Expression data from sleep deprivation experiment in mouse hippocampus
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Lucia Peixoto
PROVIDER: E-GEOD-33302 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus.
Vecsey Christopher G CG Peixoto Lucia L Choi Jennifer H K JH Wimmer Mathieu M Jaganath Devan D Hernandez Pepe J PJ Blackwell Jennifer J Meda Karuna K Park Alan J AJ Hannenhalli Sridhar S Abel Ted T
Physiological genomics 20120828 20
Sleep deprivation is a common problem of considerable health and economic impact in today's society. Sleep loss is associated with deleterious effects on cognitive functions such as memory and has a high comorbidity with many neurodegenerative and neuropsychiatric disorders. Therefore, it is crucial to understand the molecular basis of the effect of sleep deprivation in the brain. In this study, we combined genome-wide and traditional molecular biological approaches to determine the cellular and ...[more]
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Project description:Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence, however, indicates that sleep is necessary for normal brain function and that the need to sleep is a tightly regulated process. Surprisingly molecular mechanisms that determine the need to sleep are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. In this study we present an integrated 2 cross-laboratory analysis of the effects of sleep deprivation (SD) in gene expression in the mouse cortex. We also evaluate changes in gene expression genome-wide following various lengths of subsequent recovery sleep. (RS). We demonstrate that changes in gene expression specifically linked to SD or RS, and not to technical factors (e.g. the assay used), requires a novel analysis methodology not previously utilized in the field of sleep research. Cortical samples from mice were analyzed, from groups that were sleep deprived, sleep deprived and allowed to recover for 1, 2, 3, or 6 hours, and circadian control animals that were not sleep deprived. The experimental protocol began at lights on (ZT0) with 13 mice: 1 sacrificed, 4 control mice left undisturbed, and 8 mice kept awake with gentle brushing when attempting to sleep. After 5 hours of sleep deprivation the mice were randomly assigned to recovery sleep or continued sleep deprivation, and at fixed intervals the mice were sacrificed, dissected and the left cortex retained. The experimental protocol was repeated 7 times, one animal per timepoint per experimental day, so that 7 independent experiments are represented for each timepoint. All animals were acclimated to the brushing and tapping on cages used during sleep deprivationfor 6 days, and dissections and tissue collection were performed by a single experimenter.
2016-09-07 | E-GEOD-78215 | biostudies-arrayexpress
Project description:Sleep deprivation (SD) in young adults is associated with metabolic, stress and cognitive responses that are also characteristic of brain aging. Given that sleep architecture changes with age, including increased fragmentation and decreased slow wave activity, it seems reasonable to investigate potential molecular relationships between SD and aging in brain tissue. Here, we tested the hypothesis that young rats exposed to 24 or 72 hour SD would respond with stress and aging-like shifts in brain hippocampal CA1 gene expression. SD animals showed blood corticosterone and weight changes consistent with a stress response. Microarray results, validated by Western blot and comparison to prior SD studies, pointed to disruptions in neurotransmission, sleep pressure signaling, and macromolecular synthesis. In a separate experiment, animals exposed to 24 or 72 hour novel environment stress recapitulated nearly one third of the SD transcriptional profile, particularly upregulated apoptotic and immune signaling pathways. Compared to aging (based on three previously published independent hippocampal aging studies), SD transcriptional profiles agreed for neurogenesis and energy pathways. However, immune signaling, glial activity, macromolecular synthesis and neuronal function all showed an SD profile that was, at least in part, opposed by aging. We conclude that while stress and SD have discrete molecular signatures, they do show a subset of highly similar changes. However, the same could not be said of aging and SD, where a similar subset of genes is changed, but in partially divergent directions. Finally, this work identifies presynaptic vesicular release and intercellular adhesion molecular signatures as novel targets for future SD-countering therapeutics. Subjects: Male Fischer 344 rats (3-5 months old, Harlan, Indianapolis): 37 in cohort 1 and 32 in cohort 2. Subjects were assigned to one of 5 treatment groups: Home Cage-HC n =17; 24 hour sleep deprivation- 24SD n = 16; 72 hour sleep deprivation- 72SD n = 20; 24 hour novel environment stress- 24NES n = 10; 72 hour novel environment stress- 72NES n = 6. Cohorts 1 and 2 were combined for microarray analyses. Sleep Deprivation: The multiple platform modification (Coenen and van Luijtelaar, 1985) of the classic 'flower pot' (Mendelson et al., 1974) technique in which animals are placed on an elevated platform over water was used. Pairs of SD animals (cage mates) were sleep deprived for 24 or 72 hours. Novel Environment Stress (NES): NES animals were exposed to a novel environment, but were not constrained from sleeping. These NES animals paralleled the sleep deprivation exposure duration (24 hour- n = 10, and 72 hour- n = 6). Tissue Isolation: On the day that animals were removed from the SD chambers, they were anesthetized with CO2 gas and decapitated. Brains were removed and immediately placed in oxygenated artificial cerebrospinal fluid (aCSF) containing (in mM) 114NaCl, 2.5 KCl, 2MgCl2, 30 NaHCO3, 10 Glucose and 2.2CaCl2. Hippocampi were dissected as described previously (Blalock et al., 2003; Kadish et al., 2009). Briefly, dissected hippocampi were immersed in 0C oxygenated aCSF and placed on a chilled glass petri dish. The CA1 region was dissected along the long axis of the hippocampus. CA1 tissue was flash frozen and stored at -80C until further use. Microarray Protocol: GCOS quality control measures of background signal (74.9 ± 2.1 cohort 1; 59.8 ± 2.3 cohort 2) and RawQ (2.3 ± 0.1 cohort 1; 1.9 ± 0.1 cohort 2), as well as a chip x chip correlation matrix of signal intensity data pointed to a global decrease in background signal intensity in Cohort 2. To control for this, each gene expression values for HC, 24SD and 72SD was standardized separately within cohort 1 and cohort 2, and then the two cohorts were combined. This retained the variability of each cohort, but removed the 'cohort effect' from the data. Pre-statistical filtering retained 'A' grade probe sets that were uniquely annotated (Affymetrix, June 2011) with gene symbols and had at least 6 presence calls across all 71 chips. This criterion was selected based on factorial analysis demonstrating < 5% probability of 6 or more chips being rated present for a given probe set by chance (Blalock, unpublished observations).
2012-07-16 | E-GEOD-34424 | biostudies-arrayexpress
Project description:Extended periods of waking result in physiological impairments in humans, rats, and flies. Sleep homeostasis, the increase in sleep observed following sleep loss, is believed to counter the negative effects of prolonged waking by restoring vital biological processes that are degraded during sleep deprivation. Sleep homeostasis, as with other behaviors, is influenced by both genes and environment. We report here that during periods of starvation, flies remain spontaneously awake but, in contrast to sleep deprivation, do not accrue any of the negative consequences of prolonged waking. Specifically, the homeostatic response and learning impairments that are a characteristic of sleep loss are not observed following prolonged waking induced by starvation. To identify the genes responsible for the protective effects of starvation we conducted transcription profiling of sleep deprived flies that accrue sleep debt compared to starved siblings that do not. Genes involved in lipid metabolism were highly enriched in our dataset of 84 differentially regulated transcripts. Follow up genetic studies established that 6 genes involved in lipid metabolism strongly influence sleep homeostasis. Two of these genes, brummer (bmm) and Lipid storage droplet 2 (Lsd2), are in the same lipolysis pathway but exert antagonistic effects on lipid storage. bmm mutant flies have excess fat stores and display a large homeostatic response following sleep deprivation. In contrast, Lsd2 mutant flies, which phenocopy aspects of starvation as measured by low triglyceride stores, do not exhibit a homeostatic response following sleep loss. Importantly, Lsd2 mutant flies are not learning impaired after sleep deprivation. These results provide the first genetic evidence, to our knowledge, that lipid metabolism plays an important role in regulating the homeostatic response and can protect against neuronal impairments induced by prolonged waking. Two-condition experiments: sleep deprived vs starved. RNA from 8 biological replicates for each condition was pooled in groups of 2 to create 4 samples. Each of the 4 samples is run in duplicate with untreated circadian matched controls.
2014-04-15 | E-GEOD-18550 | biostudies-arrayexpress
Project description:These studies address temporal changes in gene expression during spontaneous sleep and extended wakefulness in the mouse cerebral cortex, a neuronal target for processes that control sleep; and the hypothalamus, an important site of sleep regulatory processes. We determined these changes by comparing expression in sleeping animals sacrificed at different times during the lights on period, to that in animals sleep deprived and sacrificed at the same diurnal time. Experiment Overall Design: Experiments were performed on male mice (C57/BL6), 10 weeks of age ±1 week. Animals were housed in a light/dark cycle of 12 hrs, in a pathogen free, temperature- and humidity-controlled room (22°C and 45-55%, respectively) with water available ad libitum. Food was accessible for 12 hrs only during the active period. Animals were subjected to 14 days of acclimatization during which a nighttime feeding pattern was established. This was done to avoid differential food intake between mice that were subsequently sleep deprived during the lights on period and those allowed to sleep. Mice were sacrificed following 3, 6, 9 and 12 hrs of total sleep deprivation (n=5 at each time point). Deprivation was initiated at lights-on, and performed through gentle handling. Sleeping animals, which were left undisturbed, were sacrificed at the same diurnal time points as sleep deprived mice (n=5 at each time point). An additional control group of mice were sacrificed at time zero, i.e., at the time of lights-on (n=5). All mice were behaviorally monitored using the AccuScan infrared monitoring system that detects movement when the mouse crosses electronic beams (Columbus Instruments). Mice were sacrificed by cervical dislocation. Brain sectioning was performed according to the mouse brain atlas of Franklin and Paxinos . The primary and secondary motor areas (M1 and M2) of the cerebral cortex and broadly defined regions and zones of the hypothalamus were sampled. RNA was isolated with Trizol (Invitrogen) and further purified using RNeasy columns (Qiagen) as per the manufacturer's instructions.
2008-06-15 | E-GEOD-6514 | biostudies-arrayexpress
Project description:Although at the organismal level sleep is defined as a behavioral state, at the level of the cerebral cortex sleep has a distinct local and use-dependent aspect. This observation raises the question whether sleep is a functional property of a complex brain or occurs at the level of neuronal assemblies with populations that were active more during wakefulness needing more intense sleep to recover. Here we show that primary cortical cultures have the capacity to change between sleep- and wake-like states that share key signatures with their in vivo counterparts. Cortical cultures initially exhibit random firing activity that is gradually replaced by a M-bM-^@M-^\sleep-likeM-bM-^@M-^] synchronized burst-pause firing activity as neurons mature and make connections. When stimulated with excitatory neurotransmitters, transient tonic firing is observed, followed by the reappearance of a M-bM-^@M-^\sleep-likeM-bM-^@M-^] state. Besides electrophysiological similarities also the transcriptional profile of stimulated cortical cultures greatly resembles that of the cortex of sleep deprived animals. We then used our in vitro model to map the metabolic pathways activated by the M-bM-^@M-^\wake-likeM-bM-^@M-^] state and found evidence for increased lysolipid release, strongly suggesting that sleep plays a role in neuronal membrane homeostasis. With our in vitro model the cellular and molecular consequences of sleep loss and the genetic determinants of disturbed sleep can now be investigated in a dish. Keywords: stress response For the in vivo transcriptome analyses mice were sleep deprived for 6 hours and brain harvested immediately afterwards. For the in vitro analyses, cortical cultures were stimulated with a neurotransmitter cocktail and cells harvested 3 hours afterwards. Control mice were kept undisturbed in their home cage and control cultures were sham stimulated with water. Also, another set of sleep deprived mice as well as stimulated cultures were allowed to recover before being sampled the next day at the time of day at which sleep deprivation or stimulation started the day before).
2012-08-31 | E-GEOD-33491 | biostudies-arrayexpress
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2008-06-16 | E-GEOD-9443 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series:; GSE9441: The effect of sleep deprivation on gene expression in the brain and the liver of three inbred mouse strains; GSE9442: Molecular correlates of sleep deprivation in the brain of three inbred mouse strains in an around-the-clock experiment; GSE9443: Gene expression in brain Homer1a-expressing cells after sleep deprivation Experiment Overall Design: Refer to individual Series
2008-06-17 | E-GEOD-9444 | biostudies-arrayexpress
Project description:Transcriptomic studies revealed that hundreds of mRNAs show differential expression in the brains of sleeping versus awake rats, mice, flies, and sparrows. Although these results have offered clues regarding the molecular consequences of sleep and sleep loss, their functional significance thus far has been limited. This is because the previous studies pooled transcripts from all brain cells, including neurons and glia. In the following experiment, we studied the specific effects of sleep and wake conditions on glia cells of mouse cerebral cortex using the genetically targeted translating ribosome affinity purification (TRAP) methodology. We used bacterial artificial chromosome (BAC) transgenic mice expressing EGFP tagged ribosomal protein L10a in astrocytes which constitute a defined cellular population of the mouse brain. Using this approach, we could extract only the astrocytic mRNAs, and only those already committed to be translated into proteins (L10a is part of the translational machinery). Six mice for each vigilant state group (sleep (S), waking (W), and sleep deprivation (SD)) were considered. For each animal, cerebral cortex was dissected and immediately processed. Samples were immunoprecipitated to isolate astrocytes. The precipitated portion formed the bound sample (IP) containing astrocytes and the remaining part formed the unbound sample (UB) containing all the remaining cell types (neurons and other glia cells). Then, both IP and UB samples were processed and RNA was extracted. All the IP samples (n=18) were then hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays, while UB samples were pooled together in two biological replicates (UB1+UB2+UB3 and UB4+UB5+UB6) for each group (n=6 in total) and then hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.
2015-07-08 | E-GEOD-69079 | biostudies-arrayexpress
Project description:Transcriptomic studies revealed that hundreds of mRNAs show differential expression in the brains of sleeping versus awake rats, mice, flies, and sparrows. Although these results have offered clues regarding the molecular consequences of sleep and sleep loss, their functional significance thus far has been limited. This is because the previous studies pooled transcripts from all brain cells, including neurons and glia. In the following experiment, we studied the specific effects of sleep and wake conditions on glia cells of mouse cerebral cortex using the genetically targeted translating ribosome affinity purification (TRAP) methodology. We used bacterial artificial chromosome (BAC) transgenic mice expressing EGFP tagged ribosomal protein L10a in oligodendrocytes which constitute a defined cellular population of the mouse brain. Using this approach, we could extract only the oligodendrocitic mRNAs, and only those already committed to be translated into proteins (L10a is part of the translational machinery). Six mice for each vigilant state group (sleep (S), waking (W), and sleep deprivation (SD)) were considered. For each animal, one forebrain sample was immediately processed. Samples were immunoprecipitated to isolate oligodendrocytes. The precipitated portion formed the bound sample (IP) containing olidodendrocytes and the remaining part formed the unbound sample (UB) containing all the remaining cell types (neurons and other glia cells). Then, both IP and UB samples were processed and RNA was extracted.
2013-08-20 | E-GEOD-48369 | biostudies-arrayexpress
Project description:Despite an established link between sleep deprivation and epigenetic processes in humans, it remains unclear to what extent sleep deprivation modulates DNA methylation. We performed a within subject randomized blinded study with 16 healthy subjects to examine the effect of one night of total acute sleep deprivation (TSD) on the genome wide methylation profile in blood compared to normal sleep. Genome-wide differences in methylation between both conditions were assessed by applying a paired regression model that corrected for monocyte subpopulations (neutrophil/leukocyte ratio). Additionally, the correlations between the methylation of genes detected to be modulated by TSD and gene expression were examined in a separate, publicly available cohort of ten healthy male donors (E-GEOD-49065). Sleep deprivation significantly affected the DNA methylation profile both independently and in dependency of shifts in monocyte composition. Our study detected differential methylation of 269 probes. Notably, one CpG site was located 69bp upstream of ING5, which has been shown to be differentially expressed following sleep deprivation. Gene set enrichment analysis detected the Notch and Wnt signaling pathways to be enriched among the differentially methylated genes. These results provide evidence that total acute sleep deprivation alters the methylation profile in healthy human subjects. This is, to our knowledge, the first study that systematically investigated the impact of total acute sleep deprivation on genome-wide DNA methylation profiles in blood and related the epigenomic findings to the expression data.
2016-06-30 | E-MTAB-4664 | biostudies-arrayexpress