1
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Giri B, Kinsky N, Kaya U, Maboudi K, Abel T, Diba K. Sleep loss diminishes hippocampal reactivation and replay. Nature 2024:10.1038/s41586-024-07538-2. [PMID: 38867049 DOI: 10.1038/s41586-024-07538-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Memories benefit from sleep1, and the reactivation and replay of waking experiences during hippocampal sharp-wave ripples (SWRs) are considered to be crucial for this process2. However, little is known about how these patterns are impacted by sleep loss. Here we recorded CA1 neuronal activity over 12 h in rats across maze exploration, sleep and sleep deprivation, followed by recovery sleep. We found that SWRs showed sustained or higher rates during sleep deprivation but with lower power and higher frequency ripples. Pyramidal cells exhibited sustained firing during sleep deprivation and reduced firing during sleep, yet their firing rates were comparable during SWRs regardless of sleep state. Despite the robust firing and abundance of SWRs during sleep deprivation, we found that the reactivation and replay of neuronal firing patterns was diminished during these periods and, in some cases, completely abolished compared to ad libitum sleep. Reactivation partially rebounded after recovery sleep but failed to reach the levels found in natural sleep. These results delineate the adverse consequences of sleep loss on hippocampal function at the network level and reveal a dissociation between the many SWRs elicited during sleep deprivation and the few reactivations and replays that occur during these events.
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Affiliation(s)
- Bapun Giri
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Nathaniel Kinsky
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Utku Kaya
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kourosh Maboudi
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Kamran Diba
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA.
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2
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Nakata S, Iwasaki K, Funato H, Yanagisawa M, Ozaki H. Neuronal subtype-specific transcriptomic changes in the cerebral neocortex associated with sleep pressure. Neurosci Res 2024:S0168-0102(24)00042-7. [PMID: 38537682 DOI: 10.1016/j.neures.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/07/2024]
Abstract
Sleep is homeostatically regulated by sleep pressure, which increases during wakefulness and dissipates during sleep. Recent studies have suggested that the cerebral neocortex, a six-layered structure composed of various layer- and projection-specific neuronal subtypes, is involved in the representation of sleep pressure governed by transcriptional regulation. Here, we examined the transcriptomic changes in neuronal subtypes in the neocortex upon increased sleep pressure using single-nucleus RNA sequencing datasets and predicted the putative intracellular and intercellular molecules involved in transcriptome alterations. We revealed that sleep deprivation (SD) had the greatest effect on the transcriptome of layer 2 and 3 intratelencephalic (L2/3 IT) neurons among the neocortical glutamatergic neuronal subtypes. The expression of mutant SIK3 (SLP), which is known to increase sleep pressure, also induced profound changes in the transcriptome of L2/3 IT neurons. We identified Junb as a candidate transcription factor involved in the alteration of the L2/3 IT neuronal transcriptome by SD and SIK3 (SLP) expression. Finally, we inferred putative intercellular ligands, including BDNF, LSAMP, and PRNP, which may be involved in SD-induced alteration of the transcriptome of L2/3 IT neurons. We suggest that the transcriptome of L2/3 IT neurons is most impacted by increased sleep pressure among neocortical glutamatergic neuronal subtypes and identify putative molecules involved in such transcriptional alterations.
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Affiliation(s)
- Shinya Nakata
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kanako Iwasaki
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiromasa Funato
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan; Department of Anatomy, Graduate School of Medicine, Toho University, Tokyo, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Haruka Ozaki
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan; Center for Artificial Intelligence Research, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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3
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Shi T, Shah I, Dang Q, Taylor L, Jagannath A. Sex-specific regulation of the cortical transcriptome in response to sleep deprivation. Front Neurosci 2024; 17:1303727. [PMID: 38504908 PMCID: PMC10948409 DOI: 10.3389/fnins.2023.1303727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/07/2023] [Indexed: 03/21/2024] Open
Abstract
Multiple studies have documented sex differences in sleep behaviour, however, the molecular determinants of such differences remain unknown. Furthermore, most studies addressing molecular mechanisms have been performed only in males, leaving the current state of knowledge biased towards the male sex. To address this, we studied the differences in the transcriptome of the cerebral cortex of male and female C57Bl/6 J mice after 6 h of sleep deprivation. We found that several genes, including the neurotrophin growth factor Bdnf, immediate early genes Fosb and Fosl2, and the adenylate cyclase Adcy7 are differentially upregulated in males compared to females. We identified the androgen-receptor activating transcription factor EZH2 as the upstream regulatory element specifying sex differences in the sleep deprivation transcriptome. We propose that the pathways downstream of these transcripts, which impact on cellular re-organisation, synaptic signalling, and learning may underpin the differential response to sleep deprivation in the two sexes.
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Affiliation(s)
- Tianyi Shi
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, New Biochemistry Building, University of Oxford, Oxford, United Kingdom
| | - Ishani Shah
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Quang Dang
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, New Biochemistry Building, University of Oxford, Oxford, United Kingdom
- Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam
| | - Lewis Taylor
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, New Biochemistry Building, University of Oxford, Oxford, United Kingdom
| | - Aarti Jagannath
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, New Biochemistry Building, University of Oxford, Oxford, United Kingdom
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4
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Ford K, Zuin E, Righelli D, Medina E, Schoch H, Singletary K, Muheim C, Frank MG, Hicks SC, Risso D, Peixoto L. A Global Transcriptional Atlas of the Effect of Sleep Deprivation in the Mouse Frontal Cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569011. [PMID: 38076891 PMCID: PMC10705260 DOI: 10.1101/2023.11.28.569011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Sleep deprivation (SD) has negative effects on brain function. Sleep problems are prevalent in neurodevelopmental, neurodegenerative and psychiatric disorders. Thus, understanding the molecular consequences of SD is of fundamental importance in neuroscience. In this study, we present the first simultaneous bulk and single-nuclear (sn)RNA sequencing characterization of the effects of SD in the mouse frontal cortex. We show that SD predominantly affects glutamatergic neurons, specifically in layers 4 and 5, and produces isoform switching of thousands of transcripts. At both the global and cell-type specific level, SD has a large repressive effect on transcription, down-regulating thousands of genes and transcripts; underscoring the importance of accounting for the effects of sleep loss in transcriptome studies of brain function. As a resource we provide extensive characterizations of cell types, genes, transcripts and pathways affected by SD; as well as tutorials for data analysis.
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Affiliation(s)
- Kaitlyn Ford
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Elena Zuin
- Department of Biology, University of Padova, Italy
- Department of Statistical Sciences, University of Padova, Italy
| | - Dario Righelli
- Department of Statistical Sciences, University of Padova, Italy
| | - Elizabeth Medina
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Hannah Schoch
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Kristan Singletary
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Christine Muheim
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Marcos G Frank
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, MD, USA
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Italy
| | - Lucia Peixoto
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
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5
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Vaquer-Alicea A, Yu J, Liu H, Lucey BP. Plasma and cerebrospinal fluid proteomic signatures of acutely sleep-deprived humans: an exploratory study. SLEEP ADVANCES : A JOURNAL OF THE SLEEP RESEARCH SOCIETY 2023; 4:zpad047. [PMID: 38046221 PMCID: PMC10691441 DOI: 10.1093/sleepadvances/zpad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/06/2023] [Indexed: 12/05/2023]
Abstract
Study Objectives Acute sleep deprivation affects both central and peripheral biological processes. Prior research has mainly focused on specific proteins or biological pathways that are dysregulated in the setting of sustained wakefulness. This exploratory study aimed to provide a comprehensive view of the biological processes and proteins impacted by acute sleep deprivation in both plasma and cerebrospinal fluid (CSF). Methods We collected plasma and CSF from human participants during one night of sleep deprivation and controlled normal sleep conditions. One thousand and three hundred proteins were measured at hour 0 and hour 24 using a high-scale aptamer-based proteomics platform (SOMAscan) and a systematic biological database tool (Metascape) was used to reveal altered biological pathways. Results Acute sleep deprivation decreased the number of upregulated and downregulated biological pathways and proteins in plasma but increased upregulated and downregulated biological pathways and proteins in CSF. Predominantly affected proteins and pathways were associated with immune response, inflammation, phosphorylation, membrane signaling, cell-cell adhesion, and extracellular matrix organization. Conclusions The identified modifications across biofluids add to evidence that acute sleep deprivation has important impacts on biological pathways and proteins that can negatively affect human health. As a hypothesis-driving study, these findings may help with the exploration of novel mechanisms that mediate sleep loss and associated conditions, drive the discovery of new sleep loss biomarkers, and ultimately aid in the identification of new targets for intervention to human diseases.
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Affiliation(s)
- Ana Vaquer-Alicea
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Jinsheng Yu
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Haiyan Liu
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Brendan P Lucey
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
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6
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Vanrobaeys Y, Peterson ZJ, Walsh EN, Chatterjee S, Lin LC, Lyons LC, Nickl-Jockschat T, Abel T. Spatial transcriptomics reveals unique gene expression changes in different brain regions after sleep deprivation. Nat Commun 2023; 14:7095. [PMID: 37925446 PMCID: PMC10625558 DOI: 10.1038/s41467-023-42751-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
Sleep deprivation has far-reaching consequences on the brain and behavior, impacting memory, attention, and metabolism. Previous research has focused on gene expression changes in individual brain regions, such as the hippocampus or cortex. Therefore, it is unclear how uniformly or heterogeneously sleep loss affects the brain. Here, we use spatial transcriptomics to define the impact of a brief period of sleep deprivation across the brain in male mice. We find that sleep deprivation induced pronounced differences in gene expression across the brain, with the greatest changes in the hippocampus, neocortex, hypothalamus, and thalamus. Both the differentially expressed genes and the direction of regulation differed markedly across regions. Importantly, we developed bioinformatic tools to register tissue sections and gene expression data into a common anatomical space, allowing a brain-wide comparison of gene expression patterns between samples. Our results suggest that distinct molecular mechanisms acting in discrete brain regions underlie the biological effects of sleep deprivation.
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Affiliation(s)
- Yann Vanrobaeys
- Interdisciplinary Graduate Program in Genetics, University of Iowa, 357 Medical Research Center Iowa City, Iowa, IA, USA
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
| | - Zeru J Peterson
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Emily N Walsh
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, 356 Medical Research Center, Iowa City, IA, USA
| | - Snehajyoti Chatterjee
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
| | - Li-Chun Lin
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
- Department of Neurology, University of Iowa, Iowa City, IA, USA
| | - Lisa C Lyons
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Thomas Nickl-Jockschat
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA.
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA.
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.
| | - Ted Abel
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA.
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA.
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7
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Bernardini I, Quagliariello A, Peruzza L, Martino ME, Dalla Rovere G, Iori S, Asnicar D, Ciscato M, Fabrello J, Corami F, Cecchetto M, Giubilato E, Carrer C, Bettiol C, Semenzin E, Marcomini A, Matozzo V, Bargelloni L, Milan M, Patarnello T. Contaminants from dredged sediments alter the transcriptome of Manila clam and induce shifts in microbiota composition. BMC Biol 2023; 21:234. [PMID: 37880625 PMCID: PMC10601118 DOI: 10.1186/s12915-023-01741-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The reuse of dredged sediments in ports and lagoons is a big issue as it should not affect the quality and the equilibrium of ecosystems. In the lagoon of Venice, sediment management is of crucial importance as sediments are often utilized to built-up structures necessary to limit erosion. However, the impact of sediment reuse on organisms inhabiting this delicate area is poorly known. The Manila clam is a filter-feeding species of high economic and ecological value for the Venice lagoon experiencing a drastic decline in the last decades. In order to define the molecular mechanisms behind sediment toxicity, we exposed clams to sediments sampled from different sites within one of the Venice lagoon navigable canals close to the industrial area. Moreover, we investigated the impacts of dredged sediments on clam's microbial communities. RESULTS Concentrations of the trace elements and organic chemicals showed increasing concentrations from the city of Venice to sites close to the industrial area of Porto Marghera, where PCDD/Fs and PCBs concentrations were up to 120 times higher than the southern lagoon. While bioaccumulation of organic contaminants of industrial origin reflected sediments' chemical concentrations, metal bioaccumulation was not consistent with metal concentrations measured in sediments probably due to the activation of ABC transporters. At the transcriptional level, we found a persistent activation of the mTORC1 signalling pathway, which is central in the coordination of cellular responses to chemical stress. Microbiota characterization showed the over-representation of potential opportunistic pathogens following exposure to the most contaminated sediments, leading to host immune response activation. Despite the limited acquisition of new microbial species from sediments, the latter play an important role in shaping Manila clam microbial communities. CONCLUSIONS Sediment management in the Venice lagoon will increase in the next years to maintain and create new canals as well as to allow the operation of the new mobile gates at the three Venice lagoon inlets. Our data reveal important transcriptional and microbial changes of Manila clams after exposure to sediments, therefore reuse of dredged sediments represents a potential risk for the conservation of this species and possibly for other organisms inhabiting the Venice lagoon.
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Affiliation(s)
- Ilaria Bernardini
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Maria Elena Martino
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Silvia Iori
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Davide Asnicar
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padua, Italy
- Aquatic Bioscience, Huntsman Marine Science Centre, 1 Lower Campus Road, E5B 2L7, St Andrews, New Brunswick, Canada
| | - Maria Ciscato
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Jacopo Fabrello
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Fabiana Corami
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
- Institute of Polar Sciences, CNR-ISP, Foscari University of Venice, Campus Scientifico - CaVia Torino, 155, 30172, Venice-Mestre, Italy
| | - Martina Cecchetto
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
| | - Elisa Giubilato
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
| | - Claudio Carrer
- Thetis S.P.a. C/o laboratorio del Provveditorato Interregionale Alle Opere Pubbliche Per Il Veneto, Il Trentino Alto Adige E Il Friuli Venezia Giulia, Venice-Mestre, Italy
| | - Cinzia Bettiol
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
| | - Elena Semenzin
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
| | - Antonio Marcomini
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
| | - Valerio Matozzo
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy.
- NFBC, National Future Biodiversity Center, Palermo, Italy.
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
- NFBC, National Future Biodiversity Center, Palermo, Italy
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8
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Zong W, Seney ML, Ketchesin KD, Gorczyca MT, Liu AC, Esser KA, Tseng GC, McClung CA, Huo Z. Experimental design and power calculation in omics circadian rhythmicity detection using the cosinor model. Stat Med 2023; 42:3236-3258. [PMID: 37265194 PMCID: PMC10425922 DOI: 10.1002/sim.9803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/27/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Circadian clocks are 24-h endogenous oscillators in physiological and behavioral processes. Though recent transcriptomic studies have been successful in revealing the circadian rhythmicity in gene expression, the power calculation for omics circadian analysis have not been fully explored. In this paper, we develop a statistical method, namely CircaPower, to perform power calculation for circadian pattern detection. Our theoretical framework is determined by three key factors in circadian gene detection: sample size, intrinsic effect size and sampling design. Via simulations, we systematically investigate the impact of these key factors on circadian power calculation. We not only demonstrate that CircaPower is fast and accurate, but also show its underlying cosinor model is robust against variety of violations of model assumptions. In real applications, we demonstrate the performance of CircaPower using mouse pan-tissue data and human post-mortem brain data, and illustrate how to perform circadian power calculation using mouse skeleton muscle RNA-Seq pilot as case study. Our method CircaPower has been implemented in an R package, which is made publicly available on GitHub ( https://github.com/circaPower/circaPower).
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Affiliation(s)
- Wei Zong
- Department of Biostatistics, University of Pittsburgh, PA, USA
| | - Marianne L. Seney
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Kyle D. Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Michael T. Gorczyca
- Department of Computational and Systems Biology, University of Pittsburgh, PA, USA
| | - Andrew C. Liu
- Department of Physiology and Aging, University of Florida, FL, USA
| | - Karyn A. Esser
- Department of Physiology and Aging, University of Florida, FL, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, PA, USA
| | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, FL, USA
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9
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Lyons LC, Vanrobaeys Y, Abel T. Sleep and memory: The impact of sleep deprivation on transcription, translational control, and protein synthesis in the brain. J Neurochem 2023; 166:24-46. [PMID: 36802068 PMCID: PMC10919414 DOI: 10.1111/jnc.15787] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/20/2023]
Abstract
In countries around the world, sleep deprivation represents a widespread problem affecting school-age children, teenagers, and adults. Acute sleep deprivation and more chronic sleep restriction adversely affect individual health, impairing memory and cognitive performance as well as increasing the risk and progression of numerous diseases. In mammals, the hippocampus and hippocampus-dependent memory are vulnerable to the effects of acute sleep deprivation. Sleep deprivation induces changes in molecular signaling, gene expression and may cause changes in dendritic structure in neurons. Genome wide studies have shown that acute sleep deprivation alters gene transcription, although the pool of genes affected varies between brain regions. More recently, advances in research have drawn attention to differences in gene regulation between the level of the transcriptome compared with the pool of mRNA associated with ribosomes for protein translation following sleep deprivation. Thus, in addition to transcriptional changes, sleep deprivation also affects downstream processes to alter protein translation. In this review, we focus on the multiple levels through which acute sleep deprivation impacts gene regulation, highlighting potential post-transcriptional and translational processes that may be affected by sleep deprivation. Understanding the multiple levels of gene regulation impacted by sleep deprivation is essential for future development of therapeutics that may mitigate the effects of sleep loss.
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Affiliation(s)
- Lisa C Lyons
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Iowa Neuroscience Institute, Iowa City, Iowa, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Iowa Neuroscience Institute, Iowa City, Iowa, USA
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10
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Debès C, Papadakis A, Grönke S, Karalay Ö, Tain LS, Mizi A, Nakamura S, Hahn O, Weigelt C, Josipovic N, Zirkel A, Brusius I, Sofiadis K, Lamprousi M, Lu YX, Huang W, Esmaillie R, Kubacki T, Späth MR, Schermer B, Benzing T, Müller RU, Antebi A, Partridge L, Papantonis A, Beyer A. Ageing-associated changes in transcriptional elongation influence longevity. Nature 2023; 616:814-821. [PMID: 37046086 PMCID: PMC10132977 DOI: 10.1038/s41586-023-05922-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/07/2023] [Indexed: 04/14/2023]
Abstract
Physiological homeostasis becomes compromised during ageing, as a result of impairment of cellular processes, including transcription and RNA splicing1-4. However, the molecular mechanisms leading to the loss of transcriptional fidelity are so far elusive, as are ways of preventing it. Here we profiled and analysed genome-wide, ageing-related changes in transcriptional processes across different organisms: nematodes, fruitflies, mice, rats and humans. The average transcriptional elongation speed (RNA polymerase II speed) increased with age in all five species. Along with these changes in elongation speed, we observed changes in splicing, including a reduction of unspliced transcripts and the formation of more circular RNAs. Two lifespan-extending interventions, dietary restriction and lowered insulin-IGF signalling, both reversed most of these ageing-related changes. Genetic variants in RNA polymerase II that reduced its speed in worms5 and flies6 increased their lifespan. Similarly, reducing the speed of RNA polymerase II by overexpressing histone components, to counter age-associated changes in nucleosome positioning, also extended lifespan in flies and the division potential of human cells. Our findings uncover fundamental molecular mechanisms underlying animal ageing and lifespan-extending interventions, and point to possible preventive measures.
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Affiliation(s)
- Cédric Debès
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Antonios Papadakis
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Özlem Karalay
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Luke S Tain
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Shuhei Nakamura
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Oliver Hahn
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Carina Weigelt
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Anne Zirkel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Isabell Brusius
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Konstantinos Sofiadis
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Mantha Lamprousi
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Yu-Xuan Lu
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Wenming Huang
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Reza Esmaillie
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Torsten Kubacki
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Martin R Späth
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Bernhard Schermer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Thomas Benzing
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Roman-Ulrich Müller
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Adam Antebi
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
| | - Linda Partridge
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, UCL, London, UK.
| | - Argyris Papantonis
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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11
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Milan M, Bernardini I, Bertolini C, Dalla Rovere G, Manuzzi A, Pastres R, Peruzza L, Smits M, Fabrello J, Breggion C, Sambo A, Boffo L, Gallocchio L, Carrer C, Sorrentino F, Bettiol C, Lodi GC, Semenzin E, Varagnolo M, Matozzo V, Bargelloni L, Patarnello T. Multidisciplinary long-term survey of Manila clam grown in farming sites subjected to different environmental conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160796. [PMID: 36528093 DOI: 10.1016/j.scitotenv.2022.160796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/14/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
In recent years recurrent bivalve mass mortalities considerably increased around the world, causing the collapse of natural and farmed populations. Venice Lagoon has historically represented one of the major production areas of the Manila clam Ruditapes philippinarum in Europe. However, in the last 20 years a 75 % decrease in the annual production has been experienced. While climate change and anthropogenic interventions may have played a key role in natural and farmed stocks reductions, no studies investigated at multiple levels the environmental stressors affecting farmed Manila clam to date. In this work we carried out a long-term monitoring campaign on Manila clam reared in four farming sites located at different distances from the southern Venice Lagoon inlet, integrating (meta)genomic approaches (i.e. RNA-seq; microbiota characterization), biometric measurements and chemical-physical parameters. Our study allowed to characterize the molecular mechanisms adopted by this species to cope with the different environmental conditions characterizing farming sites and to propose hypotheses to explain mortality events observed in recent years. Among the most important findings, the disruption of clam's immune response, the spread of Vibrio spp., and the up-regulation of molecular pathways involved in xenobiotic metabolism suggested major environmental stressors affecting clams farmed in sites placed close to Chioggia's inlet, where highest mortality was also observed. Overall, our study provides knowledge-based tools for managing Manila clam farming on-growing areas. In addition, the collected data is a snapshot of the time immediately before the commissioning of MoSE, a system of mobile barriers aimed at protecting Venice from high tides, and will represent a baseline for future studies on the effects of MoSE on clams farming and more in general on the ecology of the Venice Lagoon.
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Affiliation(s)
- Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy.
| | - Ilaria Bernardini
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Camilla Bertolini
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via torino 155, 30170 Venezia, Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Alice Manuzzi
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Roberto Pastres
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via torino 155, 30170 Venezia, Italy
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Morgan Smits
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Jacopo Fabrello
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Cristina Breggion
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Andrea Sambo
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | | | - Loretta Gallocchio
- Thetis s.p.a., c /o Provveditorato Interregionale OO.PP. - Ufficio Tecnico Antinquinamento Laboratorio CSMO, Via Asconio Pediano, 9, 35127 Padova, PD, Italy
| | - Claudio Carrer
- Thetis s.p.a., c /o Provveditorato Interregionale OO.PP. - Ufficio Tecnico Antinquinamento Laboratorio CSMO, Via Asconio Pediano, 9, 35127 Padova, PD, Italy
| | - Francesco Sorrentino
- Provveditorato Interregionale OO.PP. - Ufficio Tecnico Antinquinamento, San Polo 19, 30124 Venezia, Italy)
| | - Cinzia Bettiol
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via torino 155, 30170 Venezia, Italy
| | - Giulia Carolina Lodi
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via torino 155, 30170 Venezia, Italy
| | - Elena Semenzin
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via torino 155, 30170 Venezia, Italy
| | - Maurizio Varagnolo
- Societa' Agricola Kappa S. S. di Varagnolo Maurizio E. C., Chioggia, VE, Italy
| | - Valerio Matozzo
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
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12
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Muheim CM, Ford K, Medina E, Singletary K, Peixoto L, Frank MG. Ontogenesis of the molecular response to sleep loss. Neurobiol Sleep Circadian Rhythms 2023; 14:100092. [PMID: 37020466 PMCID: PMC10068260 DOI: 10.1016/j.nbscr.2023.100092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Sleep deprivation (SD) results in profound cellular and molecular changes in the adult mammalian brain. Some of these changes may result in, or aggravate, brain disease. However, little is known about how SD impacts gene expression in developing animals. We examined the transcriptional response in the prefrontal cortex (PFC) to SD across postnatal development in male mice. We used RNA sequencing to identify functional gene categories that were specifically impacted by SD. We find that SD has dramatically different effects on PFC genes depending on developmental age. Gene expression differences after SD fall into 3 categories: present at all ages (conserved), present when mature sleep homeostasis is first emerging, and those unique to certain ages. Developmentally conserved gene expression was limited to a few functional categories, including Wnt-signaling which suggests that this pathway is a core mechanism regulated by sleep. In younger ages, genes primarily related to growth and development are affected while changes in genes related to metabolism are specific to the effect of SD in adults.
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13
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Mezzelani M, Peruzza L, d'Errico G, Milan M, Gorbi S, Regoli F. Mixtures of environmental pharmaceuticals in marine organisms: Mechanistic evidence of carbamazepine and valsartan effects on Mytilus galloprovincialis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160465. [PMID: 36427727 DOI: 10.1016/j.scitotenv.2022.160465] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/12/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Unravelling the adverse outcomes of pharmaceuticals mixture represents a research priority to characterize the risk for marine ecosystems. The present study investigated, for the first time, the interactions between two of the most largely detected pharmaceuticals in marine species: carbamazepine (CBZ) and valsartan (VAL), elucidating mechanisms that can modulate bioaccumulation, excretion and the onset of toxicity. Mytilus galloprovincialis were exposed to environmental levels of CBZ and VAL dosed alone or in combination: measurement of drug bioaccumulation was integrated with changes in the whole transcriptome and responsiveness of various biochemical and cellular biomarkers. Interactive and competing mechanisms between tested drugs were revealed by the much higher CBZ accumulation in mussels exposed to this compound alone, while an opposite trend was observed for VAL. A complex network of responses was observed as variations of gene expression, functional effects on neurotransmission, cell cycle, immune responses and redox homeostasis. The elaboration of results through a quantitative Weight of Evidence model summarized a greater biological reactivity of CBZ compared to VAL and antagonistic interactions between these compounds, resulting in a reduced effect of the antiepileptic when combined with valsartan. Overall, new perspectives are highlighted for a more comprehensive risk assessment of environmental mixtures of pharmaceuticals.
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Affiliation(s)
- Marica Mezzelani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche (60131), Ancona, Italy
| | - Luca Peruzza
- Dipartimento di Biomedicina Comparata e Alimentazione, Università di Padova, Viale dell'Università, 16 - 35020 Legnaro (PD), Polo di Agripolis, Italy
| | - Giuseppe d'Errico
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche (60131), Ancona, Italy
| | - Massimo Milan
- Dipartimento di Biomedicina Comparata e Alimentazione, Università di Padova, Viale dell'Università, 16 - 35020 Legnaro (PD), Polo di Agripolis, Italy
| | - Stefania Gorbi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche (60131), Ancona, Italy
| | - Francesco Regoli
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche (60131), Ancona, Italy.
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14
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Giri B, Kaya U, Maboudi K, Abel T, Diba K. Sleep loss diminishes hippocampal reactivation and replay. RESEARCH SQUARE 2023:rs.3.rs-2540186. [PMID: 36824950 PMCID: PMC9949250 DOI: 10.21203/rs.3.rs-2540186/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Memories benefit from sleep, and sleep loss immediately following learning has a negative impact on subsequent memory storage. Several prominent hypotheses ascribe a central role to hippocampal sharp-wave ripples (SWRs), and the concurrent reactivation and replay of neuronal patterns from waking experience, in the offline memory consolidation process that occurs during sleep. However, little is known about how SWRs, reactivation, and replay are affected when animals are subjected to sleep deprivation. We performed long duration (~12 h), high-density silicon probe recordings from rat hippocampal CA1 neurons, in animals that were either sleeping or sleep deprived following exposure to a novel maze environment. We found that SWRs showed a sustained rate of activity during sleep deprivation, similar to or higher than in natural sleep, but with decreased amplitudes for the sharp-waves combined with higher frequencies for the ripples. Furthermore, while hippocampal pyramidal cells showed a log-normal distribution of firing rates during sleep, these distributions were negatively skewed with a higher mean firing rate in both pyramidal cells and interneurons during sleep deprivation. During SWRs, however, firing rates were remarkably similar between both groups. Despite the abundant quantity of SWRs and the robust firing activity during these events in both groups, we found that reactivation of neurons was either completely abolished or significantly diminished during sleep deprivation compared to sleep. Interestingly, reactivation partially rebounded upon recovery sleep, but failed to reach the levels characteristic of natural sleep. Similarly, the number of replays were significantly lower during sleep deprivation and recovery sleep compared to natural sleep. These results provide a network-level account for the negative impact of sleep loss on hippocampal function and demonstrate that sleep loss impacts memory storage by causing a dissociation between the amount of SWRs and the replays and reactivations that take place during these events.
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Affiliation(s)
- Bapun Giri
- Dept of Anesthesiology and Neuroscience Graduate Program, 1150 W Medical Center Dr, University of Michigan Medical School, Ann Arbor, MI 48109
- Dept of Psychology, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201
| | - Utku Kaya
- Dept of Anesthesiology and Neuroscience Graduate Program, 1150 W Medical Center Dr, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Kourosh Maboudi
- Dept of Anesthesiology and Neuroscience Graduate Program, 1150 W Medical Center Dr, University of Michigan Medical School, Ann Arbor, MI 48109
- Dept of Psychology, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, USA
| | - Kamran Diba
- Dept of Anesthesiology and Neuroscience Graduate Program, 1150 W Medical Center Dr, University of Michigan Medical School, Ann Arbor, MI 48109
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15
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Obodo D, Outland EH, Hughey JJ. Sex Inclusion in Transcriptome Studies of Daily Rhythms. J Biol Rhythms 2023; 38:3-14. [PMID: 36419398 PMCID: PMC9903005 DOI: 10.1177/07487304221134160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Biomedical research on mammals has traditionally neglected females, raising the concern that some scientific findings may generalize poorly to half the population. Although this lack of sex inclusion has been broadly documented, its extent within circadian genomics remains undescribed. To address this gap, we examined sex inclusion practices in a comprehensive collection of publicly available transcriptome studies on daily rhythms. Among 148 studies having samples from mammals in vivo, we found strong underrepresentation of females across organisms and tissues. Overall, only 23 of 123 studies in mice, 0 of 10 studies in rats, and 9 of 15 studies in humans included samples from females. In addition, studies having samples from both sexes tended to have more samples from males than from females. These trends appear to have changed little over time, including since 2016, when the US National Institutes of Health began requiring investigators to consider sex as a biological variable. Our findings highlight an opportunity to dramatically improve representation of females in circadian research and to explore sex differences in daily rhythms at the genome level.
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Affiliation(s)
- Dora Obodo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Elliot H. Outland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jacob J. Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee,Jacob J. Hughey, Department of Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End Ave., Suite 1475, Nashville, TN 37232, USA; e-mail:
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16
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Vanrobaeys Y, Peterson ZJ, Walsh EN, Chatterjee S, Lin LC, Lyons LC, Nickl-Jockschat T, Abel T. Spatial transcriptomics reveals unique gene expression changes in different brain regions after sleep deprivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524406. [PMID: 36712009 PMCID: PMC9882298 DOI: 10.1101/2023.01.18.524406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Sleep deprivation has far-reaching consequences on the brain and behavior, impacting memory, attention, and metabolism. Previous research has focused on gene expression changes in individual brain regions, such as the hippocampus or cortex. Therefore, it is unclear how uniformly or heterogeneously sleep loss affects the brain. Here, we use spatial transcriptomics to define the impact of a brief period of sleep deprivation across the brain. We find that sleep deprivation induced pronounced differences in gene expression across the brain, with the greatest changes in the hippocampus, neocortex, hypothalamus, and thalamus. Both the differentially expressed genes and the direction of regulation differed markedly across regions. Importantly, we developed bioinformatic tools to register tissue sections and gene expression data into a common anatomical space, allowing a brain-wide comparison of gene expression patterns between samples. Our results suggest that distinct molecular mechanisms acting in discrete brain regions underlie the biological effects of sleep deprivation.
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Affiliation(s)
- Yann Vanrobaeys
- Interdisciplinary Graduate Program in Genetics, University of Iowa, 357 Medical Research Center Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
| | - Zeru J. Peterson
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Emily. N. Walsh
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, 356 Medical Research Center, Iowa City, IA 52242, USA
| | - Snehajyoti Chatterjee
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
| | - Li-Chun Lin
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neurology, University of Iowa, Iowa City, IA, USA
| | - Lisa C. Lyons
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Thomas Nickl-Jockschat
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
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17
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Muheim CM, Ford K, Medina E, Singletary K, Peixoto L, Frank MG. Ontogenesis of the molecular response to sleep loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524266. [PMID: 36712085 PMCID: PMC9882159 DOI: 10.1101/2023.01.16.524266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sleep deprivation (SD) results in profound cellular and molecular changes in the adult mammalian brain. Some of these changes may result in, or aggravate, brain disease. However, little is known about how SD impacts gene expression in developing animals. We examined the transcriptional response in the prefrontal cortex (PFC) to SD across postnatal development in male mice. We used RNA sequencing to identify functional gene categories that were specifically impacted by SD. We find that SD has dramatically different effects on PFC genes depending on developmental age. Gene expression differences after SD fall into 3 categories: present at all ages (conserved), present when mature sleep homeostasis is first emerging, and those unique to certain ages in adults. Developmentally conserved gene expression was limited to a few functional categories, including Wnt-signaling which suggests that this pathway is a core mechanism regulated by sleep. In younger ages, genes primarily related to growth and development are affected while changes in genes related to metabolism are specific to the effect of SD in adults.
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Affiliation(s)
- Christine M. Muheim
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA
| | - Kaitlyn Ford
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA
| | - Elizabeth Medina
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA
| | - Kristan Singletary
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA
| | - Lucia Peixoto
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,Correspondence: & , Tel.: +01-509 368 6747
| | - Marcos G. Frank
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA,Correspondence: & , Tel.: +01-509 368 6747
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18
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Jha PK, Valekunja UK, Ray S, Nollet M, Reddy AB. Single-cell transcriptomics and cell-specific proteomics reveals molecular signatures of sleep. Commun Biol 2022; 5:846. [PMID: 35986171 PMCID: PMC9391396 DOI: 10.1038/s42003-022-03800-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
Every day, we sleep for a third of the day. Sleep is important for cognition, brain waste clearance, metabolism, and immune responses. The molecular mechanisms governing sleep are largely unknown. Here, we used a combination of single-cell RNA sequencing and cell-type-specific proteomics to interrogate the molecular underpinnings of sleep. Different cell types in three important brain regions for sleep (brainstem, cortex, and hypothalamus) exhibited diverse transcriptional responses to sleep need. Sleep restriction modulates astrocyte-neuron crosstalk and sleep need enhances expression of specific sets of transcription factors in different brain regions. In cortex, we also interrogated the proteome of two major cell types: astrocytes and neurons. Sleep deprivation differentially alters the expression of proteins in astrocytes and neurons. Similarly, phosphoproteomics revealed large shifts in cell-type-specific protein phosphorylation. Our results indicate that sleep need regulates transcriptional, translational, and post-translational responses in a cell-specific manner.
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Affiliation(s)
- Pawan K Jha
- Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Utham K Valekunja
- Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sandipan Ray
- Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India
| | - Mathieu Nollet
- Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Akhilesh B Reddy
- Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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19
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Ingiosi AM, Frank MG. Noradrenergic Signaling in Astrocytes Influences Mammalian Sleep Homeostasis. Clocks Sleep 2022; 4:332-345. [PMID: 35892990 PMCID: PMC9326550 DOI: 10.3390/clockssleep4030028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/22/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023] Open
Abstract
Astrocytes influence sleep expression and regulation, but the cellular signaling pathways involved in these processes are poorly defined. We proposed that astrocytes detect and integrate a neuronal signal that accumulates during wakefulness, thereby leading to increased sleep drive. Noradrenaline (NA) satisfies several criteria for a waking signal integrated by astrocytes. We therefore investigated the role of NA signaling in astrocytes in mammalian sleep. We conditionally knocked out (cKO) β2-adrenergic receptors (β2-AR) selectively in astrocytes in mice and recorded electroencephalographic and electromyographic activity under baseline conditions and in response to sleep deprivation (SDep). cKO of astroglial β2-ARs increased active phase siesta duration under baseline conditions and reduced homeostatic compensatory changes in sleep consolidation and non-rapid eye movement slow-wave activity (SWA) after SDep. Overall, astroglial NA β2-ARs influence mammalian sleep homeostasis in a manner consistent with our proposed model of neuronal-astroglial interactions.
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Affiliation(s)
- Ashley M. Ingiosi
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA;
| | - Marcos G. Frank
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA;
- Gleason Institute for Neuroscience, Washington State University, Spokane, WA 99202, USA
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20
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Giannos P, Prokopidis K, Forbes SC, Celoch K, Candow DG, Tartar JL. Gene Expression Changes of Murine Cortex Homeostasis in Response to Sleep Deprivation Hint Dysregulated Aging-like Transcriptional Responses. Brain Sci 2022; 12:825. [PMID: 35884632 PMCID: PMC9313387 DOI: 10.3390/brainsci12070825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 12/04/2022] Open
Abstract
Sleep deprivation leads to the deterioration in the physiological functioning of the brain, cognitive decline, and many neurodegenerative diseases, all of which progress with advancing age. Sleep insufficiency and impairments in cognitive function are characterized by progressive neuronal losses in the cerebral cortex. In this study, we analyze gene expression profiles following sleep-deprived murine models and circadian matched controls to identify genes that might underlie cortical homeostasis in response to sleep deprivation. Screening of the literature resulted in three murine (Mus musculus) gene expression datasets (GSE6514, GSE78215, and GSE33491) that included cortical tissue biopsies from mice that are sleep deprived for 6 h (n = 15) and from circadian controls that are left undisturbed (n = 15). Cortical differentially expressed genes are used to construct a network of encoded proteins that are ranked based on their interactome according to 11 topological algorithms. The analysis revealed three genes-NFKBIA, EZR, and SGK1-which exhibited the highest multi-algorithmic topological significance. These genes are strong markers of increased brain inflammation, cytoskeletal aberrations, and glucocorticoid resistance, changes that imply aging-like transcriptional responses during sleep deprivation in the murine cortex. Their potential role as candidate markers of local homeostatic response to sleep loss in the murine cortex warrants further experimental validation.
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Affiliation(s)
- Panagiotis Giannos
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
- Society of Meta-Research and Biomedical Innovation, London W12 0BZ, UK;
| | - Konstantinos Prokopidis
- Society of Meta-Research and Biomedical Innovation, London W12 0BZ, UK;
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Scott C. Forbes
- Department of Physical Education Studies, Faculty of Education, Brandon University, Brandon, MB R7A 6A9, Canada;
| | - Kamil Celoch
- Department of Psychology and Neuroscience, Nova Southeastern University, Fort Lauderdale, FL 33314, USA; (K.C.); (J.L.T.)
| | - Darren G. Candow
- Faculty of Kinesiology and Health Studies, University of Regina, Regina, SK S4S 0A2, Canada;
| | - Jaime L. Tartar
- Department of Psychology and Neuroscience, Nova Southeastern University, Fort Lauderdale, FL 33314, USA; (K.C.); (J.L.T.)
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21
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TNF signaling pathway-mediated microglial activation in the PFC underlies acute paradoxical sleep deprivation-induced anxiety-like behaviors in mice. Brain Behav Immun 2022; 100:254-266. [PMID: 34915154 DOI: 10.1016/j.bbi.2021.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/08/2021] [Accepted: 12/09/2021] [Indexed: 12/24/2022] Open
Abstract
Acute sleep deprivation is a common condition in modern life and increases anxiety symptoms in healthy individuals. The neuroinflammatory response induced by microglial activation could be an important contributing factor, but its underlying molecular mechanisms are still unclear. In the present study, we first found that acute paradoxical sleep deprivation (PSD) induced by the modified multiple platform method (MMPM) for 6 h led to anxiety-like behavior in mice, as verified by the open field test, elevated plus maze test, light-dark box test, and marble burying test. In addition, bioinformatic analysis suggested an important relationship between acute sleep deprivation and brain inflammatory signaling pathways. Key genes enriched in the TNF signaling pathway were confirmed to be altered during acute PSD by qPCR and Western blot analyses, including the upregulation of the prostaglandin-endoperoxide synthase 2 (Ptgs2) and suppressor of cytokine signaling 3 protein (Socs3) genes and the downregulation of the cysteine-aspartic acid protease 3 (Casp3) gene. Furthermore, we found that microglial cells in the prefrontal cortex (PFC) were activated with significant branch structure changes and that the cell body area was increased in the PSD model. Finally, we found that minocycline, a tetracycline with anti-inflammatory properties, may ameliorate the anxiogenic effect and microglial activation. Our study reveals significant correlations of anxiety-like behavior, microglial activation, and inflammation during acute PSD.
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22
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Barahona RA, Morabito S, Swarup V, Green KN. Cortical diurnal rhythms remain intact with microglial depletion. Sci Rep 2022; 12:114. [PMID: 34997092 PMCID: PMC8742049 DOI: 10.1038/s41598-021-04079-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/01/2021] [Indexed: 12/15/2022] Open
Abstract
Microglia are subject to change in tandem with the endogenously generated biological oscillations known as our circadian rhythm. Studies have shown microglia harbor an intrinsic molecular clock which regulates diurnal changes in morphology and influences inflammatory responses. In the adult brain, microglia play an important role in the regulation of condensed extracellular matrix structures called perineuronal nets (PNNs), and it has been suggested that PNNs are also regulated in a circadian and diurnal manner. We sought to determine whether microglia mediate the diurnal regulation of PNNs via CSF1R inhibitor dependent microglial depletion in C57BL/6J mice, and how the absence of microglia might affect cortical diurnal gene expression rhythms. While we observe diurnal differences in microglial morphology, where microglia are most ramified at the onset of the dark phase, we do not find diurnal differences in PNN intensity. However, PNN intensity increases across many brain regions in the absence of microglia, supporting a role for microglia in the regulation of PNNs. Here, we also show that cortical diurnal gene expression rhythms are intact, with no cycling gene changes without microglia. These findings demonstrate a role for microglia in the maintenance of PNNs, but not in the maintenance of diurnal rhythms.
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Affiliation(s)
- Rocio A Barahona
- Department of Neurobiology and Behavior, University of California, 3208 Biological Sciences III, Irvine, CA, 92697, USA
| | - Samuel Morabito
- Mathematical, Computational and Systems Biology (MCSB) Program, University of California, Irvine, CA, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, 3208 Biological Sciences III, Irvine, CA, 92697, USA
| | - Kim N Green
- Department of Neurobiology and Behavior, University of California, 3208 Biological Sciences III, Irvine, CA, 92697, USA.
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23
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Gaine ME, Bahl E, Chatterjee S, Michaelson JJ, Abel T, Lyons LC. Altered hippocampal transcriptome dynamics following sleep deprivation. Mol Brain 2021; 14:125. [PMID: 34384474 PMCID: PMC8361790 DOI: 10.1186/s13041-021-00835-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Widespread sleep deprivation is a continuing public health problem in the United States and worldwide affecting adolescents and adults. Acute sleep deprivation results in decrements in spatial memory and cognitive impairments. The hippocampus is vulnerable to acute sleep deprivation with changes in gene expression, cell signaling, and protein synthesis. Sleep deprivation also has long lasting effects on memory and performance that persist after recovery sleep, as seen in behavioral studies from invertebrates to humans. Although previous research has shown that acute sleep deprivation impacts gene expression, the extent to which sleep deprivation affects gene regulation remains unknown. Using an unbiased deep RNA sequencing approach, we investigated the effects of acute sleep deprivation on gene expression in the hippocampus. We identified 1,146 genes that were significantly dysregulated following sleep deprivation with 507 genes upregulated and 639 genes downregulated, including protein coding genes and long non-coding RNAs not previously identified as impacted by sleep deprivation. Notably, genes significantly upregulated after sleep deprivation were associated with RNA splicing and the nucleus. In contrast, downregulated genes were associated with cell adhesion, dendritic localization, the synapse, and postsynaptic membrane. Furthermore, we found through independent experiments analyzing a subset of genes that three hours of recovery sleep following acute sleep deprivation was sufficient to normalize mRNA abundance for most genes, although exceptions occurred for some genes that may affect RNA splicing or transcription. These results clearly demonstrate that sleep deprivation differentially regulates gene expression on multiple transcriptomic levels to impact hippocampal function.
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Affiliation(s)
- 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
| | - Ethan Bahl
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jacob J Michaelson
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA, USA
- Department of Communication Sciences and Disorders, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Human Genetics, 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
| | - Lisa C Lyons
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL, USA.
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24
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Yang Y, Sun H, Zhang Y, Zhang T, Gong J, Wei Y, Duan YG, Shu M, Yang Y, Wu D, Yu D. Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data. Cell Rep 2021; 36:109442. [PMID: 34320340 DOI: 10.1016/j.celrep.2021.109442] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/01/2021] [Accepted: 07/01/2021] [Indexed: 12/13/2022] Open
Abstract
Transcriptomic analysis plays a key role in biomedical research. Linear dimensionality reduction methods, especially principal-component analysis (PCA), are widely used in detecting sample-to-sample heterogeneity, while recently developed non-linear methods, such as t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP), can efficiently cluster heterogeneous samples in single-cell RNA sequencing analysis. Yet, the application of t-SNE and UMAP in bulk transcriptomic analysis and comparison with conventional methods have not been achieved. We compare four major dimensionality reduction methods (PCA, multidimensional scaling [MDS], t-SNE, and UMAP) in analyzing 71 large bulk transcriptomic datasets. UMAP is superior to PCA and MDS but shows some advantages over t-SNE in differentiating batch effects, identifying pre-defined biological groups, and revealing in-depth clusters in two-dimensional space. Importantly, UMAP generates sample clusters uncovering biological features and clinical meaning. We recommend deploying UMAP in visualizing and analyzing sizable bulk transcriptomic datasets to reinforce sample heterogeneity analysis.
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Affiliation(s)
- Yang Yang
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia; Shandong Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Hongjian Sun
- Shandong Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China; School of Microelectronics, Shandong University, Jinan, China
| | - Yu Zhang
- Laboratory of Immunology for Environment and Health, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Tiefu Zhang
- University of Electronic Science and Technology of China, Chengdu, China
| | - Jialei Gong
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, University of Hong Kong, Shenzhen Hospital, Shenzhen, China
| | - Yunbo Wei
- Laboratory of Immunology for Environment and Health, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yong-Gang Duan
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, University of Hong Kong, Shenzhen Hospital, Shenzhen, China
| | - Minglei Shu
- Shandong Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yuchen Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oral and Craniofacial Health Science, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Di Yu
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia; Shandong Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China; Laboratory of Immunology for Environment and Health, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China.
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25
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Bernardini I, Matozzo V, Valsecchi S, Peruzza L, Rovere GD, Polesello S, Iori S, Marin MG, Fabrello J, Ciscato M, Masiero L, Bonato M, Santovito G, Boffo L, Bargelloni L, Milan M, Patarnello T. The new PFAS C6O4 and its effects on marine invertebrates: First evidence of transcriptional and microbiota changes in the Manila clam Ruditapes philippinarum. ENVIRONMENT INTERNATIONAL 2021; 152:106484. [PMID: 33740673 DOI: 10.1016/j.envint.2021.106484] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/16/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
There is growing concern for the wide use ofperfluorooctanoic acid (PFOA) because of its toxic effects on the environment and on human health. A new compound - the so called C6O4 (perfluoro ([5-methoxy-1,3-dioxolan-4-yl]oxy) acetic acid) - was recently introduced as one of the alternative to traditional PFOA, however this was done without any scientific evidence of the effects of C6O4 when dispersed into the environment. Recently, the Regional Agency for the Protection of the Environment of Veneto (Italy) detected high levels of C6O4 in groundwater and in the Po river, increasing the alarm for the potential effects of this chemical into the natural environment. The present study investigates for the first time the effects of C6O4 on the Manila clam Ruditapes philippinarum exposed to environmental realistic concentrations of C6O4 (0.1 µg/L and 1 µg/L) for 7 and 21 days. Furthermore, in order to better understand if C6O4 is a valid and less hazardous alternative to its substitute, microbial and transcriptomic alterations were also investigated in clams exposed to 1 µg/L ofPFOA. Results indicate that C6O4 may cause significant perturbations to the digestive gland microbiota, likely determining the impairment of host physiological homeostasis. Despite chemical analyses suggest a 5 times lower accumulation potential of C604 as compared to PFOA in clam soft tissues, transcriptional analyses reveal several alterations of gene expression profile. A large part of the altered pathways, including immune response, apoptosis regulation, nervous system development, lipid metabolism and cell membrane is the same in C6O4 and PFOA exposed clams. In addition, clams exposed to C6O4 showed dose-dependent responses as well as possible narcotic or neurotoxic effects and reduced activation of genes involved in xenobiotic metabolism. Overall, the present study suggests that the potential risks for marine organism following environmental contamination are not reduced by replacing PFOA with C6O4. In addition, the detection of both C6O4 and PFOA into tissues of clams inhabiting the Lagoon of Venice - where there are no point sources of either compounds - recommends a similar capacity to spread throughout the environment. These results prompt the urgent need to re-evaluate the use of C6O4 as it may represent not only an environmental hazard but also a potential risk for human health.
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Affiliation(s)
- Ilaria Bernardini
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Valerio Matozzo
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Sara Valsecchi
- Water Research Institute, Italian National Research Council (IRSA-CNR), Via Mulino 19, 20861 Brugherio, MB, Italy
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Stefano Polesello
- Water Research Institute, Italian National Research Council (IRSA-CNR), Via Mulino 19, 20861 Brugherio, MB, Italy
| | - Silvia Iori
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | | | - Jacopo Fabrello
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Maria Ciscato
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Luciano Masiero
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Marco Bonato
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Gianfranco Santovito
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | | | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy.
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
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26
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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: 18] [Impact Index Per Article: 4.5] [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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27
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Xu C, Li Q, Efimova O, Jiang X, Petrova M, K Vinarskaya A, Kolosov P, Aseyev N, Koshkareva K, Ierusalimsky VN, Balaban PM, Khaitovich P. Identification of Immediate Early Genes in the Nervous System of Snail Helix lucorum. eNeuro 2019; 6:ENEURO.0416-18.2019. [PMID: 31053606 PMCID: PMC6584072 DOI: 10.1523/eneuro.0416-18.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 03/02/2019] [Accepted: 03/17/2019] [Indexed: 02/06/2023] Open
Abstract
Immediate early genes (IEGs) are useful markers of neuronal activation and essential components of neuronal response. While studies of gastropods have provided many insights into the basic learning and memory mechanisms, the genome-wide assessment of IEGs has been mainly restricted to vertebrates. In this study, we identified IEGs in the terrestrial snail Helix lucorum In the absence of the genome, we conducted de novo transcriptome assembly using reads with short and intermediate lengths cumulatively covering more than 98 billion nucleotides. Based on this assembly, we identified 37 proteins corresponding to contigs differentially expressed (DE) in either the parietal ganglia (PaG) or two giant interneurons located within the PaG of the snail in response to the neuronal stimulation. These proteins included homologues of well-known mammalian IEGs, such as c-jun/jund, C/EBP, c-fos/fosl2, and Egr1, as well as homologues of genes not yet implicated in the neuronal response.
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Affiliation(s)
- Chuan Xu
- CAS Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian Li
- CAS Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Olga Efimova
- Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Xi Jiang
- CAS Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Marina Petrova
- CAS Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Alia K Vinarskaya
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Peter Kolosov
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Nikolay Aseyev
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Kira Koshkareva
- Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | | | - Pavel M Balaban
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Moscow 143026, Russia
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Comparative Biology Laboratory, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
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28
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Ingiosi AM, Schoch H, Wintler T, Singletary KG, Righelli D, Roser LG, Medina E, Risso D, Frank MG, Peixoto L. Shank3 modulates sleep and expression of circadian transcription factors. eLife 2019; 8:e42819. [PMID: 30973326 PMCID: PMC6488297 DOI: 10.7554/elife.42819] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 04/10/2019] [Indexed: 12/30/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is the most prevalent neurodevelopmental disorder in the United States and often co-presents with sleep problems. Sleep problems in ASD predict the severity of ASD core diagnostic symptoms and have a considerable impact on the quality of life of caregivers. Little is known, however, about the underlying molecular mechanisms of sleep problems in ASD. We investigated the role of Shank3, a high confidence ASD gene candidate, in sleep architecture and regulation. We show that mice lacking exon 21 of Shank3 have problems falling asleep even when sleepy. Using RNA-seq we show that sleep deprivation increases the differences in prefrontal cortex gene expression between mutants and wild types, downregulating circadian transcription factors Per3, Bhlhe41, Hlf, Tef, and Nr1d1. Shank3 mutants also have trouble regulating wheel-running activity in constant darkness. Overall, our study shows that Shank3 is an important modulator of sleep and clock gene expression.
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Affiliation(s)
- Ashley M Ingiosi
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Hannah Schoch
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Taylor Wintler
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Kristan G Singletary
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Dario Righelli
- Istituto per le Applicazioni del Calcolo “M. Picone”Consiglio Nazionale della RicercheNapoliItaly
- Dipartimento di Scienze Aziendali Management & Innovation SystemsUniversity of FuscianoFiscianoItaly
| | - Leandro G Roser
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Elizabeth Medina
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Davide Risso
- Department of Statistical SciencesUniversity of PadovaPadovaItaly
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and ResearchWeill Cornell MedicineNew YorkUnited States
| | - Marcos G Frank
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Lucia Peixoto
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
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29
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Athanasiadou R, Neymotin B, Brandt N, Wang W, Christiaen L, Gresham D, Tranchina D. A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory. PLoS Comput Biol 2019; 15:e1006794. [PMID: 30856174 PMCID: PMC6428340 DOI: 10.1371/journal.pcbi.1006794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 03/21/2019] [Accepted: 01/16/2019] [Indexed: 01/09/2023] Open
Abstract
A fundamental assumption, common to the vast majority of high-throughput transcriptome analyses, is that the expression of most genes is unchanged among samples and that total cellular RNA remains constant. As the number of analyzed experimental systems increases however, different independent studies demonstrate that this assumption is often violated. We present a calibration method using RNA spike-ins that allows for the measurement of absolute cellular abundance of RNA molecules. We apply the method to pooled RNA from cell populations of known sizes. For each transcript, we compute a nominal abundance that can be converted to absolute by dividing by a scale factor determined in separate experiments: the yield coefficient of the transcript relative to that of a reference spike-in measured with the same protocol. The method is derived by maximum likelihood theory in the context of a complete statistical model for sequencing counts contributed by cellular RNA and spike-ins. The counts are based on a sample from a fixed number of cells to which a fixed population of spike-in molecules has been added. We illustrate and evaluate the method with applications to two global expression data sets, one from the model eukaryote Saccharomyces cerevisiae, proliferating at different growth rates, and differentiating cardiopharyngeal cell lineages in the chordate Ciona robusta. We tested the method in a technical replicate dilution study, and in a k-fold validation study.
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Affiliation(s)
- Rodoniki Athanasiadou
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Benjamin Neymotin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Nathan Brandt
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Wei Wang
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York, United States of America
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Daniel Tranchina
- Department of Biology, New York University, New York, New York, United States of America
- Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
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30
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Seibt J, Frank MG. Primed to Sleep: The Dynamics of Synaptic Plasticity Across Brain States. Front Syst Neurosci 2019; 13:2. [PMID: 30774586 PMCID: PMC6367653 DOI: 10.3389/fnsys.2019.00002] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/09/2019] [Indexed: 11/13/2022] Open
Abstract
It is commonly accepted that brain plasticity occurs in wakefulness and sleep. However, how these different brain states work in concert to create long-lasting changes in brain circuitry is unclear. Considering that wakefulness and sleep are profoundly different brain states on multiple levels (e.g., cellular, molecular and network activation), it is unlikely that they operate exactly the same way. Rather it is probable that they engage different, but coordinated, mechanisms. In this article we discuss how plasticity may be divided across the sleep-wake cycle, and how synaptic changes in each brain state are linked. Our working model proposes that waking experience triggers short-lived synaptic events that are necessary for transient plastic changes and mark (i.e., 'prime') circuits and synapses for further processing in sleep. During sleep, synaptic protein synthesis at primed synapses leads to structural changes necessary for long-term information storage.
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Affiliation(s)
- Julie Seibt
- Surrey Sleep Research Centre, University of Surrey, Guildford, United Kingdom
| | - Marcos G. Frank
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University Spokane, Spokane, WA, United States
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31
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Scarpa JR, Jiang P, Gao VD, Fitzpatrick K, Millstein J, Olker C, Gotter A, Winrow CJ, Renger JJ, Kasarskis A, Turek FW, Vitaterna MH. Cross-species systems analysis identifies gene networks differentially altered by sleep loss and depression. SCIENCE ADVANCES 2018; 4:eaat1294. [PMID: 30050989 PMCID: PMC6059761 DOI: 10.1126/sciadv.aat1294] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
To understand the transcriptomic organization underlying sleep and affective function, we studied a population of (C57BL/6J × 129S1/SvImJ) F2 mice by measuring 283 affective and sleep phenotypes and profiling gene expression across four brain regions. We identified converging molecular bases for sleep and affective phenotypes at both the single-gene and gene-network levels. Using publicly available transcriptomic datasets collected from sleep-deprived mice and patients with major depressive disorder (MDD), we identified three cortical gene networks altered by the sleep/wake state and depression. The network-level actions of sleep loss and depression were opposite to each other, providing a mechanistic basis for the sleep disruptions commonly observed in depression, as well as the reported acute antidepressant effects of sleep deprivation. We highlight one particular network composed of circadian rhythm regulators and neuronal activity-dependent immediate-early genes. The key upstream driver of this network, Arc, may act as a nexus linking sleep and depression. Our data provide mechanistic insights into the role of sleep in affective function and MDD.
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Affiliation(s)
- Joseph R. Scarpa
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peng Jiang
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Vance D. Gao
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Karrie Fitzpatrick
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | | | - Christopher Olker
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Anthony Gotter
- Department of Neuroscience, Merck Research Laboratories, West Point, PA 19486, USA
| | | | - John J. Renger
- Department of Neuroscience, Merck Research Laboratories, West Point, PA 19486, USA
| | - Andrew Kasarskis
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fred W. Turek
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Martha H. Vitaterna
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
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32
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Frank MG, Seibt J. Sleep and plasticity: Waking from a fevered dream. Sleep Med Rev 2018; 39:1-2. [DOI: 10.1016/j.smrv.2017.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 12/15/2022]
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33
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Jones AC, Troy NM, White E, Hollams EM, Gout AM, Ling KM, Kicic A, Stick SM, Sly PD, Holt PG, Hall GL, Bosco A. Persistent activation of interlinked type 2 airway epithelial gene networks in sputum-derived cells from aeroallergen-sensitized symptomatic asthmatics. Sci Rep 2018; 8:1511. [PMID: 29367592 PMCID: PMC5784090 DOI: 10.1038/s41598-018-19837-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/04/2018] [Indexed: 02/08/2023] Open
Abstract
Atopic asthma is a persistent disease characterized by intermittent wheeze and progressive loss of lung function. The disease is thought to be driven primarily by chronic aeroallergen-induced type 2-associated inflammation. However, the vast majority of atopics do not develop asthma despite ongoing aeroallergen exposure, suggesting additional mechanisms operate in conjunction with type 2 immunity to drive asthma pathogenesis. We employed RNA-Seq profiling of sputum-derived cells to identify gene networks operative at baseline in house dust mite-sensitized (HDMS) subjects with/without wheezing history that are characteristic of the ongoing asthmatic state. The expression of type 2 effectors (IL-5, IL-13) was equivalent in both cohorts of subjects. However, in HDMS-wheezers they were associated with upregulation of two coexpression modules comprising multiple type 2- and epithelial-associated genes. The first module was interlinked by the hubs EGFR, ERBB2, CDH1 and IL-13. The second module was associated with CDHR3 and mucociliary clearance genes. Our findings provide new insight into the molecular mechanisms operative at baseline in the airway mucosa in atopic asthmatics undergoing natural aeroallergen exposure, and suggest that susceptibility to asthma amongst these subjects involves complex interactions between type 2- and epithelial-associated gene networks, which are not operative in equivalently sensitized/exposed atopic non-asthmatics.
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Affiliation(s)
- Anya C Jones
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, Australia
| | - Niamh M Troy
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, Australia
| | - Elisha White
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Elysia M Hollams
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Alexander M Gout
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Kak-Ming Ling
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Anthony Kicic
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, Australia.,Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Australia.,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Perth, Australia
| | - Stephen M Stick
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, Australia.,Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Australia.,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Perth, Australia
| | - Peter D Sly
- Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - Patrick G Holt
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - Graham L Hall
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,School of Physiotherapy and Exercise Science, Curtin University, Perth, Australia.,Centre of Child Health Research, The University of Western Australia, Perth, Australia
| | - Anthony Bosco
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.
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34
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Gerashchenko D, Pasumarthi RK, Kilduff TS. Plasticity-Related Gene Expression During Eszopiclone-Induced Sleep. Sleep 2017; 40:3866746. [PMID: 28605546 DOI: 10.1093/sleep/zsx098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Study Objectives Experimental evidence suggests that restorative processes depend on synaptic plasticity changes in the brain during sleep. We used the expression of plasticity-related genes to assess synaptic plasticity changes during drug-induced sleep. Methods We first characterized sleep induced by eszopiclone in mice during baseline conditions and during the recovery from sleep deprivation. We then compared the expression of 18 genes and two miRNAs critically involved in synaptic plasticity in these mice. Gene expression was assessed in the cerebral cortex and hippocampus by the TaqMan reverse transcription polymerase chain reaction and correlated with sleep parameters. Results Eszopiclone reduced the latency to nonrapid eye movement (NREM) sleep and increased NREM sleep amounts. Eszopiclone had no effect on slow wave activity (SWA) during baseline conditions but reduced the SWA increase during recovery sleep (RS) after sleep deprivation. Gene expression analyses revealed three distinct patterns: (1) four genes had higher expression either in the cortex or hippocampus in the group of mice with increased amounts of wakefulness; (2) a large proportion of plasticity-related genes (7 out of 18 genes) had higher expression during RS in the cortex but not in the hippocampus; and (3) six genes and the two miRNAs showed no significant changes across conditions. Even at a relatively high dose (20 mg/kg), eszopiclone did not reduce the expression of plasticity-related genes during RS period in the cortex. Conclusions These results indicate that gene expression associated with synaptic plasticity occurs in the cortex in the presence of a hypnotic medication.
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Affiliation(s)
| | - Ravi K Pasumarthi
- Center for Neuroscience, Biosciences Division, SRI International, Menlo Park, CA
| | - Thomas S Kilduff
- Center for Neuroscience, Biosciences Division, SRI International, Menlo Park, CA
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35
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Timofeev I, Chauvette S. Sleep slow oscillation and plasticity. Curr Opin Neurobiol 2017; 44:116-126. [PMID: 28453998 DOI: 10.1016/j.conb.2017.03.019] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/31/2017] [Indexed: 11/25/2022]
Abstract
It is well documented that sleep contributes to memory consolidation and it is also accepted that long-term synaptic plasticity plays a critical role in memory formation. The mechanisms of this sleep-dependent memory formation are unclear. Two main hypotheses are proposed. According to the first one, synapses are potentiated during wake; and during sleep they are scaled back to become available for the learning tasks in the next day. The other hypothesis is that sleep slow oscillations potentiate synapses that were depressed due to persistent activities during the previous day and that potentiation provides physiological basis for memory consolidation. The objective of this review is to group information on whether cortical synapses are up-scaled or down-scaled during sleep. We conclude that the majority of cortical synapses are up-regulated by sleep slow oscillation.
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Affiliation(s)
- Igor Timofeev
- Department of Psychiatry and Neuroscience, Université Laval Québec, QC G1V 0A6, Canada; Centre de recherche de l'Institut universitaire en santé mentale de Québec (CRIUSMQ), 2601, de la Canardière Québec, QC G1J 2G3, Canada.
| | - Sylvain Chauvette
- Centre de recherche de l'Institut universitaire en santé mentale de Québec (CRIUSMQ), 2601, de la Canardière Québec, QC G1J 2G3, Canada
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