33310754 PMCID: PMC7888222 DOI: 10.1523/jneurosci.0921-20.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 10/14/2020] [Accepted: 11/12/2020] [Indexed: 12/18/2022] Open
Abstract
The activity and the metabolism of the brain change rhythmically during the day/night cycle. Such rhythmicity is also observed in cultured neurons from the suprachiasmatic nucleus, which is a critical center in rhythm maintenance. However, this issue has not been extensively studied in cultures from areas less involved in timekeeping, as the hippocampus. Using neurons cultured from the hippocampi of newborn rats (both male and female), we observed significant time-dependent changes in global activity, in synaptic vesicle dynamics, in synapse size, and in synaptic mRNA amounts. A transcriptome analysis of the neurons, performed at different times over 24 h, revealed significant changes only for RNA-binding motif 3 (Rbm3). RBM3 amounts changed, especially in synapses. RBM3 knockdown altered synaptic vesicle dynamics and changed the neuronal activity patterns. This procedure also altered local translation in synapses, albeit it left the global cellular translation unaffected. We conclude that hippocampal cultured neurons can exhibit strong changes in their activity levels over 24 h, in an RBM3-dependent fashion. SIGNIFICANCE STATEMENT This work is important in several ways. First, the discovery of relatively regular activity patterns in hippocampal cultures implies that future studies using this common model will need to take the time parameter into account, to avoid misinterpretation. Second, our work links these changes in activity strongly to RBM3, in a fashion that is independent of the canonical clock mechanisms, which is a very surprising observation. Third, we describe here probably the first molecule (RBM3) whose manipulation affects translation specifically in synapses, and not at the whole-cell level. This is a key finding for the rapidly growing field of local synaptic translation.
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116
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Lyons LC, Chatterjee S, Vanrobaeys Y, Gaine ME, Abel T. Translational changes induced by acute sleep deprivation uncovered by TRAP-Seq. Mol Brain 2020; 13:165. [PMID: 33272296 PMCID: PMC7713217 DOI: 10.1186/s13041-020-00702-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Sleep deprivation is a global health problem adversely affecting health as well as causing decrements in learning and performance. Sleep deprivation induces significant changes in gene transcription in many brain regions, with the hippocampus particularly susceptible to acute sleep deprivation. However, less is known about the impacts of sleep deprivation on post-transcriptional gene regulation. To identify the effects of sleep deprivation on the translatome, we took advantage of the RiboTag mouse line to express HA-labeled Rpl22 in CaMKIIα neurons to selectively isolate and sequence mRNA transcripts associated with ribosomes in excitatory neurons. We found 198 differentially expressed genes in the ribosome-associated mRNA subset after sleep deprivation. In comparison with previously published data on gene expression in the hippocampus after sleep deprivation, we found that the subset of genes affected by sleep deprivation was considerably different in the translatome compared with the transcriptome, with only 49 genes regulated similarly. Interestingly, we found 478 genes differentially regulated by sleep deprivation in the transcriptome that were not significantly regulated in the translatome of excitatory neurons. Conversely, there were 149 genes differentially regulated by sleep deprivation in the translatome but not in the whole transcriptome. Pathway analysis revealed differences in the biological functions of genes exclusively regulated in the transcriptome or translatome, with protein deacetylase activity and small GTPase binding regulated in the transcriptome and unfolded protein binding, kinase inhibitor activity, neurotransmitter receptors and circadian rhythms regulated in the translatome. These results indicate that sleep deprivation induces significant changes affecting the pool of actively translated mRNAs.
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Affiliation(s)
- Lisa C Lyons
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Marie E Gaine
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Pharmaceutical Sciences and Experimental Therapeutics (PSET), College of Pharmacy, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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117
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Griffin P, Sheehan PW, Dimitry JM, Guo C, Kanan MF, Lee J, Zhang J, Musiek ES. REV-ERBα mediates complement expression and diurnal regulation of microglial synaptic phagocytosis. eLife 2020; 9:e58765. [PMID: 33258449 PMCID: PMC7728439 DOI: 10.7554/elife.58765] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 11/27/2020] [Indexed: 01/01/2023] Open
Abstract
The circadian clock regulates various aspects of brain health including microglial and astrocyte activation. Here, we report that deletion of the master clock protein BMAL1 in mice robustly increases expression of complement genes, including C4b and C3, in the hippocampus. BMAL1 regulates expression of the transcriptional repressor REV-ERBα, and deletion of REV-ERBα causes increased expression of C4b transcript in neurons and astrocytes as well as C3 protein primarily in astrocytes. REV-ERBα deletion increased microglial phagocytosis of synapses and synapse loss in the CA3 region of the hippocampus. Finally, we observed diurnal variation in the degree of microglial synaptic phagocytosis which was antiphase to REV-ERBα expression. This daily variation in microglial synaptic phagocytosis was abrogated by global REV-ERBα deletion, which caused persistently elevated synaptic phagocytosis. This work uncovers the BMAL1-REV-ERBα axis as a regulator of complement expression and synaptic phagocytosis in the brain, linking circadian proteins to synaptic regulation.
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MESH Headings
- ARNTL Transcription Factors/deficiency
- ARNTL Transcription Factors/genetics
- Animals
- CA3 Region, Hippocampal/cytology
- CA3 Region, Hippocampal/metabolism
- Cells, Cultured
- Circadian Rhythm
- Complement C3/genetics
- Complement C3/metabolism
- Complement C4/genetics
- Complement C4/metabolism
- Complement System Proteins/genetics
- Complement System Proteins/metabolism
- Female
- Male
- Mice, Inbred C57BL
- Mice, Knockout
- Microglia/metabolism
- Nuclear Receptor Subfamily 1, Group D, Member 1/deficiency
- Nuclear Receptor Subfamily 1, Group D, Member 1/genetics
- Nuclear Receptor Subfamily 1, Group D, Member 1/metabolism
- Phagocytosis
- Signal Transduction
- Synapses/metabolism
- Time Factors
- Up-Regulation
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Affiliation(s)
- Percy Griffin
- Department of Neurology, Washington University School of Medicine in St. LouisSt. LouisUnited States
| | - Patrick W Sheehan
- Department of Neurology, Washington University School of Medicine in St. LouisSt. LouisUnited States
| | - Julie M Dimitry
- Department of Neurology, Washington University School of Medicine in St. LouisSt. LouisUnited States
| | - Chun Guo
- Department of Pharmacological and Physiological Science, Saint Louis University School of MedicineSt. LouisUnited States
| | - Michael F Kanan
- Department of Neurology, Washington University School of Medicine in St. LouisSt. LouisUnited States
| | - Jiyeon Lee
- Department of Neurology, Washington University School of Medicine in St. LouisSt. LouisUnited States
| | - Jinsong Zhang
- Department of Pharmacological and Physiological Science, Saint Louis University School of MedicineSt. LouisUnited States
| | - Erik S Musiek
- Department of Neurology, Washington University School of Medicine in St. LouisSt. LouisUnited States
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. LouisSt. LouisUnited States
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118
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D’Arcy BR, Silver DL. Local gene regulation in radial glia: Lessons from across the nervous system. Traffic 2020; 21:737-748. [PMID: 33058331 PMCID: PMC7723028 DOI: 10.1111/tra.12769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/16/2020] [Accepted: 10/12/2020] [Indexed: 01/15/2023]
Abstract
Radial glial cells (RGCs) are progenitors of the cerebral cortex which produce both neurons and glia during development. Given their central role in development, RGC dysfunction can result in diverse neurodevelopmental disorders. RGCs have an elongated bipolar morphology that spans the entire radial width of the cortex and ends in basal endfeet connected to the pia. The basal process and endfeet are important for proper guidance of migrating neurons and are implicated in signaling. However, endfeet must function at a great distance from the cell body. This spatial separation suggests a role for local gene regulation in endfeet. Endfeet contain a local transcriptome enriched for cytoskeletal and signaling factors. These localized mRNAs are actively transported from the cell body and can be locally translated in endfeet. Yet, studies of local gene regulation in RGC endfeet are still in their infancy. Here, we draw comparisons of RGCs with foundational work in anatomically and phylogenetically related cell types, neurons and astrocytes. Our review highlights a striking overlap in the types of RNAs localized, as well as principles of local translation between these three cell types. Thus, studies in neurons, astrocytes and RGCs can mutually inform an understanding of RNA localization across the nervous system.
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Affiliation(s)
- Brooke R. D’Arcy
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina
| | - Debra L. Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina
- Duke Institute for Brain Sciences, Duke University Medical Center, Durham, North Carolina
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119
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Time is of the essence: Coupling sleep-wake and circadian neurobiology to the antidepressant effects of ketamine. Pharmacol Ther 2020; 221:107741. [PMID: 33189715 DOI: 10.1016/j.pharmthera.2020.107741] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/03/2020] [Indexed: 12/28/2022]
Abstract
Several studies have demonstrated the effectiveness of ketamine in rapidly alleviating depression and suicidal ideation. Intense research efforts have been undertaken to expose the precise mechanism underlying the antidepressant action of ketamine; however, the translation of findings into new clinical treatments has been slow. This translational gap is partially explained by a lack of understanding of the function of time and circadian timing in the complex neurobiology around ketamine. Indeed, the acute pharmacological effects of a single ketamine treatment last for only a few hours, whereas the antidepressant effects peak at around 24 hours and are sustained for the following few days. Numerous studies have investigated the acute and long-lasting neurobiological changes induced by ketamine; however, the most dramatic and fundamental change that the brain undergoes each day is rarely taken into consideration. Here, we explore the link between sleep and circadian regulation and rapid-acting antidepressant effects and summarize how diverse phenomena associated with ketamine's antidepressant actions - such as cortical excitation, synaptogenesis, and involved molecular determinants - are intimately connected with the neurobiology of wake, sleep, and circadian rhythms. We review several recently proposed hypotheses about rapid antidepressant actions, which focus on sleep or circadian regulation, and discuss their implications for ongoing research. Considering these aspects may be the last piece of the puzzle necessary to gain a more comprehensive understanding of the effects of rapid-acting antidepressants on the brain.
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120
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Abstract
Circadian rhythms govern a large array of physiological and metabolic functions. Perturbations of the daily cycle have been linked to elevated risk of developing cancer as well as poor prognosis in patients with cancer. Also, expression of core clock genes or proteins is remarkably attenuated particularly in tumours of a higher stage or that are more aggressive, possibly linking the circadian clock to cellular differentiation. Emerging evidence indicates that metabolic control by the circadian clock underpins specific hallmarks of cancer metabolism. Indeed, to support cell proliferation and biomass production, the clock may direct metabolic processes of cancer cells in concert with non-clock transcription factors to control how nutrients and metabolites are utilized in a time-specific manner. We hypothesize that the metabolic switch between differentiation or stemness of cancer may be coupled to the molecular clockwork. Moreover, circadian rhythms of host organisms appear to dictate tumour growth and proliferation. This Review outlines recent discoveries of the interplay between circadian rhythms, proliferative metabolism and cancer, highlighting potential opportunities in the development of future therapeutic strategies.
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Affiliation(s)
- Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
- Department of Endocrinology, Metabolism, and Nephrology, School of Medicine, Keio University, Tokyo, Japan.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
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121
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Bernard C. Circadian/multidien Molecular Oscillations and Rhythmicity of Epilepsy (MORE). Epilepsia 2020; 62 Suppl 1:S49-S68. [PMID: 33063860 DOI: 10.1111/epi.16716] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 12/26/2022]
Abstract
The occurrence of seizures at specific times of the day has been consistently observed for centuries in individuals with epilepsy. Electrophysiological recordings provide evidence that seizures have a higher probability of occurring at a given time during the night and day cycle in individuals with epilepsy here referred to as the seizure rush hour. Which mechanisms underlie such circadian rhythmicity of seizures? Why don't they occur every day at the same time? Which mechanisms may underlie their occurrence outside the rush hour? In this commentary, I present a hypothesis: MORE - Molecular Oscillations and Rhythmicity of Epilepsy, a conceptual framework to study and understand the mechanisms underlying the circadian rhythmicity of seizures and their probabilistic nature. The core of the hypothesis is the existence of ~24-hour oscillations of gene and protein expression throughout the body in different cells and organs. The orchestrated molecular oscillations control the rhythmicity of numerous body events, such as feeding and sleep. The concept developed here is that molecular oscillations may favor seizure genesis at preferred times, generating the condition for a seizure rush hour. However, the condition is not sufficient, as other factors are necessary for a seizure to occur. Studying these molecular oscillations may help us understand seizure genesis mechanisms and find new therapeutic targets and predictive biomarkers. The MORE hypothesis can be generalized to comorbidities and the slower multidien (week/month period) rhythmicity of seizures, a phenomenon addressed in another article in this issue of Epilepsia.
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Affiliation(s)
- Christophe Bernard
- Inserm, INS, Institut de Neurosciences des Systèmes, Aix Marseille Univ, Marseille, France
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122
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Abstract
Sleep is a fundamental property conserved across species. The homeostatic induction of sleep indicates the presence of a mechanism that is progressively activated by the awake state and that induces sleep. Several lines of evidence support that such function, namely, sleep need, lies in the neuronal assemblies rather than specific brain regions and circuits. However, the molecular mechanism underlying the dynamics of sleep need is still unclear. This review aims to summarize recent studies mainly in rodents indicating that protein phosphorylation, especially at the synapses, could be the molecular entity associated with sleep need. Genetic studies in rodents have identified a set of kinases that promote sleep. The activity of sleep-promoting kinases appears to be elevated during the awake phase and in sleep deprivation. Furthermore, the proteomic analysis demonstrated that the phosphorylation status of synaptic protein is controlled by the sleep-wake cycle. Therefore, a plausible scenario may be that the awake-dependent activation of kinases modifies the phosphorylation status of synaptic proteins to promote sleep. We also discuss the possible importance of multisite phosphorylation on macromolecular protein complexes to achieve the slow dynamics and physiological functions of sleep in mammals.
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Affiliation(s)
- Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics, Osaka, Japan
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123
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Abstract
Sleep is evolutionarily conserved across all species, and impaired sleep is a common trait of the diseased brain. Sleep quality decreases as we age, and disruption of the regular sleep architecture is a frequent antecedent to the onset of dementia in neurodegenerative diseases. The glymphatic system, which clears the brain of protein waste products, is mostly active during sleep. Yet the glymphatic system degrades with age, suggesting a causal relationship between sleep disturbance and symptomatic progression in the neurodegenerative dementias. The ties that bind sleep, aging, glymphatic clearance, and protein aggregation have shed new light on the pathogenesis of a broad range of neurodegenerative diseases, for which glymphatic failure may constitute a therapeutically targetable final common pathway.
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Affiliation(s)
- Maiken Nedergaard
- Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Steven A Goldman
- Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
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124
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Debski KJ, Ceglia N, Ghestem A, Ivanov AI, Brancati GE, Bröer S, Bot AM, Müller JA, Schoch S, Becker A, Löscher W, Guye M, Sassone-Corsi P, Lukasiuk K, Baldi P, Bernard C. The circadian dynamics of the hippocampal transcriptome and proteome is altered in experimental temporal lobe epilepsy. SCIENCE ADVANCES 2020; 6:eaat5979. [PMID: 33036982 PMCID: PMC10764101 DOI: 10.1126/sciadv.aat5979] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Gene and protein expressions display circadian oscillations, which can be disrupted in diseases in most body organs. Whether these oscillations occur in the healthy hippocampus and whether they are altered in epilepsy are not known. We identified more than 1200 daily oscillating transcripts in the hippocampus of control mice and 1600 in experimental epilepsy, with only one-fourth oscillating in both conditions. Comparison of gene oscillations in control and epilepsy predicted time-dependent alterations in energy metabolism, which were verified experimentally. Although aerobic glycolysis remained constant from morning to afternoon in controls, it increased in epilepsy. In contrast, oxidative phosphorylation increased in control and decreased in epilepsy. Thus, the control hippocampus shows circadian molecular remapping, which is altered in epilepsy. We suggest that the hippocampus operates in a different functioning mode in epilepsy. These alterations need to be considered when studying epilepsy mechanisms, designing drug treatments, and timing their delivery.
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Affiliation(s)
- K J Debski
- Epileptogenesis Laboratory, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
- Bioinformatics Laboratory, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - N Ceglia
- Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697-3435, USA
| | - A Ghestem
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - A I Ivanov
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - G E Brancati
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - S Bröer
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Hannover, Germany
| | - A M Bot
- Epileptogenesis Laboratory, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - J A Müller
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - S Schoch
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - A Becker
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - W Löscher
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Hannover, Germany
| | - M Guye
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France
- APHM, Hôpital Universitaire Timone, CEMEREM, Marseille, France
| | - P Sassone-Corsi
- Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - K Lukasiuk
- Epileptogenesis Laboratory, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - P Baldi
- Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697-3435, USA
| | - C Bernard
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France.
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125
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Zhang L, Yan R, Wu Z. Metagenomics analysis of intestinal flora modulatory effect of green tea polyphenols by a circadian rhythm dysfunction mouse model. J Food Biochem 2020; 44:e13430. [PMID: 32776532 DOI: 10.1111/jfbc.13430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 12/16/2022]
Abstract
The present study investigated the regulatory mechanism of green tea polyphenols (GTP) on the circadian rhythm of gut flora. The administration of GTP mitigated the variations in the serum and liver level of constant dark (CD)-induced circadian rhythm disorder mouse model. For the gut microbial population, GTP promoted the relative abundance of Bacteroidetes while inhibited Firmicutes. Furthermore, KEGG pathways of biosynthesis of amino acids, two-component system and ATP-binding cassette translocators enriched the most differentially expressed genes after GTP interference. It indicated GTP may prevent CD-induced circadian rhythm disorder, which has an enormous potential to be utilized as prebiotic-like ingredients in food industry. PRACTICAL APPLICATIONS: The findings underscore the capacity of GTP to modulate circadian rhythm by modulating the structure and functional characteristics of host gut microbiota and influencing metabolism, conducing to the melioration of human microecology. The prebiotic function of GTP indicated it can be used to prevent metabolic disturbance related to circadian rhythm disorder.
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Affiliation(s)
- Li Zhang
- Department of Physical Education, China University of Mining and Technology, Beijing, P.R. China
| | - Ruonan Yan
- Department of Food Science and Engineering, Ningbo University, Ningbo, P.R. China
| | - Zufang Wu
- Department of Food Science and Engineering, Ningbo University, Ningbo, P.R. China
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126
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Wang HB, Tahara Y, Luk SHC, Kim YS, Hitchcock ON, MacDowell Kaswan ZA, In Kim Y, Block GD, Ghiani CA, Loh DH, Colwell CS. Melatonin treatment of repetitive behavioral deficits in the Cntnap2 mouse model of autism spectrum disorder. Neurobiol Dis 2020; 145:105064. [PMID: 32889171 PMCID: PMC7597927 DOI: 10.1016/j.nbd.2020.105064] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/04/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023] Open
Abstract
Nighttime light pollution is linked to metabolic and cognitive dysfunction. Many patients with autism spectrum disorders (ASD) show disturbances in their sleep/wake cycle, and may be particularly vulnerable to the impact of circadian disruptors. In this study, we examined the impact of exposure to dim light at night (DLaN, 5 lx) in a model of ASD: the contactin associated protein-like 2 knock out (Cntnap2 KO) mice. DLaN was sufficient to disrupt locomotor activity rhythms, exacerbate the excessive grooming and diminish the social preference in Cntnap2 mutant mice. On a molecular level, DLaN altered the phase and amplitude of PER2:LUC rhythms in a tissue-specific manner in vitro. Daily treatment with melatonin reduced the excessive grooming of the mutant mice to wild-type levels and improved activity rhythms. Our findings suggest that common circadian disruptors such as light at night should be considered in the management of ASD.
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Affiliation(s)
- Huei Bin Wang
- Molecular, Cellular, Integrative Physiology Graduate Program, David Geffen School of Medicine, University of California Los Angeles, USA; Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, USA
| | - Yu Tahara
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, USA
| | - Shu Hon Christopher Luk
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, USA
| | - Yoon-Sik Kim
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, USA
| | - Olivia N Hitchcock
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, USA
| | - Zoe A MacDowell Kaswan
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, USA
| | - Yang In Kim
- Department of Physiology and Neuroscience Research Institute, Korea University College of Medicine, Seoul, Republic of Korea
| | - Gene D Block
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, USA
| | - Cristina A Ghiani
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, USA
| | - Dawn H Loh
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, USA
| | - Christopher S Colwell
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, USA.
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127
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Cao J, Herman AB, West GB, Poe G, Savage VM. Unraveling why we sleep: Quantitative analysis reveals abrupt transition from neural reorganization to repair in early development. SCIENCE ADVANCES 2020; 6:6/38/eaba0398. [PMID: 32948580 PMCID: PMC7500925 DOI: 10.1126/sciadv.aba0398] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Sleep serves disparate functions, most notably neural repair, metabolite clearance and circuit reorganization. Yet the relative importance remains hotly debated. Here, we create a novel mechanistic framework for understanding and predicting how sleep changes during ontogeny and across phylogeny. We use this theory to quantitatively distinguish between sleep used for neural reorganization versus repair. Our findings reveal an abrupt transition, between 2 and 3 years of age in humans. Specifically, our results show that differences in sleep across phylogeny and during late ontogeny (after 2 or 3 years in humans) are primarily due to sleep functioning for repair or clearance, while changes in sleep during early ontogeny (before 2 or 3 years) primarily support neural reorganization and learning. Moreover, our analysis shows that neuroplastic reorganization occurs primarily in REM sleep but not in NREM. This developmental transition suggests a complex interplay between developmental and evolutionary constraints on sleep.
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Affiliation(s)
- Junyu Cao
- Department of Information, Risk and Operations Management, McCombs School of Business, The University of Texas at Austin, TX, USA
| | | | - Geoffrey B West
- Santa Fe Institute, Santa Fe, NM, USA
- Department of Mathematics, Imperial College, London, UK
| | - Gina Poe
- Department of Integrative Biology and Physiology University of California, Los Angeles, CA, USA
| | - Van M Savage
- Santa Fe Institute, Santa Fe, NM, USA.
- Departments of Computational Medicine and Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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128
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Bjorness TE, Kulkarni A, Rybalchenko V, Suzuki A, Bridges C, Harrington AJ, Cowan CW, Takahashi JS, Konopka G, Greene RW. An essential role for MEF2C in the cortical response to loss of sleep in mice. eLife 2020; 9:e58331. [PMID: 32851972 PMCID: PMC7490011 DOI: 10.7554/elife.58331] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
Neuronal activity and gene expression in response to the loss of sleep can provide a window into the enigma of sleep function. Sleep loss is associated with brain differential gene expression, an increase in pyramidal cell mEPSC frequency and amplitude, and a characteristic rebound and resolution of slow wave sleep-slow wave activity (SWS-SWA). However, the molecular mechanism(s) mediating the sleep-loss response are not well understood. We show that sleep-loss regulates MEF2C phosphorylation, a key mechanism regulating MEF2C transcriptional activity, and that MEF2C function in postnatal excitatory forebrain neurons is required for the biological events in response to sleep loss in C57BL/6J mice. These include altered gene expression, the increase and recovery of synaptic strength, and the rebound and resolution of SWS-SWA, which implicate MEF2C as an essential regulator of sleep function.
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Affiliation(s)
- Theresa E Bjorness
- Department of Psychiatry, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Research Service, North Texas VA Health Care SystemDallasUnited States
| | - Ashwinikumar Kulkarni
- Department of Neuroscience, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Volodymyr Rybalchenko
- Department of Psychiatry, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Ayako Suzuki
- Department of Psychiatry, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Catherine Bridges
- Department of Neuroscience, Medical University of South CarolinaCharlestonUnited States
| | - Adam J Harrington
- Department of Neuroscience, Medical University of South CarolinaCharlestonUnited States
| | - Christopher W Cowan
- Department of Neuroscience, Medical University of South CarolinaCharlestonUnited States
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Genevieve Konopka
- Department of Neuroscience, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Robert W Greene
- Department of Psychiatry, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Neuroscience, Peter O’Donnell Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
- International Institute of Integrative Sleep Medicine, University of TsukubaTsukubaJapan
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129
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Marti AR, Pedersen TT, Wisor JP, Mrdalj J, Holmelid Ø, Patil S, Meerlo P, Bramham CR, Grønli J. Cognitive function and brain plasticity in a rat model of shift work: role of daily rhythms, sleep and glucocorticoids. Sci Rep 2020; 10:13141. [PMID: 32753733 PMCID: PMC7403587 DOI: 10.1038/s41598-020-69969-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023] Open
Abstract
Many occupations require operations during the night-time when the internal circadian clock promotes sleep, in many cases resulting in impairments in cognitive performance and brain functioning. Here, we use a rat model to attempt to identify the biological mechanisms underlying such impaired performance. Rats were exposed to forced activity, either in their rest-phase (simulating night-shift work; rest work) or in their active-phase (simulating day-shift work; active work). Sleep, wakefulness and body temperature rhythm were monitored throughout. Following three work shifts, spatial memory performance was tested on the Morris Water Maze task. After 4 weeks washout, the work protocol was repeated, and blood and brain tissue collected. Simulated night-shift work impaired spatial memory and altered biochemical markers of cerebral cortical protein synthesis. Measures of daily rhythm strength were blunted, and sleep drive increased. Individual variation in the data suggested differences in shift work tolerance. Hierarchical regression analyses revealed that type of work, changes in daily rhythmicity and changes in sleep drive predict spatial memory performance and expression of brain protein synthesis regulators. Moreover, serum corticosterone levels predicted expression of brain protein synthesis regulators. These findings open new research avenues into the biological mechanisms that underlie individual variation in shift work tolerance.
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Affiliation(s)
- Andrea R Marti
- Bergen Stress and Sleep Group, Department of Biological and Medical Psychology, Faculty of Psychology, University of Bergen, Jonas Liesvei 91, 5009, Bergen, Norway. .,Bergen Stress and Sleep Group, Department of Biological and Medical Psychology, Faculty of Psychology, University of Bergen, Jonas Liesvei 91, 5009, Bergen, Norway.
| | - Torhild T Pedersen
- Bergen Stress and Sleep Group, Department of Biological and Medical Psychology, Faculty of Psychology, University of Bergen, Jonas Liesvei 91, 5009, Bergen, Norway
| | - Jonathan P Wisor
- College of Medicine, Washington State University, Spokane, WA, USA
| | - Jelena Mrdalj
- Bergen Stress and Sleep Group, Department of Biological and Medical Psychology, Faculty of Psychology, University of Bergen, Jonas Liesvei 91, 5009, Bergen, Norway
| | - Øystein Holmelid
- Bergen Stress and Sleep Group, Department of Biological and Medical Psychology, Faculty of Psychology, University of Bergen, Jonas Liesvei 91, 5009, Bergen, Norway
| | - Sudarshan Patil
- Department of Biomedicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Peter Meerlo
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Clive R Bramham
- Department of Biomedicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Janne Grønli
- Bergen Stress and Sleep Group, Department of Biological and Medical Psychology, Faculty of Psychology, University of Bergen, Jonas Liesvei 91, 5009, Bergen, Norway
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130
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Impact of circadian and diurnal rhythms on cellular metabolic function and neurodegenerative diseases. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 154:393-412. [PMID: 32739012 DOI: 10.1016/bs.irn.2020.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The 24-h rotational period of the earth has driven evolution of biological systems that serve to synchronize organismal physiology and behavior to this predictable environmental event. In mammals, the circadian (circa, "about" and dia, "a day") clock keeps 24-h time at the organismal and cellular level, optimizing biological function for a given time of day. The most obvious circadian output is the sleep-wake cycle, though countless bodily functions, ranging from hormone levels to cognitive function, are influenced by the circadian clock. Here we discuss the regulation of metabolic pathways by the circadian clock, discuss the evidence implicating circadian and sleep disruption in neurodegenerative diseases, and suggest some possible connections between the clock, metabolism, and neurodegenerative disease.
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131
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Hartsock MJ, Spencer RL. Memory and the circadian system: Identifying candidate mechanisms by which local clocks in the brain may regulate synaptic plasticity. Neurosci Biobehav Rev 2020; 118:134-162. [PMID: 32712278 DOI: 10.1016/j.neubiorev.2020.07.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 07/14/2020] [Accepted: 07/18/2020] [Indexed: 12/11/2022]
Abstract
The circadian system is an endogenous biological network responsible for coordinating near-24-h cycles in behavior and physiology with daily timing cues from the external environment. In this review, we explore how the circadian system regulates memory formation, retention, and recall. Circadian rhythms in these memory processes may arise through several endogenous pathways, and recent work highlights the importance of genetic timekeepers found locally within tissues, called local clocks. We evaluate the circadian memory literature for evidence of local clock involvement in memory, identifying potential nodes for direct interactions between local clock components and mechanisms of synaptic plasticity. Our discussion illustrates how local clocks may pervasively modulate neuronal plastic capacity, a phenomenon that we designate here as circadian metaplasticity. We suggest that this function of local clocks supports the temporal optimization of memory processes, illuminating the potential for circadian therapeutic strategies in the prevention and treatment of memory impairment.
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Affiliation(s)
- Matthew J Hartsock
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado 80309, United States.
| | - Robert L Spencer
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado 80309, United States.
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132
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133
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Umemura Y, Yagita K. Development of the Circadian Core Machinery in Mammals. J Mol Biol 2020; 432:3611-3617. [DOI: 10.1016/j.jmb.2019.11.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 01/20/2023]
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134
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Havekes R, Aton SJ. Impacts of Sleep Loss versus Waking Experience on Brain Plasticity: Parallel or Orthogonal? Trends Neurosci 2020; 43:385-393. [PMID: 32459991 DOI: 10.1016/j.tins.2020.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/12/2020] [Accepted: 03/25/2020] [Indexed: 12/21/2022]
Abstract
Recent studies on the effects of sleep deprivation on synaptic plasticity have yielded discrepant results. Sleep deprivation studies using novelty exposure as a means to keep animals awake suggests that sleep (compared with wake) leads to widespread reductions in net synaptic strength. By contrast, sleep deprivation studies using approaches avoiding novelty-induced arousal (i.e., gentle handling) suggest that sleep can promote synaptic growth and strengthening. How can these discrepant findings be reconciled? Here, we discuss how varying methodologies for the experimental disruption of sleep (with differential introduction of novel experiences) could fundamentally alter the experimental outcome with regard to synaptic plasticity. Thus, data from experiments aimed at assessing the relative impact of sleep versus wake on the brain may instead reflect the quality of the waking experience itself. The highlighted work suggests that brain plasticity resulting from novel experiences versus wake per se has unique and distinct features.
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Affiliation(s)
- Robbert Havekes
- Neurobiology Expertise Group, Groningen Institute for Evolutionary Life Sciences, Groningen, The Netherlands.
| | - Sara J Aton
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
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135
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Brüning F, Noya SB, Bange T, Koutsouli S, Rudolph JD, Tyagarajan SK, Cox J, Mann M, Brown SA, Robles MS. Sleep-wake cycles drive daily dynamics of synaptic phosphorylation. Science 2020; 366:366/6462/eaav3617. [PMID: 31601740 DOI: 10.1126/science.aav3617] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 09/04/2019] [Indexed: 12/14/2022]
Abstract
The circadian clock drives daily changes of physiology, including sleep-wake cycles, through regulation of transcription, protein abundance, and function. Circadian phosphorylation controls cellular processes in peripheral organs, but little is known about its role in brain function and synaptic activity. We applied advanced quantitative phosphoproteomics to mouse forebrain synaptoneurosomes isolated across 24 hours, accurately quantifying almost 8000 phosphopeptides. Half of the synaptic phosphoproteins, including numerous kinases, had large-amplitude rhythms peaking at rest-activity and activity-rest transitions. Bioinformatic analyses revealed global temporal control of synaptic function through phosphorylation, including synaptic transmission, cytoskeleton reorganization, and excitatory/inhibitory balance. Sleep deprivation abolished 98% of all phosphorylation cycles in synaptoneurosomes, indicating that sleep-wake cycles rather than circadian signals are main drivers of synaptic phosphorylation, responding to both sleep and wake pressures.
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Affiliation(s)
- Franziska Brüning
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany.,Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Sara B Noya
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Tanja Bange
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany
| | - Stella Koutsouli
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany
| | - Jan D Rudolph
- Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Shiva K Tyagarajan
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Jürgen Cox
- Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
| | - Maria S Robles
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany.
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136
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Song D, Yang CS, Zhang X, Wang Y. The relationship between host circadian rhythms and intestinal microbiota: A new cue to improve health by tea polyphenols. Crit Rev Food Sci Nutr 2020; 61:139-148. [PMID: 31997655 DOI: 10.1080/10408398.2020.1719473] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Under the control of the host circadian rhythms, intestinal microbiota undergoes dietary-dependent diurnal fluctuations in composition and function. In addition, microbiome plays a critical role in maintaining the host circadian rhythms and metabolic homeostasis. The interactions between host circadian rhythms and intestinal microbiota suggest that intervention with prebiotics or probiotic is a possible way to alleviate circadian rhythm misalignment and related metabolic diseases. This review discusses the circadian rhythm oscillations of gut flora, relationship between host circadian rhythms and microbiome and related effects on metabolism. The influence on circadian rhythms by the interactions between tea polyphenols (TP) and intestinal microbiota is highlighted.
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Affiliation(s)
- Dan Song
- Department of Food Science and Engineering, Ningbo University, Ningbo University, Ningbo, P.R. China
| | - Chung S Yang
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Xin Zhang
- Department of Food Science and Engineering, Ningbo University, Ningbo University, Ningbo, P.R. China.,State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, P.R. China
| | - Ying Wang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, P.R. China
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137
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Mauvoisin D, Gachon F. Proteomics in Circadian Biology. J Mol Biol 2019; 432:3565-3577. [PMID: 31843517 DOI: 10.1016/j.jmb.2019.12.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 02/06/2023]
Abstract
The circadian clock is an endogenous molecular timekeeping system that allows organisms to adjust their physiology and behavior to the time of day in an anticipatory fashion. In different organisms, the circadian clock coordinates physiology and metabolism through regulation of gene expression at the transcriptional and post-transcriptional levels. Until now, circadian gene expression studies have mostly focused primarily on transcriptomics approaches. This type of analyses revealed that many protein-encoding genes show circadian expression in a tissue-specific manner. During the last three decades, a long way has been traveled since the pioneering work on dinoflagellates, and new advances in mass spectrometry offered new perspectives in the characterization of the circadian dynamics of the proteome. Altogether, these efforts highlighted that rhythmic protein oscillation is driven equally by gene transcription, post-transcriptional and post-translational regulations. The determination of the role of the circadian clock in these three levels of regulation appears to be the next major challenge in the field.
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Affiliation(s)
- Daniel Mauvoisin
- L'institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France.
| | - Frédéric Gachon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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138
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Abstract
Day and night, the amounts of many synaptic proteins vary according to sleep pressure
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Affiliation(s)
- Chiara Cirelli
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI 53719, USA.
| | - Giulio Tononi
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI 53719, USA
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139
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Noya SB, Colameo D, Brüning F, Spinnler A, Mircsof D, Opitz L, Mann M, Tyagarajan SK, Robles MS, Brown SA. The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep. Science 2019; 366:366/6462/eaav2642. [DOI: 10.1126/science.aav2642] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 09/03/2019] [Indexed: 12/13/2022]
Abstract
Neurons have adapted mechanisms to traffic RNA and protein into distant dendritic and axonal arbors. Taking a biochemical approach, we reveal that forebrain synaptic transcript accumulation shows overwhelmingly daily rhythms, with two-thirds of synaptic transcripts showing time-of-day–dependent abundance independent of oscillations in the soma. These transcripts formed two sharp temporal and functional clusters, with transcripts preceding dawn related to metabolism and translation and those anticipating dusk related to synaptic transmission. Characterization of the synaptic proteome around the clock demonstrates the functional relevance of temporal gating for synaptic processes and energy homeostasis. Unexpectedly, sleep deprivation completely abolished proteome but not transcript oscillations. Altogether, the emerging picture is one of a circadian anticipation of messenger RNA needs in the synapse followed by translation as demanded by sleep-wake cycles.
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Affiliation(s)
- Sara B. Noya
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - David Colameo
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Franziska Brüning
- Institute of Medical Psychology, Medical Faculty, LMU Munich, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andrea Spinnler
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Dennis Mircsof
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, University of Zurich–Eidgenosissche Technische Hochschule, Zurich, Switzerland
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Shiva K. Tyagarajan
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Maria S. Robles
- Institute of Medical Psychology, Medical Faculty, LMU Munich, Germany
| | - Steven A. Brown
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
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