Differences in brain gene expression between sleep and waking as revealed by mRNA differential display and cDNA microarray technology

REM-Sleep Deprivation Induces Mitochondrial Biogenesis in the Rat Hippocampus

BACKGROUND/AIM

Sleep loss is proposed as a trigger for manic episodes in bipolar disorder in humans. It has been shown that sleep and wakefulness can affect changes in mitochondrial gene expression, oxidative phosphorylation (OXPHOS) activity, and morphology in the brain. In this study, we investigated alterations in mitochondrial bioenergetic function in the brain of rats after 72-h rapid eye movement sleep deprivation (REM-SD).

MATERIALS AND METHODS

Alterations in the mitochondrial DNA (mtDNA) copy number were detected in the prefrontal cortex and hippocampus through amplification of mitochondrially encoded NADH dehydrogenase 1 (mt-Nd1) gene using quantitative real-time polymerase chain reaction. The expression levels of mitochondrial biogenesis-related proteins such as peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A), cytochrome c oxidase subunit 4I1 (COX4I1) and sirtuin 3 (SIRT3) were assessed using western blot analysis and immunohistochemistry.

RESULTS

We found that REM-SD significantly increased the mtDNA copy number in the hippocampus but not in the prefrontal cortex. In addition, REM-SD increased the protein expression of COX4I1 in the hippocampus. Furthermore, we observed manic-like behaviors in rats exposed to 72-h REM-SD. REM-SD increased locomotion in the open-field test and the time spent in open arms in the elevated plus-maze test.

CONCLUSION

REM-SD may induce mitochondrial dysfunction in the brain, which may be involved in the induction of mania.

The Effect of Sleep Deprivation and Subsequent Recovery Period on the Synaptic Proteome of Rat Cerebral Cortex

Sleep deprivation (SD) is commonplace in the modern way of life and has a substantial social, medical, and human cost. Sleep deprivation induces cognitive impairment such as loss of executive attention, working memory decline, poor emotion regulation, increased reaction times, and higher cognitive functions are particularly vulnerable to sleep loss. Furthermore, SD is associated with obesity, diabetes, cardiovascular diseases, cancer, and a vast majority of psychiatric and neurodegenerative disorders are accompanied by sleep disturbances. Despite the widespread scientific interest in the effect of sleep loss on synaptic function, there is a lack of investigation focusing on synaptic transmission on the proteome level. In the present study, we report the effects of SD and recovery period (RP) on the cortical synaptic proteome in rats. Synaptosomes were isolated after 8 h of SD performed by gentle handling and after 16 h of RP. The purity of synaptosome fraction was validated with western blot and electron microscopy, and the protein abundance alterations were analyzed by mass spectrometry. We observed that SD and RP have a wide impact on neurotransmitter-related proteins at both the presynaptic and postsynaptic membranes. The abundance of synaptic proteins has changed to a greater extent in consequence of SD than during RP: we identified 78 proteins with altered abundance after SD and 39 proteins after the course of RP. Levels of most of the altered proteins were upregulated during SD, while RP showed the opposite tendency, and three proteins (Gabbr1, Anks1b, and Decr1) showed abundance changes with opposite direction after SD and RP. The functional cluster analysis revealed that a majority of the altered proteins is related to signal transduction and regulation, synaptic transmission and synaptic assembly, protein and ion transport, and lipid and fatty acid metabolism, while the interaction network analysis revealed several connections between the significantly altered proteins and the molecular processes of synaptic plasticity or sleep. Our proteomic data implies suppression of SNARE-mediated synaptic vesicle exocytosis and impaired endocytic processes after sleep deprivation. Both SD and RP altered GABA neurotransmission and affected protein synthesis, several regulatory processes and signaling pathways, energy homeostatic processes, and metabolic pathways.

Exploring phylogeny to find the function of sleep

During sleep, animals do not eat, reproduce or forage. Sleeping animals are vulnerable to predation. Yet, the persistence of sleep despite evolutionary pressures, and the deleterious effects of sleep deprivation, indicate that sleep serves a function or functions that cannot easily be bypassed. Recent research demonstrates sleep to be phylogenetically far more pervasive than previously appreciated; it is possible that the very first animals slept. Here, we give an overview of sleep across various species, with the aim of determining its original purpose. Sleep exists in animals without cephalized nervous systems and can be influenced by non-neuronal signals, including those associated with metabolic rhythms. Together, these observations support the notion that sleep serves metabolic functions in neural and non-neural tissues.

Sleep Deprivation and the Epigenome

Sleep deprivation disrupts the lives of millions of people every day and has a profound impact on the molecular biology of the brain. These effects begin as changes within a neuron, at the DNA and RNA level, and result in alterations in neuronal plasticity and dysregulation of many cognitive functions including learning and memory. The epigenome plays a critical role in regulating gene expression in the context of memory storage. In this review article, we begin by describing the effects of epigenetic alterations on the regulation of gene expression, focusing on the most common epigenetic mechanisms: (i) DNA methylation; (ii) histone modifications; and (iii) non-coding RNAs. We then discuss evidence suggesting that sleep loss impacts the epigenome and that these epigenetic alterations might mediate the changes in cognition seen following disruption of sleep. The link between sleep and the epigenome is only beginning to be elucidated, but clear evidence exists that epigenetic alterations occur following sleep deprivation. In the future, these changes to the epigenome could be utilized as biomarkers of sleep loss or as therapeutic targets for sleep-related disorders.

Molecular Mechanisms of Sleep Homeostasis in Flies and Mammals

Sleep is homeostatically regulated with sleep pressure accumulating with the increasing duration of prior wakefulness. Yet, a clear understanding of the molecular components of the homeostat, as well as the molecular and cellular processes they sense and control to regulate sleep intensity and duration, remain a mystery. Here, we will discuss the cellular and molecular basis of sleep homeostasis, first focusing on the best homeostatic sleep marker in vertebrates, slow wave activity; second, moving to the molecular genetic analysis of sleep homeostasis in the fruit fly Drosophila; and, finally, discussing more systemic aspects of sleep homeostasis.

Gene Chips: Applications to Neuroscience

A convergence between molecular biological technique and the technology of miniaturization has produced the "gene chip" or microhybridization array. This device multiplies by several thousand fold the power of the northern blot for studying gene expression. Now, it is possible to survey simultaneously a large fraction of all genes in an experimental organism, and within a few years all of the approximately 140,000 human genes will be within reach of the technique. This capability is not only accelerating the rate of research into gene expression and function, it is changing the perspective of inquiry from single genes in isolation to networks of genes operating as a system. Many neurological diseases, from hydrocephalus to schizophrenia, have a genetic component, and individual responses to therapeutic drugs can vary with the genetic background of patients. In neurology and neurobiology, the ability to obtain "gene expression profiles" from nervous tissue promises to illuminate interactions between neuronal genes and the environment, development, disease, aging, and response to drugs and injury.

A review of sleep deprivation studies evaluating the brain transcriptome

Epidemiological studies show a positive association between adequate sleep and good health. Further, disrupted sleep may increase the risk for CNS diseases, such as stroke and Alzheimer’s disease. However, there has been limited progress in determining how sleep is linked to brain health or how sleep disruption may increase susceptibility to brain insult and disease. Animal studies can aid in understanding these links. In reviewing the animal literature related to the effects of sleep disruption on the brain, we found most of the work was directed toward investigating and characterizing the role of various brain areas or structures in initiating and regulating sleep. In contrast, limited effort has been directed towards understanding how sleep disruption alters the brain’s health or susceptibility to insult. We also note many current studies have determined the changes in the brain following compromised sleep by examining, for example, the brain transcriptome or to a more limited extent the proteome. However, these studies have utilized almost exclusively total sleep deprivation (e.g., 24 out of 24 hours) paradigms or single short periods of limited acute sleep deprivation (e.g., 3 out of 24 hours). While such strategies are beneficial in understanding how sleep is controlled, they may not have much translational value for determining links between sleep and brain health or for determining how sleep disruption may increase brain susceptibility to insult. Surprisingly, few studies have determined how the duration and recurrence of sleep deprivation influence the effects seen after sleep deprivation. Our aim in this review was to identify relevant rodent studies from 1980 through 2012 and analyze those that use varying durations of sleep deprivation or restriction in their effort to evaluate the effects of sleep deprivation on the brain transcriptome and to a more limited extent the proteome. We examined how differences in the duration of sleep deprivation affect gene and protein expression to better understand the full consequences of repeated sleep disruption on the brain. Future research needs to consider and emphasize how the type and extent of the sleep deprivation exposure impacts the conclusions reached concerning the influence of sleep disruption on the brain.

We identified relevant studies between 1980 and 2012 by searching the electronic databases of PubMed, Medline (Ovid), Embase (Ovid), and Web of Science using the terms “sleep” AND “disrupt”, “deprivation”, “restrict”, “fragment”, “loss”, “disturb”, “disorder”, “dysfunction”, “brain”, “cortex”, striatum”, hypothalamus”, “hippocampus”, “gene”, “protein”, “genomics”, “proteomics”, “polymerase chain reaction”, “pcr”, “microarray”, “molecular”, “rodent” “rat”, “rats”, “mouse”, “mice”. All searches were limited to rodent studies in English and the reference lists of retrieved articles were searched for additional pertinent studies.

Introduction to sequencing the brain transcriptome

High-throughput next-generation sequencing is now entering its second decade. However, it was not until 2008 that the first report of sequencing the brain transcriptome appeared (Mortazavi, Williams, Mccue, Schaeffer, & Wold, 2008). These authors compared short-read RNA-Seq data for mouse whole brain with microarray results for the same sample and noted both the advantages and disadvantages of the RNA-Seq approach. While RNA-Seq provided exon level resolution, the majority of the reads were provided by a small proportion of highly expressed genes and the data analysis was exceedingly complex. Over the past 6 years, there have been substantial improvements in both RNA-Seq technology and data analysis. This volume contains 11 chapters that detail various aspects of sequencing the brain transcriptome. Some of the chapters are very methods driven, while others focus on the use of RNA-Seq to study such diverse areas as development, schizophrenia, and drug abuse. This chapter briefly reviews the transition from microarrays to RNA-Seq as the preferred method for analyzing the brain transcriptome. Compared with microarrays, RNA-Seq has a greater dynamic range, detects both coding and noncoding RNAs, is superior for gene network construction, detects alternative spliced transcripts, and can be used to extract genotype information, e.g., nonsynonymous coding single nucleotide polymorphisms. RNA-Seq embraces the complexity of the brain transcriptome and provides a mechanism to understand the underlying regulatory code; the potential to inform the brain-behavior-disease relationships is substantial.

Genes, behavior and next-generation RNA sequencing

Advances in next-generation sequencing suggest that RNA-Seq is poised to supplant microarray-based approaches for transcriptome analysis. This article briefly reviews the use of microarrays in the brain-behavior context and then illustrates why RNA-Seq is a superior strategy. Compared with microarrays, RNA-Seq has a greater dynamic range, detects both coding and noncoding RNAs, is superior for gene network construction, detects alternative spliced transcripts, detects allele specific expression and can be used to extract genotype information, e.g. nonsynonymous coding single nucleotide polymorphisms. Examples of where RNA-Seq has been used to assess brain gene expression are provided. Despite the advantages of RNA-Seq, some disadvantages remain. These include the high cost of RNA-Seq and the computational complexities associated with data analysis. RNA-Seq embraces the complexity of the transcriptome and provides a mechanism to understand the underlying regulatory code; the potential to inform the brain-behavior relationship is substantial.

Key electrophysiological, molecular, and metabolic signatures of sleep and wakefulness revealed in primary cortical cultures

Although sleep is defined as a behavioral state, at the cortical level sleep has local and use-dependent features suggesting that it is a property of neuronal assemblies requiring sleep in function of the activation experienced during prior wakefulness. Here we show that mature cortical cultured neurons display a default state characterized by synchronized burst-pause firing activity reminiscent of sleep. This default sleep-like state can be changed to transient tonic firing reminiscent of wakefulness when cultures are stimulated with a mixture of waking neurotransmitters and spontaneously returns to sleep-like state. In addition to electrophysiological similarities, the transcriptome of stimulated cultures strikingly resembles the cortical transcriptome of sleep-deprived mice, and plastic changes as reflected by AMPA receptors phosphorylation are also similar. We used our in vitro model and sleep-deprived animals to map the metabolic pathways activated by waking. Only a few metabolic pathways were identified, including glycolysis, aminoacid, and lipids. Unexpectedly large increases in lysolipids were found both in vivo after sleep deprivation and in vitro after stimulation, strongly suggesting that sleep might play a major role in reestablishing the neuronal membrane homeostasis. With our in vitro model, the cellular and molecular consequences of sleep and wakefulness can now be investigated in a dish.

Roles of endoplasmic reticulum and energetic stress in disturbed sleep

Sleep disturbances are contributing factors to health risk for several diseases including hypertension, diabetes, obesity, depression, and stroke. On a molecular level, sleep disturbances that incur sleep loss and sleep fragmentation result in cellular stress, inflammation, and an impaired immune system. It has been hypothesized that sleep deprivation or prolonged waking leads to increased energy demand and thus energetic stress. Sleep loss and sleep fragmentation are also known to lead to cellular stress specifically endoplasmic reticulum (ER) stress. This review will summarize the current knowledge of the roles of ER and energetic stress during sleep loss and fragmentation that are characteristics of many sleep disturbances. Sleep research pertinent to these specific pathways will be discussed.

Sleep and plasticity

While there is ample agreement that the cognitive role of sleep is explained by sleep-dependent synaptic changes, consensus is yet to be established as to the nature of these changes. Some researchers believe that sleep promotes global synaptic downscaling, leading to a non-Hebbian reset of synaptic weights that is putatively necessary for the acquisition of new memories during ensuing waking. Other investigators propose that sleep also triggers experience-dependent, Hebbian synaptic upscaling able to consolidate recently acquired memories. Here, I review the molecular and physiological evidence supporting these views, with an emphasis on the calcium signaling pathway. I argue that the available data are consistent with sleep promoting experience-dependent synaptic embossing, understood as the simultaneous non-Hebbian downscaling and Hebbian upscaling of separate but complementary sets of synapses, heterogeneously activated at the time of memory encoding and therefore differentially affected by sleep.

Changes in components of energy regulation in mouse cortex with increases in wakefulness

STUDY OBJECTIVES

Increases in ATP production machinery have been described in brain after 3 h of sleep deprivation. Whether this is sustained with longer durations of extended wakefulness is unknown. We hypothesized that energy depletion could be a mechanism leading to difficulty maintaining wakefulness and assessed changes in components of the electron transport chain.

DESIGN

Protein levels of key subunits of complexes IV and V of the electron transport chain (COXI, COXIV, ATP5B) and uncoupling protein 2 (UCP2) in isolated mitochondria by Westerns in mouse cerebral cortex after 3 and 12 h of sleep deprivation were compared to that in control mice. Activity of complex IV enzyme and relevant transcription factors-Nrf1, Nrf2 (Gabp), and phosphorylation of AMP-dependent kinase (AMPK)-were also assessed.

PARTICIPANTS

8-10 week old C57BL/6J male mice (n = 91).

INTERVENTIONS

3, 6, and 12 h of sleep deprivation.

MEASUREMENTS AND RESULTS

After both 3 and 12 h of sleep deprivation, complex IV proteins and enzyme activity were significantly increased. The complex V catalytic subunit was significantly increased after 12 h of sleep deprivation only. Increased levels of UCP2 protein after 12 h of sleep deprivation suggests that there might be alterations in the ATP/AMP ratio as wakefulness is extended. That phosphorylation of AMPK is increased after 6 h of sleep deprivation supports this assertion. The increase in Nrf1 and Nrf2 (Gabp) mRNA after 6 h of sleep deprivation provides a mechanism by which there is up-regulation of key proteins.

CONCLUSIONS

There are complex dynamic changes in brain energy regulation with extended wakefulness.

Refined anatomical isolation of functional sleep circuits exhibits distinctive regional and circadian gene transcriptional profiles

Powerful new approaches to study molecular variation in distinct neuronal populations have recently been developed enabling a more precise investigation of the control of neural circuits involved in complex behaviors such as wake and sleep. We applied laser capture microdissection (LCM) to isolate precise brain nuclei from rat CNS at opposing circadian time points associated with wake and sleep. Discrete anatomical and temporal analysis was performed to examine the extent of variation in the transcriptional control associated with both identifiable anatomical nuclei and with light/dark cycle. Precise isolation of specific brain nuclei regulating sleep and arousal, including the LC, SCN, TMN, VTA, and VLPO, demonstrated robust changes in gene expression. Many of these differences were not observed in previous studies where whole brain lysates or gross dissections were used to probe for changes in gene expression. The robust and differential profiles of genomic data obtained from the approaches used herein underscore the requirement for careful anatomical refinement in CNS gene expression studies designed to understand genomic control within behaviorally-linked, but functionally isolated brain nuclei.

Drosophila melanogaster: an insect model for fundamental studies of sleep

In 2000, Drosophila melanogaster joined the ranks of vertebrates and invertebrates with a defined behavioral sleep state. The characterization of this sleep state revealed striking similarities to sleep in humans: sleep in flies has both circadian and homeostatic components, it is influenced by sex and age, and it is affected by pharmacological agents such as caffeine and antihistamines. As in mammals, arousal thresholds in flies increase with sleep deprivation. Furthermore, changes in brain electrical activity accompany the change from wake to sleep states. Not only do flies and vertebrates share these behavioral and physiological traits of sleep, but they are likely to share at least some genetic mechanisms underlying the regulation of sleep as well. This article reviews the methods currently used to identify and characterize the Drosophila sleep state. As these methods become more refined and our understanding of Drosophila sleep more detailed, the powerful techniques afforded by this organism are likely to unveil deep insights into the function(s) and regulatory mechanisms of sleep.

Differences in the sleep architecture of forager and young honeybees(Apis mellifera)

Honeybee (Apis mellifera) foragers are among the first invertebrates for which sleep behavior has been described. Foragers (typically older than 21 days) have strong circadian rhythms; they are active during the day, and sleep during the night. We explored whether young bees (∼3 days of age), which are typically active around-the-clock with no circadian rhythms, also exhibit sleep behavior. We combined 24-hour video recordings,detailed behavioral observations, and analyses of response thresholds to a light pulse for individually housed bees in various arousal states. We characterized three sleep stages in foragers on the basis of differences in body posture, bout duration, antennae movements and response threshold. Young bees exhibited sleep behavior consisting of the same three stages as observed in foragers. Sleep was interrupted by brief awakenings, which were as frequent in young bees as in foragers. Beyond these similarities, we found differences in the sleep architecture of young bees and foragers. Young bees passed more frequently between the three sleep stages, and stayed longer in the lightest sleep stage than foragers. These differences in sleep architecture may represent developmental and/or environmentally induced variations in the neuronal network underlying sleep in honeybees. To the best of our knowledge,this is the first evidence for plasticity in sleep behavior in insects.

Molecular analysis of sleep: wake cycles in Drosophila

Sleep is controlled by two major regulatory systems: a circadian system that drives it with a 24-hour periodicity and a home-ostatic system that ensures that adequate amounts of sleep are obtained. We are using the fruit fly Drosophila melanogaster to understand both types of regulation. With respect to circadian control, we have identified molecular mechanisms that are critical for the generation of a clock. Our recent efforts have focused on the analysis of posttranslational mechanisms, specifically the action of different phosphatases that control the phosphorylation and thereby the stability and/or nuclear localization of circadian clock proteins period (PER) and timeless (TIM). Resetting the clock in response to light is also mediated through posttranslational events that target TIM for degradation by the proteasome pathway; a recently identified ubiquitin ligase, jet lag (JET), is required for this response. Our understanding of the homeostatic control of sleep is in its early stages. We have found that mushroom bodies, which are a site of synaptic plasticity in the fly brain, are important for the regulation of sleep. In addition, through analysis of genes expressed under different behavioral states, we have identified some that are up-regulated during sleep deprivation. Thus, the Drosophila model allows the use of cellular and molecular approaches that should ultimately lead to a better understanding of sleep biology.

Sleep: dozy worms and sleepy flies

Recent work on quiescent states in Caenorhabditis elegans suggests that worms exhibit behaviours reminiscent of satiety and sleep in mammals. At a molecular level, signalling through the EGF receptor and protein kinase G promotes quiescent states in both worms and flies, suggesting conserved mechanisms for sleep-like behaviours.

Genetic analyses on DNA microarrays

A great stir has coursed through the genetics community with the advent in 1996 of "chip technologies," a series of related techniques that allow DNA hybridization-based studies to be performed with unprecedented speed and parallelism. All chip technologies have in common a microarray, a small glass chip approximately one square centimeter in area, to which nucleotide sequences are bound. Fluorescently labeled nucleic acids are hybridized to the microarray and imaged with a laser scanner or fluorescence microscope. This unit offers an overview of the two dominant technologies, cDNA microarrays and oligonucleotide chips. It concludes with a discussion regarding how well microarrays perform real-world expression analysis.

The role of protein synthesis in memory consolidation: progress amid decades of debate

A major component of consolidation theory holds that protein synthesis is required to produce the synaptic modification needed for long-term memory storage. Protein synthesis inhibitors have played a pivotal role in the development of this theory. However, these commonly used drugs have unintended effects that have prompted some to reevaluate the role of protein synthesis in memory consolidation. Here we review the role of protein synthesis in memory formation as proposed by consolidation theory calling special attention to the controversy involving the non-specific effects of a group of protein synthesis inhibitors commonly used to study memory formation in vivo. We argue that molecular and genetic approaches that were subsequently applied to the problem of memory formation confirm the results of less selective pharmacological studies. Thus, to a certain extent, the debate over the role of protein synthesis in memory based on interpretational difficulties inherent to the use of protein synthesis inhibitors may be somewhat moot. We conclude by presenting avenues of research we believe will best provide answers to both long-standing and more recent questions facing field of learning and memory.

Metabolic mechanism of wakefulness (and hunger) and sleep (and satiety): Role of adenosine triphosphate and hypocretin and other peptides

The concurrent background level of metabolic activity may control state of vigilance, promoting wakefulness (and hunger) when it is low, or sleep (and satiety) when it is high. In a series of experiments, we have shown that sleep is dependent on feeding, but only because of the metabolic consequences of food ingestion. These consequences are sensed by glioneuronal populations (at least in the rostromedial hypothalamus), which probably respond to channel-bound adenosine triphosphate/diphosphate turnover (ischymetric monitoring) rather than to the binding of such downstream molecules as adenosine and cytochrome c oxidase. This basic signal is communicated to the vigilance-controlling centers by a cascade of peptidic and nonpeptidic messengers-messengers that promote wakefulness and hunger, possibly via a hypometabolic action (as in the case of neuropeptide Y or hypocretins), or somnolence and satiety, possibly via a hypermetabolic action (as in the case of leptin or certain serotonergic agents).

From synapse to gene product: prolonged expression of c-fos induced by a single microinjection of carbachol in the pontomesencephalic tegmentum

It is not known how the brain modifies its regulatory systems in response to the application of a drug, especially over the long term of weeks and months. We have developed a model system approach to this question by manipulating cholinergic cell groups of the laterodorsal and pedunculopontine tegmental (LDT/PPT) nuclei in the pontomesencephalic tegmentum (PMT), which are known to be actively involved in the timing and quantity of rapid eye movement (REM) sleep. In a freely moving feline model, a single microinjection of the cholinergic agonist carbachol conjugated to a latex nanosphere delivery system into the caudolateral PMT elicits a long-term enhancement of one distinguishing phasic event of REM sleep, ponto-geniculo-occipital (PGO) waves, lasting 5 days but without any significant change in REM sleep or other behavioral state. Here, we test the hypothesis that cholinergic activation within the caudolateral PMT alters the postsynaptic excitability of the PGO network, stimulating the prolonged expression of c-fos that underlies this long-term PGO enhancement (LTPE) effect. Using quantitative Fos immunohistochemistry, we found that the number of Fos-immunoreactive (Fos-IR) neurons surrounding the caudolateral PMT injection site decreased sharply by postcarbachol day 03, while the number of Fos-IR neurons in the more rostral LDT/PPT increased >30-fold and remained at a high level following the course of LTPE. These results demonstrate a sustained c-fos expression in response to pharmacological stimulation of the brain and suggest that carbachol's acute effects induce LTPE via cholinergic receptors, with subsequent transsynaptic activation of the LDT/PPT maintaining the LTPE effect.

Functional genomics of sleep

Functional genomics is a systematic and high-throughput effort to analyze the functions of genes and gene products. Functional genomics is divided into gene- and phenotype-driven approaches. Gene-driven approaches to the functional genomics of sleep have demonstrated that transcripts of many genes change as a function of behavioral state. A phenotype-driven approach includes identification and characterization of gene function through the analyses of natural polygenic traits, creation of transgenic animals or high-throughput mutagenesis. Identification of a gene for narcolepsy through QTL analyses and concomitantly using a transgenic approach is one example of the phenotype-driven approach to the functional genomics of sleep. Though the majority of functional genomics is currently performed in mice, the rat is emerging as an important model for genomic research. Since rest in Drosophila shares many features with mammalian sleep, this allows a comparative functional genomics approach to the study of rest and sleep. The concepts outlined here for the functional genomics of sleep are applicable to respiration research.

Altered expression of randomly selected genes in mouse hippocampus after traumatic brain injury

Using a cDNA microarray method, we analyzed gene expression profiles in mouse hippocampus after traumatic brain injury (TBI). Of 6,400 randomly selected arrayed genes and expressed sequence tags from a mouse cDNA library, 253 were found to be differentially expressed (106 increased and 147 decreased). Genes involved in cell homeostasis and calcium signaling were primarily up-regulated while those encoding mitochondrial enzymes, metabolic molecules, and structural proteins were predominantly down-regulated. Equal numbers of genes related to inflammatory reactions showed increased or decreased expression. Importantly, a large proportion of the dysregulated genes we identified have not been reported as differentially expressed in TBI models. Semiquantitative reverse-transcriptase polymerase chain reaction (RT-PCR) analyses of representative genes confirmed the validity of the corresponding microarray findings. Thus, our microarray-based evaluation of gene expression in traumatically injured hippocampus identified both known and novel genes that respond to TBI. Further investigation of these candidate molecules may suggest new ways to attenuate the traumatic effects of brain injury.

Perchance to dream: solving the mystery of sleep through genetic analysis

Sleep has been identified in all mammals and nonmammalian vertebrates that have been critically evaluated. In addition, sleep-like states have also been identified and described in several invertebrates. Despite this prevalence throughout the animal kingdom, the function of sleep remains a mystery. The completion of several genome sequencing projects has led to the expectation that fundamental aspects of sleep can be elucidated through genetic dissection. Indeed, studies in both the mouse and fly have begun to reveal tantalizing suggestions about the underlying principles that regulate sleep homeostasis. In this article we will review recent studies that have used genetic techniques to evaluate sleep in the fruit fly and the mouse.

The implications of microarray technology for animal use in scientific research

Microarray technology has the potential to affect the number of laboratory animals used, the severity of animal experiments, and the development of non-animal alternatives in several areas scientific research. Microarrays can contain hundreds or thousands of microscopic spots of DNA, immobilised on a solid support, and their use enables global patterns of gene expression to be determined in a single experiment. This technology is being used to improve our understanding of the operation of biological systems during health and disease, and their responses to chemical insults. Although it is impossible to predict with certainty any future trends regarding animal use, microarray technology might not initially reduce animal use, as is often claimed to be the case. The accelerated pace of research as a result of the use of microarrays could increase overall animal use in basic and applied biological research, by increasing the numbers of interesting genes identified for further analysis, and the number of potential targets for drug development. Each new lead will require further evaluation i n studies that could involve animals. In toxicity testing, microarray studies could lead to increases in animal studies, if further confirmatory and other studies are performed. However, before such technology can be used more extensively, several technical problems need to be overcome, and the relevance of the data to biological processes needs to be assessed. Were microarray technology to be used in the manner envisaged by its protagonists, there need to be efforts to increase the likelihood that its application will create new opportunities for reducing, refining and replacing animal use. This comment is a critical assessment of the possible implications of the application of microarray technology on animal experimentation in various research areas, and makes some recommendations for maximising the application of the Three Rs.

Approaches to the analysis of gene expression using mRNA: a technical overview

Messenger RNA is the blueprint for all proteins expressed within living systems. Therefore, the study of mRNA expression within normal and diseased tissues is central to our understanding of biological systems. However, blueprints, in themselves, perform no function unless they are used to produce the material for which they code. Spurious results may frequently result from poorly designed or inappropriate studies. This review seeks to highlight both the pitfalls and the promise of various approaches to the analysis of mRNA in different systems and to place these studies in the wider context of research approaches aimed at understanding the function of living systems. The various techniques for the analysis of mRNA are discussed, with particular reference to their potential uses and problems and relevant examples are cited from the literature. It is hoped that this overview of the uses of analytical approaches will allow both the novice researcher and the more experienced scientist to better structure research approaches.

Morbidity of obstructive sleep apnea in children: facts and theory

Sleep-disordered breathing (SDB) is a frequent, albeit underdiagnosed, problem in children. If left untreated, SDB may lead to substantial morbidities affecting multiple target organs and systems. This review provides a detailed and current description of the current status of our understanding of SDB-associated morbidity in children, and provides recommendations of future research directions necessary for increasing our knowledge and awareness on the short- and long-term consequences of SDB during childhood.

Sex-related differences in gene expression in neonatal rat hypothalamus assessed by cDNA microarray analysis

Sexual differentiation of the rodent brain is recognized to involve transcriptional activation of multiple genes induced by gonadal steroids at developmental stages. To identify the genes differing in expression level between sexes, we analyzed gene expression in male and female rat hypothalami at postnatal day 5 by means of a cDNA microarray consisting of 2352 genes. By comparing the expression pattern between sexes, we identified 12 male-enriched genes and 20 female-enriched genes. Among them, the expression pattern of 1 male-enriched gene, jagged homolog 1, and those of 2 female-enriched genes, p27Kip1 and p130, were confirmed to be consistent with microarray data by RT-PCR. Investigation of these genes should help to elucidate the molecular and cellular mechanisms underlying sexual differentiation of the rodent central nervous system.

A novel sensitive microarray approach for differential screening using probes labelled with two different radioelements

We have developed a novel microarray approach for differential screening using probes labelled with two different radioelements. The complementary DNAs from the reverse transcription of mRNAs from two different biological samples were labelled with radioelements of significantly different energies (3H and 35S or 33P). Radioactive images corresponding to the expressed genes were acquired with a MicroImager, a real time, high resolution digital autoradiography system. An algorithm was used to process the data such that the initially acquired radioactive image was filtered into two subimages, each representative of the hybridisation result specific for one probe. The simultaneous screening of gene expression in two different biological samples requires <100 ng mRNA without any amplification. In such conditions, the technique is sensitive enough to directly quantify the amount of mRNA even when present in small amounts: 10(7) molecules in the probe as assessed with an added control sequence and 2 x 10(5) molecules with an endogenous tyrosine hydroxylase mRNA. This novel technique of double radioactive labelling on a microarray is thus suitable for the comparison of gene expression in two different biological samples available in only small quantities. Consequently, it has great potential for various biological fields, such as neuroscience.

Sleep enhances plasticity in the developing visual cortex

During a critical period of brain development, occluding the vision of one eye causes a rapid remodeling of the visual cortex and its inputs. Sleep has been linked to other processes thought to depend on synaptic remodeling, but a role for sleep in this form of cortical plasticity has not been demonstrated. We found that sleep enhanced the effects of a preceding period of monocular deprivation on visual cortical responses, but wakefulness in complete darkness did not do so. The enhancement of plasticity by sleep was at least as great as that produced by an equal amount of additional deprivation. These findings demonstrate that sleep and sleep loss modify experience-dependent cortical plasticity in vivo. They suggest that sleep in early life may play a crucial role in brain development.

Microarray applications in neuroscience

Advances in all facets of technology from molecular biology to imaging and computational biology offer unprecedented opportunities for improving our understanding of the brain in health and disease. Oligonucleotide and cDNA microarray analysis, using a variety of "DNA chips," is a recently developed high-throughput technique that allows for tour-de-force analysis of gene expression. We review this powerful technique, developed in genetics laboratories, with reference to applications in neurologic diseases in humans and the use of animal models. The typical microarray experiment is multistaged and includes preparation or purchase of arrays, preparation of target DNA and probe, target DNA hybridization, microarray scanning, and image analysis. The power and pitfalls of this technology are discussed in the context of neuroscience paradigms. Since unprecedented amounts of data are produced from microarray experiments, bioinformatics and modeling expertise are increasingly becoming critical components of this approach.

Gene expression in the brain across the sleep-waking cycle

Sleep and waking differ significantly in terms of behavior, metabolism, and neuronal activity. Recent evidence indicates that sleep and waking also differ with respect to the expression of certain genes. To systematically investigate such changes, we used mRNA differential display and cDNA microarrays to screen approximately 10000 transcripts expressed in the cerebral cortex of rats after 8 h of sleep, spontaneous waking, or sleep deprivation. We found that 44 genes had higher mRNA levels after waking and/or sleep deprivation relative to sleep, while 10 were upregulated after sleep. Known genes that were upregulated in waking and sleep deprivation can be grouped into the following categories: immediate early genes/transcription factors (Arc, CHOP, IER5, NGFI-A, NGFI-B, N-Ras, Stat3), genes related to energy metabolism (glucose type I transporter Glut1, Vgf), growth factors/adhesion molecules (BDNF, TrkB, F3 adhesion molecule), chaperones/heat shock proteins (BiP, ERP72, GRP75, HSP60, HSP70), vesicle- and synapse-related genes (chromogranin C, synaptotagmin IV), neurotransmitter/hormone receptors (adrenergic receptor alpha(1A) and beta(2), GABA(A) receptor beta(3), glutamate NMDA receptor 2A, glutamate AMPA receptor GluR2 and GluR3, nicotinic acetylcholine receptor beta(2), thyroid hormone receptor TRbeta), neurotransmitter transporters (glutamate/aspartate transporter GLAST, Na(+)/Cl(-) transporter NTT4/Rxt1), enzymes (aryl sulfotransferase, c-jun N-terminal kinase 1, serum/glucocorticoid-induced serine/threonine kinase), and a miscellaneous group (calmodulin, cyclin D2, LMO-4, metallothionein 3). Several other genes that were upregulated in waking and all the genes upregulated in sleep, with the exception of the one coding for membrane protein E25, did not match any known sequence. Thus, significant changes in gene expression occur across behavioral states, which are likely to affect basic cellular functions such as RNA and protein synthesis, neural plasticity, neurotransmission, and metabolism.

Detection of differentially expressed genes in lymphomas using cDNA arrays: identification of clusterin as a new diagnostic marker for anaplastic large-cell lymphomas

This study reports the first use of gene array technology for the identification of a tumor-specific marker in lymphoid neoplasms. The differential gene expression of 31 hematopoietic cell lines, representing most major lymphoma subgroups of B- and T-cell origin, was assessed by hybridizing labeled complementary DNA to Atlas human expression arrays containing 588 genes. Genes known to be specific for B, T, or myelomonocytic lineages were appropriately identified in the arrays, validating the general utility of this approach. One gene,clusterin, not previously known to be expressed in lymphoid neoplasms, was specifically found in all 4 anaplastic large-cell lymphoma (ALCL) cell lines, but not in any of the 27 remaining tumor lines. Using a monoclonal antibody against clusterin, its differential expression was confirmed by Western blotting and immunohistochemistry. A total of 198 primary lymphomas (representing most major lymphoma subtypes), including 36 cases of systemic ALCL, were surveyed for clusterin expression by immunohistochemistry and Western blotting. All of the 36 ALCL cases marked for clusterin, with most cases showing moderate to strong staining in the majority of neoplastic cells. Clusterin expression was not related to expression of anaplastic lymphoma kinase-1. With 2 exceptions, none of the remaining 162 non-ALCL cases marked with the clusterin antibody, including Hodgkin disease and primary cutaneous ALCL. In reactive lymphoid tissues, only follicular dendritic cells and fibroblastic reticular cells exhibited staining. Clusterin is a highly conserved glycoprotein implicated in intercellular and cell matrix interactions, regulation of the complement system, lipid transport, stress responses, and apoptosis. Although its function in ALCL is unknown, the unique expression of clusterin within this category of lymphoma provides an additional marker for the diagnosis of ALCL. This study illustrates the enormous potential of gene array technologies for diagnostic marker discovery.

Detection of differentially expressed genes in lymphomas using cDNA arrays: identification of clusterin as a new diagnostic marker for anaplastic large-cell lymphomas

This study reports the first use of gene array technology for the identification of a tumor-specific marker in lymphoid neoplasms. The differential gene expression of 31 hematopoietic cell lines, representing most major lymphoma subgroups of B- and T-cell origin, was assessed by hybridizing labeled complementary DNA to Atlas human expression arrays containing 588 genes. Genes known to be specific for B, T, or myelomonocytic lineages were appropriately identified in the arrays, validating the general utility of this approach. One gene,clusterin, not previously known to be expressed in lymphoid neoplasms, was specifically found in all 4 anaplastic large-cell lymphoma (ALCL) cell lines, but not in any of the 27 remaining tumor lines. Using a monoclonal antibody against clusterin, its differential expression was confirmed by Western blotting and immunohistochemistry. A total of 198 primary lymphomas (representing most major lymphoma subtypes), including 36 cases of systemic ALCL, were surveyed for clusterin expression by immunohistochemistry and Western blotting. All of the 36 ALCL cases marked for clusterin, with most cases showing moderate to strong staining in the majority of neoplastic cells. Clusterin expression was not related to expression of anaplastic lymphoma kinase-1. With 2 exceptions, none of the remaining 162 non-ALCL cases marked with the clusterin antibody, including Hodgkin disease and primary cutaneous ALCL. In reactive lymphoid tissues, only follicular dendritic cells and fibroblastic reticular cells exhibited staining. Clusterin is a highly conserved glycoprotein implicated in intercellular and cell matrix interactions, regulation of the complement system, lipid transport, stress responses, and apoptosis. Although its function in ALCL is unknown, the unique expression of clusterin within this category of lymphoma provides an additional marker for the diagnosis of ALCL. This study illustrates the enormous potential of gene array technologies for diagnostic marker discovery.

High throughput gene expression screening: its emerging role in drug discovery

The genetic makeup and the environment influences the health and welfare of an individual. At both the tissue and cellular level, physiological function can be correlated with the transcription of genes, whose protein products contribute and influence the activity of biological systems. In order to understand these processes, it is therefore essential to determine the temporal and spatial patterns of gene expression, and, with particular relevance to drug discovery, define changes that occur during development of disease or treatment with therapeutic agents.

Effects of sleep deprivation on sleep and sleep EEG in three mouse strains: empirical data and simulations

Gene targeted mice can be used as models to investigate the mechanisms underlying sleep regulation. Three commonly used background strains for gene targeting (129/Ola, 129/SvJ and C57BL/6J) were subjected to 4-h and 6-h sleep deprivation (SD), and their sleep and sleep EEG were continuously recorded. The two-process model of sleep regulation has predicted the time course of slow-wave activity (SWA) in nonREM sleep after several sleep-wake manipulations in humans and the rat [3] [9]. We tested the capacity of the model to predict SWA in nonREM sleep on the basis of the temporal organization of sleep in mice. The strains differed in the amount and distribution of sleep and the time course of SWA. After spontaneous waking episodes of 10-30 min as well as after SD, SWA was invariably increased. Simulations of the time course of SWA were successful for 129/SvJ and C57BL/6J, but were not satisfactory for 129/Ola. Since the time constants are assumed to reflect the dynamics of the physiological processes involved in sleep regulation, the results provide a basis for the use of gene targeted mice to investigate the underlying mechanisms.

High throughput analysis of gene expression in the human brain

The human brain is thought to have the greatest complexity of gene expression of any region of the body, reflecting the diverse functions of neurons and glia. Studies of gene expression in the human brain may yield fundamental information about the phenotype of brain cells in different stages of development, in different brain regions, and in different physiological and pathological states. As the human genome project nears completion, several technological advances allow the analysis of thousands of expressed genes in a small brain sample. This review describes available sources of human brain material, and several high throughput techniques used to measure the expression of thousands of genes. These techniques include expressed sequence tag (EST) sequencing of cDNA libraries; differential display; subtractive hybridization; serial analysis of gene expression (SAGE); and the emerging technology of high density DNA microarrays. Measurement of gene expression with microarrays and other technologies has potential applications in the study of human brain diseases, including cognitive disorders for which animal models are typically not available. Gene expression measurements may be used to identify genes that are abnormally regulated as a secondary consequence of a disease state, or to identify the response of brain cells to pharmacological treatments.

Identification of genes responsive to BPDE treatment in HeLa cells using cDNA expression assays

Genotoxic stresses induce cellular responses that can be observed at the level of gene expression. We have studied changes in gene expression following BPDE exposure in HeLa cells by using a cDNA expression array of 597 human genes. After a 53-hr exposure to 0.4 microM BPDE, nine genes were upregulated. The protein products of these genes are: fos-related antigen 2, apoptotic cysteine protease MCH4, DB1 (zinc finger protein 91), transcription factor ETR103, integrin alpha, interleukin-4, interleukin-6, 23-kDa highly basic protein, and ribosomal protein S9. We observed the downregulation of gene expression of three genes: heat-shock protein 27, DNA-binding protein TAX, and NADH-ubiquinone oxidoreductase B18 subunit. These results suggest unknown functions or regulatory circuits for several of the responsive genes and demonstrate the complexity of cellular responses to genotoxic insults.