Biology subjects

Franken, P.

Publications and source records attributed to Franken, P..

13 recordsLinked to original sources

bioRxiv2025

Vagal afferent activation induces a NREM-sleep-like state with brain-body cooling, but locus coeruleus activation

Parasympathetic nervous system activity, vital for restorative sleep, is influenced by vagal sensory afferents, but how these shape brain-body correlates of sleep remains open. We investigated this by combining vagal sensory neuron (VSN) stimulation with EEG/EMG, heart rate, brain-body temperature, and noradrenergic locus coeruleus (LC) neuron population activity measures. Opto-/chemogenetic VSN manipulations in Vglut2-Cre mice were validated via in vitro synaptic physiology, cFos expression, and heart rate measures. Chemogenetic VSN stimulation during the resting phase induced a non-rapid-eye-movement sleep (NREMS)-like state with enriched, but homeostatically regulated, low-frequency (0.75-4 Hz) EEG activity, yet suppressed REMS. Simultaneously, brain-body temperatures dropped while LC activity increased. Recovery was gradual towards normal NREMS-REMS-cycles but accelerated by external warming, identifying cooling as key factor. We conclude that VSN activation can promote brain-body correlates as a continuum of normal NREM sleep while engaging forebrain neuromodulation, offering insights into mechanisms of sleep disruptions linked to autonomic dysregulation.

neuroscience↗

bioRxiv2023

Model integration of circadian and sleep-wake driven contributions to rhythmic gene expression reveals novel regulatory principles

Transcriptome studies aim at gaining insight into the molecular pathways underlying biological processes. Analyses of gene-expression dynamics in research on circadian rhythms and sleep homeostasis describe these two processes independently, using separate models such as sinusoidal oscillations and exponential saturating functions. Rhythmically expressed genes are, however, influenced by both processes. We therefore implemented a driven, damped harmonic oscillator model which can accommodate both types of dynamics by varying the degree of damping. This makes it possible to estimate the contribution of circadian and sleep-wake driven influences on the expression of a gene within the framework of a single model. We applied the model to cortex, liver, and blood data obtained in mice and humans. The model reliably captured a wide range of rhythmic dynamics under various experimental conditions, including the long-term amplitude reduction of cortical clock-gene rhythms observed after sleep deprivation. Cortical gene expression was generally influenced more by sleep-wake driven than circadian factors, while the opposite was observed in liver and blood. Importantly, the model suggested that sleep-wake state can alter gene expression with a delayed, long-lasting response not previously considered. Our model further predicted that, perhaps paradoxically, the gain in sleep time after sleep deprivation, delayed re-establishing baseline expression rhythms of intrinsically oscillatory transcripts indicating that similar to insufficient sleep, also excess sleep can impact rhythmic gene expression. Because of the tissue- and gene-specific responses, sleep deprivation led to a profound intra- and inter-tissue desynchronization which in the cortex lasted well beyond phenotypic sleep-wake recovery. The results demonstrate that analyzing rhythmic gene expression must take the complex interactions between circadian and sleep-wake influences into account. The model is a versatile tool with a low number of free parameters to fit and predict gene expression under a variety of conditions relevant to society.

systems biology↗

bioRxiv2022

Cortical miR-709 links glutamatergic signaling to NREM sleep EEG slow waves in an activity-dependent manner

MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression that have been implicated in a plethora of neuronal processes. Nevertheless, their role in regulating brain activity in the context of sleep has so far received little attention. To test their involvement, we deleted mature miRNAs in post-mitotic neurons at two developmental ages, i.e., in early adulthood using conditional Dicer knockout (cKO) mice and in adult mice using an inducible conditional Dicer cKO (icKO) line. In both models, electroencephalographic (EEG) activity was affected and the response to sleep deprivation (SD), altered; while rapid-eye-movement sleep (REMS) rebound was compromised in both, EEG delta (1-4 Hz) power during non-REM sleep (NREMS) was reduced in cKO mice and increased in icKO mice. We subsequently investigated the effects of SD on the miRNA transcriptome and found that the expression of 48 forebrain miRNAs was affected, in particular, the activity-dependent miRNA miR-709. In vivo inhibition of miR-709 in the brain increased EEG power during NREMS in the slow-delta (0.75-1.75 Hz) range, particularly after periods of prolonged wakefulness. Transcriptome analysis of primary cortical neurons in vitro revealed that miR-709 regulates endosomal trafficking and glutamatergic receptor activity. A subset of the genes involved in glutamatergic transmission was affected also in the cortices of sleep-deprived, miR-709-inhibited mice. Our data implicate miRNAs in the regulation of EEG activity and indicate that miR-709 links neuronal excitability during wakefulness to brain synchrony during sleep, likely through the regulation of endosomal trafficking and glutamatergic signaling. Significance StatementMicroRNAs (miRNAs) are key regulators of gene expression playing vital roles both in postnatal brain development and its functioning in adult organisms. Here, we highlight a fundamental role for miRNAs in shaping EEG slow waves, which reflect synchronous neuronal firing, characteristic of NREM sleep (NREMS) in the adult murine cortex. Disruption of the miRNA-biogenesis machinery affected brain synchrony differently, depending on when it occurred during development. Moreover, sleep deprivation altered the expression of several miRNAs in a brain-region specific manner. Among those, we identified miR-709 to affect the expression of genes involved in endosomal-trafficking and glutamatergic-transmission, thereby linking neuronal activity during wakefulness to slow EEG waves during subsequent sleep. The current study causally implicates this specific miRNA and the molecular pathways it targets in modifying the generation of NREMS EEG slow waves, which are important in synaptic plasticity and brain functioning.

neuroscience↗

bioRxiv2021

Depriving mice of sleep also deprives of food

Both sleep-wake behavior and circadian rhythms are tightly coupled to energy metabolism and food intake. Altered feeding times in mice are known to entrain clock-gene rhythms in brain and liver and sleep-deprived humans tend to eat more and gain weight. Previous observations in mice showing that sleep deprivation (SD) changes clock-gene expression might thus relate to altered food intake and not to the loss of sleep per se. Whether SD affects food intake in the mouse and how this might affect clock-gene expression is, however, unknown. We therefore quantified i) the cortical expression of the clock genes Per1, Per2, Dbp, and Cry1 in mice that had access to food or not during a 6h SD, and ii) food intake during baseline, SD, and recovery sleep. We found that food deprivation did not modify the SD-incurred clock-gene changes in the cortex. Moreover, we discovered that although food intake during SD did not differ from baseline, mice lost weight and increased food intake during subsequent recovery. We conclude that SD is associated with food deprivation and that the resulting energy deficit might contribute to the effects of SD that are commonly interpreted as a response to sleep loss.

physiology↗

bioRxiv2021

Towards mouse genetic-specific RNA-sequencing read mapping

Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using RNA-sequencing (RNA-seq). Paradoxically, these variants between the samples are usually ignored at the beginning of RNA-seq analyses of many model organisms. This can skew the transcriptome estimates that are used later for downstream analyses, such as expression quantitative trait locus (eQTL) detection. Here, we assessed the impact of reference-based analysis on the transcriptome and eQTLs in a widely-used mouse genetic population: the BXD panel of recombinant inbred lines. We highlight existing reference bias in the transcriptome data analysis and propose practical solutions which combine available genetic variants, genotypes, and genome reference sequence. The use of custom BXD line references improved downstream analysis compared to classical genome reference. These insights would likely benefit genetic studies with a transcriptomic component and demonstrate that genome references might need to be reassessed and improved.

bioinformatics↗

bioRxiv2020

A Sub-Minute Resolution Prediction of Brain Temperature Based on Sleep-Wake State in the Mouse

While brain temperature is of neurobiological and clinical importance, it is still unclear which factors contribute to its daily dynamics and to what degree. We recorded cortical temperature in mice alongside sleep-wake state during 4 days including a 6h sleep deprivation, and developed a mathematical tool to simulate temperature based on the sleep-wake sequence. The model estimated temperature with remarkable precision accounting for 91% of its variance based on three main factors with the sleep-wake sequence accounting for most of the variance (74%) and time-of-day ( circadian) the least (9%). As third factor, prior wake prevalence, was discovered to up-regulate temperature, explaining 43% of the variance. With similar accuracy the model predicted cortical temperature in a second, independent cohort using the parameters optimized for the first. Our model corroborates the profound influence of sleep-wake state on brain temperature, and can help differentiate thermoregulatory from sleep-wake driven effects in experiments affecting both.

neuroscience↗

bioRxiv2020

The sleep-wake distribution contributes to the peripheral rhythms in PERIOD-2

In the mouse, Period-2 (Per2) expression in tissues peripheral to the suprachiasmatic nuclei (SCN) increases during sleep deprivation and at times of the day when animals are predominantly awake spontaneously, suggesting that the circadian sleep-wake distribution directly contributes to the daily rhythms in Per2. We found support for this hypothesis by recording sleep-wake state alongside PER2 bioluminescence in freely behaving mice, demonstrating that PER2 increases during spontaneous waking and decreases during sleep. The temporary reinstatement of PER2 rhythmicity in behaviorally arrhythmic SCN-lesioned mice submitted to daily recurring sleep deprivations substantiates our hypothesis. Mathematical modelling revealed that PER2 dynamics can be described by a damped harmonic oscillator driven by two forces: a sleep-wake-dependent force and a SCN-independent circadian force. Our work underscores the notion that in peripheral tissues the clock gene circuitry integrates sleep-wake information and could thereby contribute to behavioral adaptability to respond to homeostatic requirements.

physiology↗

bioRxiv2020

Melanopsin-dependent direct photic effects are equal to clock-driven effects in shaping the nychthemeral sleep-wake cycle

Nychthemeral sleep-wake cycles (SWc) are known to be generated by the circadian clock in suprachiasmatic nuclei (SCN), entrained to the light-dark cycle. Light also exerts direct acute effects on sleep and waking. However, under longer photic exposure such as the 24-hour day, the precise significance of sustained direct light effects (SDLE) and circuitry involved have been neither clarified nor quantified, as disentangling them from circadian influence is difficult. Recording sleep in mice lacking a circadian pacemaker and/or melanopsin-based phototransduction, we uncovered, contrary to prevailing assumptions, that circadian-driven input shapes only half of SWc, with SDLE being equally important. SDLE were primarily mediated (>80%) through melanopsin, of which half were relayed through SCN, independent of clock function. These findings were used for a model that predicted SWc under simulated jet-lag, and revealed SDLE as a crucial mechanism influencing behavior, and should be considered for circadian/sleep disorder management and societal lighting optimization.

neuroscience↗

bioRxiv2019

Reassessing the validity of slow-wave dynamics as a proxy for NREM sleep homeostasis

Sleep-wake driven changes in NREM sleep (NREMS) EEG delta ({delta}: [~]0.75-4.5Hz) power are widely used as proxy for a sleep homeostatic process. We noted frequency increases in {delta}-waves in sleep-deprived (SD) mice, prompting us to re-evaluate how slow-wave characteristics relate to prior sleep-wake history. We discovered two types of {delta}-waves; one responding to SD with high initial power and fast, discontinuous decay ({delta}2: [~]2.5-3.5Hz) and another unrelated to time-spent-awake with slow, linear decays ({delta}1: [~]0.75-1.75Hz). Human experiments confirmed this {delta}-band heterogeneity. Similar to SD, silencing of centromedial thalamus neurons boosted {delta}2-waves, specifically. {delta}2-dynamics paralleled that of temperature, muscle tone, heart-rate, and neuronal UP/DOWN state lengths, all reverting to characteristic NREMS levels within the first recovery hour. Thus, prolonged waking seems to necessitate a physiological recalibration before typical NREMS can be reinstated. These short-lasting {delta}2-dynamics challenge accepted models of sleep regulation and function based on the merged {delta}-band as sleep-need proxy.

neuroscience↗

bioRxiv2019

Simple and complex interactions between sleep-wake driven and circadian processes shape daily genome regulatory dynamics in the mouse

The timing and duration of sleep results from the interaction between a sleep-wake driven, or homeostatic, process (S) and a circadian process (C), and involves changes in gene expression and genomic regulation. Unraveling the respective contributions of S and C, and their interaction, to transcriptional and epigenomic regulatory dynamics requires sampling over time under unperturbed conditions and conditions of perturbed sleep. Here, we profiled mRNA expression and chromatin accessibility in the cerebral cortex of mice over a three-day period, including a 6-hour sleep deprivation (SD) on day two. Mathematical modeling established that a large proportion of rhythmic genes are actually governed by Process S with varying degrees of interaction with Process C, sometimes working in opposition. Remarkably, SD causes long-term effects on gene expression dynamics, outlasting phenotypic recovery, most strikingly illustrated by a dampening of the oscillation of most core clock genes, including Bmal1, suggesting that enforced wakefulness directly impacts the molecular clock machinery. Chromatin accessibility proved highly plastic and dynamically affected by SD. Distal regions, rather than promoters, display dynamics corresponding to gene transcription, implying that changes in mRNA expression result from constantly accessible promoters under the influence of distal enhancers or repressors. Srf was predicted as a transcriptional regulator driving immediate response, suggesting that Srf activity mirrors the build-up and release of sleep pressure. Our results demonstrate that a single, short SD has long-term aftereffects at the genomic regulatory level. Such effects might accumulate with repeated sleep restrictions, thereby contributing to their adverse health effects.\n\nSignificance statementWhen and how long we sleep is determined by the time-of-day and how long we have been awake, which are tracked molecularly by a circadian and a sleep-wake driven process, respectively. We measured the long-term consequences of a short-term sleep deprivation (SD) on gene expression and regulation in the mouse brain, and used mathematical models to determine the relative contributions of the circadian and sleep-wake driven processes. We find that many genes, including most of the genes that constitute the molecular circadian clock, are perturbed by SD long after the mice ceased showing behavioral signs of sleep loss. Our results have implications for human health, given the high prevalence of insufficient and poor quality sleep in our contemporary society.

genomics↗

bioRxiv2019

A multi-omics digital research object for the genetics of sleep regulation.

More and more researchers make use of multi-omics approaches to tackle complex cellular and organismal systems. It has become apparent that the potential for re-use and integrate data generated by different labs can enhance knowledge. However, a meaningful and efficient re-use of data generated by others is difficult to achieve without in depth understanding of how these datasets were assembled. We therefore designed and describe in detail a digital research object embedding data, documentation and analytics on mouse sleep regulation. The aim of this study was to bring together electrophysiological recordings, sleep-wake behavior, metabolomics, genetics, and gene regulatory data in a systems genetics model to investigate sleep regulation in the BXD panel of recombinant inbred lines. We here showcase both the advantages and limitations of providing such multi-modal data and analytics. The reproducibility of the results was tested by a bioinformatician not implicated in the original project and the robustness of results was assessed by re-annotating genetic and transcriptome data from the mm9 to the mm10 mouse genome assembly.

bioinformatics↗

bioRxiv2018

Cold Inducible RNA-binding protein (CIRBP) adjusts clock gene expression and REM sleep recovery after sleep deprivation

Sleep depriving mice affects clock gene expression, suggesting that these genes partake in sleep homeostasis. The mechanisms linking wakefulness to clock gene expression are, however, not well understood. We propose CIRBP because its rhythmic expression is i) sleep-wake driven and ii) necessary for high-amplitude clock gene expression in vitro. We therefore expect Cirbp knock-out (KO) mice to exhibit attenuated sleep-deprivation (SD) induced changes in clock gene expression, and consequently to differ in their sleep homeostatic regulation. Lack of CIRBP indeed blunted the SD-incurred changes in cortical expression of the clock gene Rev-erb whereas it amplified the changes in Per2 and Clock. Concerning sleep homeostasis, KO mice accrued only half the extra REM sleep wild-type (WT) littermates obtained during recovery. Unexpectedly, KO mice were more active during lights-off which was accompanied by an acceleration of theta oscillations. Thus, CIRBP adjusts cortical clock gene expression after SD and expedites REM sleep recovery.

neuroscience↗

bioRxiv2017

Altered allostatic regulation of wakefulness and slow-wave-sleep spectral quality in mice with hypocretin (orexin) receptor 1 inactivation in noradrenergic cells

Noradrenaline (NA) and hypocretins/orexins (HCRT), and their receptors, dynamically modulate the circuits that configure behavioral states, and their associated oscillatory activities. Salient stimuli activate spiking of locus coeruleus noradrenergic (NALC) cells, inducing NA release and brain-wide noradrenergic signalling, thus resetting network activity, and mediating an orienting response. Hypothalamic HCRT neurons provide one of the densest input to NALC cells. To functionally address the HCRT-to-NA connection, we selectively disrupted the Hcrtr1 gene in NA neurons, and analyzed resulting (Hcrtr1Dbh-CKO) mice, and their control littermates electrocortical response in several contexts of enhanced arousal. Under enforced wakefulness (EW), or after cage change (CC), Hcrtr1Dbh-CKO mice exhibited a weakened ability to lower infra-{theta} frequencies (1-7 Hz), and mount a robust, narrow-bandwidth, high-frequency {theta} rhythm (~8.5 Hz). A fast-{gamma} (55-80 Hz) response, whose dynamics closely parallelled {theta}, also diminished, while {beta}/slow-{gamma} activity (15-45 Hz) increased. Furthermore, EW-associated locomotion was lower. Surprisingly, nestbuilding-associated wakefulness, inversely, featured enhanced {theta} and fast-{gamma} activities. Thus HCRT-to-NA signalling may fine-tune arousal, up in alarming conditions, and down during self-motivated, goal-driven behaviors. Lastly, slow-wave-sleep following EW and CC, but not nestbuilding, was severely deficient in slow-{delta} waves (0.75-2.25 Hz), suggesting that HCRT-to-NA signalling regulates the slow-{delta} rebound characterizing sleep after stress-associated arousal.

neuroscience↗