Daniel S. Whittaker

Diurnal rhythms in brain transcription align neural, immune, and metabolic processes with the light–dark cycle and are profoundly disrupted in Alzheimer’s disease (AD). However, the regional organization of diurnal transcription in the healthy and diseased brain remains poorly defined. Using large-scale spatial transcriptomics, we mapped 24-hour rhythmic transcription across cortical and subcortical regions of the mouse brain. We identified marked regional differences in rhythmicity, including distinct oscillatory signatures across cortical areas and along the rostro–caudal axis. In the APP23 mouse model of AD, pathology-vulnerable brain regions exhibited early, region-specific disruption of diurnal transcription prior to substantial amyloid plaque deposition. These findings reveal a spatially organized architecture of brain diurnal rhythms and identify early rhythmic dysregulation as a feature of Alzheimer’s disease pathogenesis.

Background: Fetal alcohol spectrum disorders (FASD) is an umbrella term used to describe physical, neuropathological, and behavioral alterations caused by prenatal alcohol exposure. Caretakers often report that children with FASD experience sleep problems. However, interventions to improve sleep have not been well‐studied in this population. Interestingly, supplementation with the essential nutrient choline can attenuate many behavioral alterations associated with prenatal alcohol exposure. Moreover, choline is a precursor to acetylcholine, a neurochemical that is also involved in sleep–wake modulation. Using an animal model, this study investigated the effects of developmental alcohol exposure on sleep and examined whether postnatal choline supplementation can modulate sleep alterations associated with FASD. Methods: Sprague–Dawley rat pups received ethanol (5.25 g/kg/day, 11.9% v/v) or sham intubations from postnatal days (PD) 4–9, a period of development equivalent to the human third‐trimester brain growth spurt. Subjects then received subcutaneous injections with choline chloride (100 mg/kg/day) or saline from PD 10–30. On PD 32–37, subjects were individually housed to measure sleep–wake behaviors using the PiezoSleep Adapt‐A‐Base System. Sleep parameters, including sleep time, bout length, and number, were recorded. Results: Ethanol‐exposed subjects, particularly females, slept less during the dark cycle. In addition, females exposed to developmental alcohol exhibited more night‐to‐night variability in sleep duration, consistent with findings from clinical populations. In contrast, choline supplementation increased sleep duration, particularly among males exposed to developmental alcohol. Choline specifically increased sleep bout duration in ethanol‐exposed subjects during the dark cycle, suggesting that choline can modify sleep patterns among subjects exposed to prenatal alcohol. Conclusions: These results illustrate that alcohol exposure during late gestation may lead to sleep disturbances and suggest that postnatal choline supplementation affects sleep quality. Importantly, this nutritional intervention was administered after the alcohol insult, suggesting that nutritional supplements in children with FASD may impact sleep problems.

Metatranscriptome (MetaT) sequencing is a critical tool for profiling the dynamic metabolic functions of microbiomes. In addition to taxonomic information, MetaT also provides real-time gene expression data of both host and microbial populations, thus permitting authentic quantification of the functional (enzymatic) output of the microbiome and its host. The main challenge to effective and accurate MetaT analysis is the removal of highly abundant rRNA transcripts from these complex mixtures of microbes, which can number in the thousands of individual species. Regardless of methodology for rRNA depletion, the design of rRNA removal probes based solely upon taxonomic content of the microbiome typically requires very large numbers of individual probes, making this approach complex to commercially manufacture, costly, and frequently technically infeasible. In previous work [1], we designed a set of depletion probes for human stool samples using a design strategy based solely on sequence abundance, completely agnostic of the microbiomal species present. Here, we show that the human-based probes are less effective when used with mouse cecal samples. However, adapting additional rRNA depletion probes specifically to cecal content provides both greater efficiency and consistency for MetaT analysis of mouse samples. Importance Sequencing total RNA from microbiome samples is seriously impaired by the overwhelming proportion of rRNA to mRNA content. As much as 99% of sequencing reads can be assigned to the rRNA content, thus removal of these abundant transcripts is critical to MetaT analysis. The use of Ribo Zero Plus rRNA depletion probes designed for human gut microbiomes proved to be less effective and more inconsistent across mouse cecal donor samples, a common experimental system for microbiome studies. In the present work, we have extended and refined a taxonomically-neutral probe design method for mouse cecal content. The additional probes were carefully chosen to limit the number needed for effective depletion to reduce both the cost and risk of introducing bias to MetaT analysis. Our results demonstrate this method as efficient and consistent for rRNA removal in mouse cecal samples, thus providing a significant increase in the number of mRNA-rich sequencing reads for MetaT analysis.

Subcortical white matter stroke (WMS) is a progressive disorder which is demarcated by the formation of small ischemic lesions along white matter tracts in the CNS. As lesions accumulate, patients begin to experience severe motor and cognitive decline. Despite its high rate of incidence in the human population, our understanding of the cause and outcome of WMS is extremely limited. As such, viable therapies for WMS remain to be seen. This study characterizes myelin recovery following stroke and motor learning-based rehabilitation in a mouse model of subcortical WMS. Following WMS, a transient increase in differentiating oligodendrocytes occurs within the peri-infarct in young male adult mice, which is completely abolished in male aged mice. Compound action potential recording demonstrates a decrease in conduction velocity of myelinated axons at the peri-infarct. Animals were then tested on one of three distinct motor learning-based rehabilitation strategies (skilled reach, restricted access to a complex running wheel, and unrestricted access to a complex running wheel) for their capacity to induce repair. These studies determined that unrestricted access to a complex running wheel alone increases the density of differentiating oligodendrocytes in infarcted white matter in young adult male mice, which is abolished in aged male mice. Unrestricted access to a complex running wheel was also able to enhance conduction velocity of myelinated axons at the peri-infarct to a speed comparable to naive controls suggesting functional recovery. However, there was no evidence of motor rehabilitation-induced remyelination or myelin protection. SIGNIFICANCE STATEMENT White matter stroke is a common disease with no medical therapy. A form of motor rehabilitation improves some aspects of white matter repair and recovery.

Introduction Disturbances in the daily sleep-wake cycle are common in individuals with neurodegenerative disorders. Huntington’s disease (HD) is a genetic neurodegenerative disorder in which patients exhibit a variety of impairments that include, poor motor function, disrupted circadian rhythms, and sleep abnormalities such as difficulty initiating sleep at bedtime and more frequent nighttime arousals. In the BACHD mouse model time restricted feeding (TRF) has been successful at improving motor functions and circadian rhythms. The BACHD mouse model has a bacterial artificial chromosome that expresses the full-length human mutant huntingtin gene. Methods In order to determine the effects of TRF on sleep-wake architecture, EEG/EMG polysomnographic records were examined in mice between 3-4 months old bearing the BAC knock-in of a human genetic mutation of HD and WT litter mates, first during ad libitum (ad lib) feeding then during an 18 hour fasting protocol. TRF protocol consisted of 6 hours of food access limited between ZT15-ZT21 and 18 hours of fasting. Results A two-way ANOVA revealed that TRF significantly decreased the amount of total sleep (p=0.04) and NREM sleep (p=0.04) in the dark phase in both WT and BACHD mice. TRF did not significantly affect sleep in the light phase, however trends suggest that BACHD mice have more sleep in the light phase under TRF than ad lib. Conclusion This data suggests that TRF improves sleep by consolidating sleep to the light phase and wake to the dark phase. In conclusion, TRF may be a promising tool that can improve the negative effects of neurodegenerative diseases on sleep-wake processes. Support These experiments were supported by R01-NS078410 and UCLA start-up funds.

Mice lacking a functional Biogenesis of Lysosome-related Organelles Complex 1 (BLOC-1), such as those of the pallid line, display cognitive and behavioural impairments reminiscent of those presented by individuals with intellectual and developmental disabilities. Although disturbances in the sleep/wake cycle are commonly lamented by these individuals, the underlying mechanisms, including the possible role of the circadian timing system, are still unknown. In this paper, we have explored sleep/circadian malfunctions and underlying mechanisms in BLOC-1-deficient pallid mice. These mutants exhibited less sleep behaviour in the beginning of the resting phase than wild-type mice with a more broken sleeping pattern in normal light-dark conditions. Furthermore, the strength of the activity rhythms in the mutants were reduced with significantly more fragmentation and lower precision than in age-matched controls. These symptoms were accompanied by an abnormal preference for the open arm in the elevated plus maze in the day and poor performance in the novel object recognition at night. At the level of the central circadian clock (the suprachiasmatic nucleus, SCN), loss of BLOC-1 caused subtle morphological changes including a larger SCN and increased expression of the relative levels of the clock gene Per2 product during the day but did not affect the neuronal activity rhythms. In the hippocampus, the pallid mice presented with anomalies in the cytoarchitecture of the Dentate Gyrus granule cells, but not in CA1 pyramidal neurones, along with altered PER2 protein levels as well as reduced pCREB/tCREB ratio during the day. Our findings suggest that lack of BLOC-1 in mice disrupts the sleep/wake cycle and performance in behavioural tests associated with specific alterations in cytoarchitecture and protein expression.

Huntington’s disease (HD) patients suffer from progressive neurodegeneration that results in cognitive, psychiatric, cardiovascular, and motor dysfunction. Disturbances in sleep-wake cycles are common among HD patients with reports of delayed sleep onset, frequent bedtime awakenings, and excessive fatigue. The BACHD mouse model exhibits many HD core symptoms including circadian dysfunction. Because circadian dysfunction manifests early in the disease in both patients and mouse models, we sought to determine if early interventions that improve circadian rhythmicity could benefit HD symptoms and delay disease progression. We evaluated the effects of time-restricted feeding (TRF) on the BACHD mouse model. At 3 months of age, the animals were divided into 2 groups: ad lib and TRF. The TRF-treated BACHD mice were exposed to a 6-h feeding/18-h fasting regimen that was designed to be aligned with the middle (ZT 15-21) of the period when mice are normally active (ZT 12-24). Following 3 months of treatment (when mice reached the early disease stage), the TRF-treated BACHD mice showed improvements in their locomotor activity and sleep behavioral rhythms. Furthermore, we found improved heart rate variability, suggesting that their autonomic nervous system dysfunction was improved. On a molecular level, TRF altered the phase but not the amplitude of the PER2::LUC rhythms measured in vivo and in vitro. Importantly, treated BACHD mice exhibited improved motor performance compared with untreated BACHD controls, and the motor improvements were correlated with improved circadian output. It is worth emphasizing that HD is a genetically caused disease with no known cure. Lifestyle changes that not only improve the quality of life but also delay disease progression for HD patients are greatly needed. Our study demonstrates the therapeutic potential of circadian-based treatment strategies in a preclinical model of HD.

Huntington’s disease (HD) patients suffer from a progressive neurodegeneration that results in cognitive, psychiatric, cardiovascular and motor dysfunction. Disturbances in sleep/wake cycles are common among HD patients with reports of delayed sleep onset, frequent bedtime awakenings, and fatigue during the day. The heterozygous Q175 mouse model of HD has been shown to phenocopy many HD core symptoms including circadian dysfunctions. Because circadian dysfunction manifests early in the disease in both patients and mouse models, we sought to determine if early intervention that improve circadian rhythmicity can benefit HD and delay disease progression. We determined the effects of time-restricted feeding (TRF) on the Q175 mouse model. At 6 months of age, the animals were divided into two groups: ad lib and TRF. The TRF-treated Q175 mice were exposed to a 6-hr feeding/18-hr fasting regimen that was designed to be aligned with the middle of the time when mice are normally active. After 3 months of treatment (when mice reached the early disease stage), the TRF-treated Q175 mice showed improvements in their locomotor activity rhythm and sleep awakening time. Furthermore, we found improved heart rate variability (HRV), suggesting that their autonomic nervous system dysfunction was improved. Importantly, treated Q175 mice exhibited improved motor performance compared to untreated Q175 controls, and the motor improvements were correlated with improved circadian output. Finally, we found that the expression of several HD-relevant markers were restored to WT levels in the striatum of the treated mice using NanoString gene expression assays. Significance Statement HD is a genetically caused disease with no known cure. Lifestyle changes that not only improve the quality of life but also delay disease progression for HD patients are greatly needed. In this study, we found that time restricted feeding (TRF) improves activity/rest rhythms in the Q175 mouse model of HD. This treatment also improved motor performance and heart rate variability in the HD mice. Finally, TRF altered the expression of HD relevant markers in the striatum. Our study demonstrates the therapeutic potential of circadian-based treatment strategies in a pre-clinical model of HD.

Huntington's disease (HD) is an autosomal dominant, neurodegenerative disorder characterized by motor as well as nonmotor symptoms for which there is currently no cure. The Q175 mouse model of HD recapitulates many of the symptoms identified in HD patients including disruptions of the sleep/wake cycle. In this study, we sought to determine if the daily administration of the histamine‐3 receptor (H3R) antagonist/inverse agonist 6‐[(3‐cyclobutyl‐2,3,4,5‐tetrahydro‐1H‐3‐benzazepin‐7‐yl)oxy]‐N‐methyl‐3‐pyridinecarboxamide hydrochloride (GSK189254) would improve nonmotor symptoms in the Q175 line. This class of drugs acts on autoreceptors found at histaminergic synapses and results in increased levels of histamine (HA). HA is a neuromodulator whose levels vary with a daily rhythm with peak release during the active cycle and relatively lower levels during sleep. H3Rs are widely expressed in brain regions involved in cognitive processes and activation of these receptors promotes wakefulness. We administered GSK189254 nightly to homozygote and heterozygote Q175 mice for 4 weeks and confirmed that the plasma levels of the drug were elevated to a therapeutic range. We demonstrate that daily treatment with GSK189254 improved several behavioral measures in the Q175 mice including strengthening activity rhythms, cognitive performance and mood as measured by the tail suspension test. The treatment also reduced inappropriate activity during the normal sleep time. The drug treatment did not alter motor performance and coordination as measured by the challenging beam test. Our findings suggest that drugs targeting the H3R system may show benefits as cognitive enhancers in the management of HD.