Beyond circadian rhythms: emerging roles of ultradian rhythms in control of liver functions

Circadian clock-independent ultradian rhythms in lipid metabolism in the Drosophila fat body

The role of circadian clocks in regulating metabolic processes is well known; however, their impact on metabolic states across species and life stages remains largely unexplored. This study investigates the relationship between circadian rhythms and metabolic regulation in the Drosophila larval fat body, a metabolic hub analogous to the mammalian liver and adipose tissue. Surprisingly, the fat body of period null mutants, which lack a functional circadian clock in all tissues, exhibited 12-hour rhythms in gene expression, particularly those involved in peroxisome function, lipid metabolism, and oxidative stress response. These transcriptomic rhythms were aligned with 12-hour oscillations in peroxisome biogenesis and activity, reactive oxygen species levels, and lipid peroxidation. Furthermore, period mutants exhibited 12-hour rhythms in body fat storage, ultimately leading to a net reduction in body fat levels. Collectively, our results identify clock-independent ultradian rhythms in lipid metabolism that are essential for larval survival and development.

Circadian clock controlled glycolipid metabolism and its relevance to disease management

The circadian clock is a critical regulator of physiological rhythms, orchestrating metabolic processes to adapt to daily environmental changes. This review focuses on the intricate relationship between circadian regulation and glycolipid metabolism, with implications for metabolic diseases. Central and peripheral clocks coordinate the rhythmic expression of key enzymes and transporters, ensuring glycolipid homeostasis. Disruptions to these rhythms can result in metabolic disorders characterized by altered glucose utilization, insulin sensitivity, and lipid storage. The molecular mechanisms underlying these processes include transcriptional-translational feedback loops involving clock factors that regulate glycolipid metabolism. Emerging therapeutic strategies, such as pharmacological and dietary interventions, highlight the translational potential of circadian biology. This review underscores the importance of circadian rhythm maintenance for glycolipid metabolism and its role in preventing metabolic disorders. Further elucidation of the molecular mechanisms linking circadian regulation to glycolipid metabolism could pave the way for precision medicine approaches tailored to individual circadian profiles.

Single and Multiple Doses of Seladelpar Decrease Diurnal Markers of Bile Acid Synthesis in Mice

Peroxisome proliferator-activated receptors (PPARs) modulate bile metabolism and are important therapeutic options in cholestatic diseases. This study was aimed at understanding the effects of single and multiple doses of seladelpar, a PPARδ (peroxisome proliferator-activated receptor delta) agonist, on plasma C4 (a freely diffusible metabolite accepted as a proxy for de novo bile acid biosynthesis), Fibroblast Growth Factor 21 (Fgf21), and gene expression changes in the liver of male and female mice. C57BL/6 mice were treated with seladelpar 10 mg/kg/day or vehicle through oral gavage before lights out on Day 1 (single dose) or from Day 1 to Day 7 (multiple doses). Liver samples were obtained at 0, 1, 2, 4, 8, 12, 16, and 24 h postdosing, and plasma C4 and Fgf21 levels were measured. In vehicle-treated mice, C4 levels were higher in the dark cycle compared to the light cycle, with higher levels in females than in males. Plasma Fgf21 did not vary substantially over the dark-light cycle or show a sex-specific expression pattern. Seladelpar treatment significantly reduced plasma C4 and increased Fgf21 levels in both sexes, which coincided with a decrease in cholesterol 7α-hydroxylase mRNA and an increase in Fgf21 mRNA in the livers. Untargeted RNA sequencing revealed a strong correlation between the genes differentially expressed after single- and multiple-dose seladelpar treatment. PPAR-responsive genes, including pyruvate dehydrogenase kinase 4, acyl-CoA thioesterase 2, and angiopoietin-like 4, were upregulated. No changes in nuclear receptors, clock genes, and sex-specific genes were observed. Overall, these results are consistent with a model where seladelpar treatment reduces bile acid synthesis by upregulating Fgf21 and modulating other PPAR-responsive genes.

Ultradian Rest-activity Rhythms Induced by Quinpirole in Mice Using Wavelet Analysis

Objective

Ultradian rhythms are biological rhythms with periods of a few seconds to a few hours. Along with circadian rhythms, ultradian rhythms influence human physiology. However, such rhythms have not been studied as intensively as circadian rhythms. This study aimed to identify ultradian rest-activity rhythms induced by the dopamine D2/D3 agonist quinpirole in mice.

Methods

We used 10 mice from the Institute of Cancer Research. Quinpirole was administered at a dose of 0.5 mg/kg. We assessed free rest-activity using infrared detectors and conducted wavelet analysis to measure the period and its variation. We also used the paired t test to compare ultradian rhythm patterns.

Results

Quinpirole did not significantly change total 24-hour locomotor activity (p = 0.065). However, it significantly increased locomotor activity during the dark phase (p = 0.001) and decreased it during the light phase (p = 0.016). In the continuous wavelet transform analysis, the mean period was 5.618 hours before quinpirole injection and 4.523 hours after injection. The period showed a significant decrease (p = 0.040), while the variation remained relatively consistent before and after quinpirole injection.

Conclusion

This study demonstrated ultradian rest-activity rhythms induced by quinpirole using wavelet analysis. Quinpirole-induced ultradian rhythms exhibited rapid oscillations with shortened periods and increased activity during the dark phase. To better understand these changes in ultradian rhythms caused by quinpirole, it is essential to compare them with the effects of other psychopharmacological agents. Furthermore, investigating the pharmacological impact on ultradian rest-activity rhythms may have valuable applications in clinical studies.

Sleep and diurnal alternative polyadenylation sites associated with human APA-linked brain disorders

Disruption of sleep and circadian rhythms are a comorbid feature of many pathologies, and can negatively influence many health conditions, including neurodegenerative disease, metabolic illness, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. The interaction between sleep and/or circadian rhythms with the use of Alternative Polyadenylation (APA) has been largely undescribed, particularly in the context of other disorders. APA generates transcript isoforms by utilizing various polyadenylation sites (PASs) from the same gene affecting its mRNA translation, stability, localization, and subsequent function. Here we identified unique APAs expressed in rat brain over time-of-day, immediately following sleep deprivation, and the subsequent recovery period. From these data, we performed a secondary analysis of these sleep- or time-of-day associated PASs with recently described APA-linked human brain disorder susceptibility genes.

SON-dependent nuclear speckle rejuvenation alleviates proteinopathies

Current treatments targeting individual protein quality control have limited efficacy in alleviating proteinopathies, highlighting the prerequisite for a common upstream druggable target capable of global proteostasis modulation. Building on our prior research establishing nuclear speckles as a pivotal membrane-less organelle responsible for global proteostasis transcriptional control, we aim to alleviate proteinopathies through nuclear speckle rejuvenation. We identified pyrvinium pamoate as a small-molecule nuclear speckle rejuvenator that enhances protein quality control while suppressing YAP1 signaling via decreasing the surface/interfacial tension of nuclear speckle condensates through interaction with the intrinsically disordered region of nuclear speckle scaffold protein SON. In pre-clinical models, nanomolar pyrvinium pamoate alleviated retina degeneration and reduced tauopathy by promoting autophagy and ubiquitin-proteasome system in a SON-dependent manner without causing cellular stress. Aberrant nuclear speckle morphology, reduced protein quality control and increased YAP1 activity were also observed in human tauopathies. Our study uncovers novel therapeutic targets for tackling protein misfolding disorders within an expanded proteostasis framework encompassing nuclear speckles and YAP1.

The relationship between oxidative balance score and circadian syndrome: evidence from the NHANES 2005-2018

Background

The oxidative balance score (OBS) is a composite indicator that evaluates the balance between pro-oxidants and antioxidants in one's diet and lifestyle. However, the relationship between OBS and circadian syndrome (CircS) has remained unexplored. This investigation aimed to determine a correlation between OBS and CircS.

Methods

This population-based study examined 7,202 participants from the 2005 to 2018 National Health and Nutrition Examination Survey (NHANES), 1,433 of whom had CircS. We utilized weighted multivariate logistic regression, trend tests, subgroup analysis, and interaction tests to evaluate the correlation between OBS (total OBS, dietary OBS, and lifestyle OBS) and CircS. Restricted cubic splines (RCS) models and threshold effect analysis were used to explore nonlinear relationships.

Results

Multivariate logistic regression analysis indicated that the protective factor for CircS was a high OBS level (total OBS: Odds ratio (OR) = 0.95, 95% Confidence interval (CI): 0.93-0.97; dietary OBS: OR = 0.98, 95% CI: 0.96-1.00; lifestyle OBS: OR = 0.65, 95% CI: 0.61-0.69). Compared to the quartile 1 group, OBS (total OBS, dietary OBS, and lifestyle OBS) was negatively and statistically significantly associated with the risk of developing Circs in the quartile 4 group (total OBS: OR = 0.47, 95% CI: 0.32-0.70; dietary OBS: OR = 0.69, 95% CI: 0.48-0.99; lifestyle OBS: OR = 0.07, 95% CI: 0.04-0.11). According to subgroup analysis and interaction tests, there was an interaction effect between the association of lifestyle OBS and CircS in terms of education level (p for interaction = 0.01). Furthermore, we observed a nonlinear negative relationship between lifestyle OBS and CircS prevalence, with inflection points at 6 (p for nonlinearity = 0.002).

Conclusion

The results showed a substantial negative connection between OBS and CircS. Encouraging foods filled with antioxidants and antioxidant-rich lifestyles may reduce the risk of CircS.

Epigenetic regulation of global proteostasis dynamics by RBBP5 ensures mammalian organismal health

Proteostasis is vital for cellular health, with disruptions leading to pathologies including aging, neurodegeneration and metabolic disorders. Traditionally, proteotoxic stress responses were studied as acute reactions to various noxious factors; however, recent evidence reveals that many proteostasis stress-response genes exhibit ~12-hour ultradian rhythms under physiological conditions in mammals. These rhythms, driven by an XBP1s-dependent 12h oscillator, are crucial for managing proteostasis. By exploring the chromatin landscape of the murine 12h hepatic oscillator, we identified RBBP5, a key subunit of the COMPASS complex writing H3K4me3, as an essential epigenetic regulator of proteostasis. RBBP5 is indispensable for regulating both the hepatic 12h oscillator and transcriptional response to acute proteotoxic stress, acting as a co-activator for proteostasis transcription factor XBP1s. RBBP5 ablation leads to increased sensitivity to proteotoxic stress, chronic inflammation, and hepatic steatosis in mice, along with impaired autophagy and reduced cell survival in vitro. In humans, lower RBBP5 expression is associated with reduced adaptive stress-response gene expression and hepatic steatosis. Our findings establish RBBP5 as a central regulator of proteostasis, essential for maintaining mammalian organismal health.

Evidence for ~12-h ultradian gene programs in humans

Mice and many marine organisms exhibit ~12-h ultradian rhythms, however, direct evidence of ~12-h ultradian rhythms in humans is lacking. Here, we performed prospective, temporal transcriptome profiling of peripheral white blood cells from three healthy humans. All three participants independently exhibited robust ~12-h transcriptional rhythms in molecular programs involved in RNA and protein metabolism, with strong homology to circatidal gene programs previously identified in Cnidarian marine species.

Sleep and diurnal alternative polyadenylation sites associated with human APA-linked brain disorders

Disruption of sleep and circadian rhythms are a comorbid feature of many pathologies, and can negatively influence many health conditions, including neurodegenerative disease, metabolic illness, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. The interaction between sleep and/or circadian rhythms with the use of Alternative Polyadenylation (APA) has been largely undescribed, particularly in the context of other disorders. APA is a process that generates various transcript isoforms of the same gene affecting its mRNA translation, stability, localization, and subsequent function. Here we identified unique APAs expressed in rat brain over time-of-day, immediately following sleep deprivation, and the subsequent recovery period. From these data, we performed a secondary analysis of these sleep- or time-of-day associated PASs with recently described APA-linked human brain disorder susceptibility genes.

Identification of sleep and circadian alternative polyadenylation sites associated with APA-linked human brain disorders

Sleep and circadian rhythm disruptions are comorbid features of many pathologies and can negatively influence numerous health conditions, including degenerative diseases, metabolic illnesses, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. Thus, associations between sleep and/or circadian rhythm and alternative polyadenylation (APA), particularly in the context of other health challenges, are largely undescribed. APA is a process that generates various transcript isoforms from the same gene, resulting in effects on mRNA translation, stability, localization, and subsequent function. Here, we have identified unique APAs in rat brain that exhibit time-of-day-dependent oscillations in expression as well as APAs that are altered by sleep deprivation and the subsequent recovery period. Genes affected by APA usage include Mapt/Tau, Ntrk2, Homer1A, Sin3band Sorl. Sorl1 has two APAs which cycle with a 24 h period, one additional APA cycles with a 12 h period and one more that is reduced during recovery sleep. Finally, we compared sleep- or circadian-associated APAs with recently described APA-linked brain disorder susceptibility genes and found 46 genes in common.

Temporal dynamics and composition of ocular surface microbiota in C57BL/6J mice: uncovering a 12h ultradian rhythm

Purpose

This study aimed to investigate the presence of rhythmic fluctuations in the composition, abundance, and functions of commensal core bacteria on the ocular surface of C57BL/6J mice.

Methods

Male C57BL/6J mice, aged 12 weeks, were subjected to a 12-hour light/12-hour dark cycle. Ocular surface tissue samples were collected at four time points (ZT) over a 24-hour period at six-hour intervals. The core ocular surface microbiota's oscillation cycles and frequencies were assessed using 16S rRNA gene sequencing targeting the V3-V4 region, along with the JTK_CYCLE algorithm. Functional predictions of these bacteria were conducted using PICRUSt2.

Results

Deep sequencing of the ocular surface microbiota highlighted the high abundance of commensal bacteria, with Proteobacteria, Actinobacteriota, and Firmicutes collectively constituting over 90% of the total sample abundance. Among the 22 core bacterial genera, 11 exhibited robust 12-hour rhythms, including Halomonas, Pelagibacterium, Pseudomonas, Nesterenkonia, norank_f_Hyphomonadaceae, Stenotrophomonas, Anoxybacillus, Acinetobacter, Zoogloea, Brevibacillus, and Ralstonia. Further taxonomic analysis indicated significant intra-cluster similarities and inter-cluster differences at the order, family, and genus levels during ZT0/12 and ZT6/18. Community interaction networks and functional prediction analyses revealed synchronized 12-hour rhythmic oscillations in neural, immune, metabolic, and other pathways associated with symbiotic bacteria.

Conclusion

This study demonstrates the presence of ultradian rhythmic oscillations in commensal bacteria on the ocular surface of normal C57BL/6J mice, with a 12-hour cycle. These findings suggest a crucial role for ultradian rhythms in maintaining ocular surface homeostasis in the host.

Reduced glucose concentration enhances ultradian rhythms in Pdcd5 promoter activity in vitro

Intrinsically driven ultradian rhythms in the hourly range are often co-expressed with circadian rhythms in various physiological processes including metabolic processes such as feeding behaviour, gene expression and cellular metabolism. Several behavioural observations show that reduced energy intake or increased energy expenditure leads to a re-balancing of ultradian and circadian timing, favouring ultradian feeding and activity patterns when energy availability is limited. This suggests a close link between ultradian rhythmicity and metabolic homeostasis, but we currently lack models to test this hypothesis at a cellular level. We therefore transduced 3T3-L1 pre-adipocyte cells with a reporter construct that drives a destabilised luciferase via the Pdcd5 promotor, a gene we previously showed to exhibit robust ultradian rhythms in vitro. Ultradian rhythmicity in Pdcd5 promotor driven bioluminescence was observed in >80% of all cultures that were synchronised with dexamethasone, whereas significantly lower numbers exhibited ultradian rhythmicity in non-synchronised cultures (∼11%). Cosine fits to ultradian bioluminescence rhythms in cells cultured and measured in low glucose concentrations (2 mM and 5 mM), exhibited significantly higher amplitudes than all other cultures, and a shorter period (6.9 h vs. 8.2 h, N = 12). Our findings show substantial ultradian rhythmicity in Pdcd5 promotor activity in cells in which the circadian clocks have been synchronised in vitro, which is in line with observations of circadian synchronisation of behavioural ultradian rhythms. Critically, we show that the amplitude of ultradian rhythms is enhanced in low glucose conditions, suggesting that low energy availability enhances ultradian rhythmicity at the cellular level in vitro.

Preservation of ∼12-h ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock

Introduction: Besides the ∼24-h circadian rhythms, ∼12-h ultradian rhythms of gene expression, metabolism and behaviors exist in animals ranging from crustaceans to mammals. Three major hypotheses were proposed on the origin and mechanisms of regulation of ∼12-h rhythms, namely, that they are not cell-autonomous and controlled by a combination of the circadian clock and environmental cues, that they are regulated by two anti-phase circadian transcription factors in a cell autonomous manner, or that they are established by a cell-autonomous ∼12-h oscillator. Methods: To distinguish among these possibilities, we performed a post hoc analysis of two high temporal resolution transcriptome dataset in animals and cells lacking the canonical circadian clock. Results: In both the liver of BMAL1 knockout mice and Drosophila S2 cells, we observed robust and prevalent ∼12-h rhythms of gene expression enriched in fundamental processes of mRNA and protein metabolism that show large convergence with those identified in wild-type mice liver. Bioinformatics analysis further predicted ELF1 and ATF6B as putative transcription factors regulating the ∼12-h rhythms of gene expression independently of the circadian clock in both fly and mice. Discussion: These findings provide additional evidence to support the existence of an evolutionarily conserved 12-h oscillator that controls ∼12-h rhythms of gene expression of protein and mRNA metabolism in multiple species.

Preservation of ∼12-hour ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock

Besides the ∼24-hour circadian rhythms, ∼12-hour ultradian rhythms of gene expression, metabolism and behaviors exist in animals ranging from crustaceans to mammals. Three major hypotheses were proposed on the origin and mechanisms of regulation of ∼12-hour rhythms, namely that they are not cell-autonomous and controlled by a combination of the circadian clock and environmental cues, that they are regulated by two anti-phase circadian transcriptional factors in a cell-autonomous manner, or that they are established by a cell-autonomous ∼12-hour oscillator. To distinguish among these possibilities, we performed a post-hoc analysis of two high temporal resolution transcriptome dataset in animals and cells lacking the canonical circadian clock. In both the liver of BMAL1 knockout mice and Drosophila S2 cells, we observed robust and prevalent ∼12-hour rhythms of gene expression enriched in fundamental processes of mRNA and protein metabolism that show large convergence with those identified in wild-type mice liver. Bioinformatics analysis further predicted ELF1 and ATF6B as putative transcription factors regulating the ∼12-hour rhythms of gene expression independently of the circadian clock in both fly and mice. These findings provide additional evidence to support the existence of an evolutionarily conserved 12-hour oscillator that controls ∼12-hour rhythms of gene expression of protein and mRNA metabolism in multiple species.

Data integration and analysis for circadian medicine

Data integration, data sharing, and standardized analyses are important enablers for data-driven medical research. Circadian medicine is an emerging field with a particularly high need for coordinated and systematic collaboration between researchers from different disciplines. Datasets in circadian medicine are multimodal, ranging from molecular circadian profiles and clinical parameters to physiological measurements and data obtained from (wearable) sensors or reported by patients. Uniquely, data spanning both the time dimension and the spatial dimension (across tissues) are needed to obtain a holistic view of the circadian system. The study of human rhythms in the context of circadian medicine has to confront the heterogeneity of clock properties within and across subjects and our inability to repeatedly obtain relevant biosamples from one subject. This requires informatics solutions for integrating and visualizing relevant data types at various temporal resolutions ranging from milliseconds and seconds to minutes and several hours. Associated challenges range from a lack of standards that can be used to represent all required data in a common interoperable form, to challenges related to data storage, to the need to perform transformations for integrated visualizations, and to privacy issues. The downstream analysis of circadian rhythms requires specialized approaches for the identification, characterization, and discrimination of rhythms. We conclude that circadian medicine research provides an ideal environment for developing innovative methods to address challenges related to the collection, integration, visualization, and analysis of multimodal multidimensional biomedical data.

Circadian rhythms and the liver

This narrative review briefly describes the mammalian circadian timing system, the specific features of the liver clock, also by comparison with other peripheral clocks, the role of the liver clock in the preparation of food intake, and its relationship with energy metabolism. It then goes on to provide a chronobiological perspective of the pathophysiology and management of several types of liver disease, with a particular focus on metabolic-associated fatty liver disease (MAFLD), decompensated cirrhosis and liver transplantation. Finally, it provides some insight into the potential contribution of circadian principles and circadian hygiene practices in preventing MAFLD, improving the prognosis of advanced liver disease and modulating liver transplantation outcomes.