A circadian gene expression atlas in mammals: implications for biology and medicine

The role of the multiplicity of circadian clocks in mammalian systems

Circadian clocks regulate rhythmic biological processes in nearly every tissue, aligning physiology and behavior with the 24-h light-dark cycle. While the central circadian clock in the suprachiasmatic nucleus (SCN) has been extensively studied, emerging evidence indicates that virtually every cell in the body possesses its own locally autonomous circadian clock. This raises a fundamental question: why do multicellular organisms utilize multiple circadian clocks instead of a single master clock broadcasting time cues? Here, we examine how distributed local clocks differ from phase-resettable cycles and ensure robust temporal scheduling of physiological processes. We discuss how internal entrainment among local clocks governs self-sustained, yet flexible, circadian organization of tissue-specific responses to environmental changes. We also examine how the organization of clocks contributes to seasonal homeostasis, and the implications for disease when coordination among these clocks is disrupted.

Circadian disruption upon painful peripheral nerve injury in mice: Temporal effects on transcriptome in pain-regulating sensory tissues

BACKGROUND

Neuropathic pain (NP) resulting from nerve damage shows diurnal fluctuation of intensity in patients, indicating circadian regulation. However, mechanisms linking NP and circadian regulation remain unclear. This study aimed to investigate time-dependent transcriptomic changes during a 24-hour period using a spared nerve injury (SNI) mouse model of NP.

METHODS

Pain-related behaviours were assessed at baseline and on days 7, 14, and 21 after SNI and control sham surgeries in C57BL/6JRJ mice. Spinal cord (SC) and periaqueductal gray (PAG) were collected 4-hourly over 24 h upon completion of behavioural testing.

RESULTS

RNA sequencing revealed 111 up- and 21 downregulated differentially expressed genes (DEGs) in the SC, and 35 up- and 33 downregulated DEGs in the PAG, across all six time points. The large majority of DEGs, 245 in the SC and 191 in the PAG, are involved in regulation of immunity. Among the top expressed genes, five DEGs in the SC, Atf3, Anxa10, Gpr151, Cxcl10, Sprr1a, and two DEGs in the PAG, Igf2 and Wnt6, were previously reported to regulate pain. Circadian analysis using CircaCompare identified 383 SC transcripts and 261 PAG transcripts with altered rhythmicity. Variability of gene expression during circadian day was increased in the SC and decreased in the PAG from the SNI mice.

CONCLUSION

These findings suggest that NP disrupts the circadian expression of rhythmic transcripts in the SC and PAG, potentially revealing new targets for chronotherapy of NP.

Circadian clock regulation of myofibroblast fate

Fibrosis-related disorders represent an increasing medical and economic burden on a worldwide scale, accounting for one-third of all disease-related deaths with limited therapeutic options. As central mediators in fibrosis development, myofibroblasts have been gaining increasing attention in the last 20 years as potential targets for fibrosis attenuation and reversal. While various aspects of myofibroblast physiology have been proposed as treatment targets, many of these approaches have shown limited long-term efficacy so far. However, ongoing research is uncovering new potential strategies for targeting myofibroblast activity, offering hope for more effective treatments in the future. The circadian molecular clock is a feature of almost every cell in the human body that dictates the rhythmic nature of various aspects of human physiology and behavior in response to changes in the surrounding environment. The dysregulation of these rhythms with aging is considered to be one of the underlying reasons behind the development of multiple aging-related chronic disorders, with fibrotic tissue scarring being a common pathological complication among the majority of them. Myofibroblast dysregulation due to skewed circadian clockwork might significantly contribute to fibrotic scar persistence. In the current review, we highlight the role of the circadian clock in the context of myofibroblast activation and deactivation and examine its dysregulation as a driver of fibrogenesis.

Dosing Time of Day Impacts the Safety of Antiarrhythmic Drugs in a Computational Model of Cardiac Electrophysiology

Circadian clocks regulate many aspects of human physiology, including cardiovascular function and drug metabolism. Administering drugs at optimal times of the day may enhance effectiveness and reduce side effects. Certain cardiac antiarrhythmic drugs have been withdrawn from the market due to unexpected proarrhythmic effects such as fatal Torsade de Pointes (TdP) ventricular tachycardia. The Comprehensive in vitro Proarrhythmia Assay (CiPA) is a recent global initiative to create guidelines for the assessment of drug-induced arrhythmias that recommends a central role for computational modeling of ion channels and in silico evaluation of compounds for TdP risk. We simulated circadian regulation of cardiac excitability and explored how dosing time of day affects TdP risk for 11 drugs previously classified into risk categories by CiPA. The model predicts that a high-risk drug taken at the most optimal time of day may actually be safer than a low-risk drug taken at the least optimal time of day. Based on these proof-of-concept results, we advocate for the incorporation of circadian clock modeling into the CiPA paradigm for assessing drug-induced TdP risk. Since cardiotoxicity is the leading cause of drug discontinuation, modeling cardiac-related chronopharmacology has significant potential to improve therapeutic outcomes.

Temporal mineralocorticoid receptor activation regulates the molecular clock and transcription of cardiovascular disease modulators in myeloid cells

Inappropriate mineralocorticoid receptor (MR) activation in monocytes/macrophages promotes cardiac inflammation and fibrosis. However, the specific pathways whereby the MR regulates macrophage phenotype are not fully defined. We recently identified bidirectional regulation of the MR and the molecular circadian clock in cardiac cells. Given that immune cells are important regulators of cardiac pathology, we investigated whether MR regulates the molecular circadian clock and time of day expression of inflammatory mediators in splenic monocytes/macrophages using myeloid MR null mice (MyMRKO). RNAseq and real-time quantitative PCR (RT-qPCR) analysis of whole spleen from floxed control (FC) or MyMRKO revealed differential expression of clock genes Per2, Cry1, REV-ERBα, and DBP at (Zeitgeber time) ZT0 versus ZT12. Time-of-day regulation of numerous gene targets was also disordered in MyMRKO spleen versus FC including iNOS2, CXCR4, FABP3, S100A8 and S100A9, and FGF1. Aldosterone induction of REV-ERBα, Cry1, iNOS, IL-1β, Arg-1, IL-10, CCL2, and Spp1 was greater when delivered at ZT0 versus ZT12, when corticosterone levels are low. Moreover, oscillating expressions of Per2, REV-ERBα, and other clock components were regulated by 10 nM aldosterone or corticosterone in immortalized bone marrow-derived cells, supporting a direct role for MR modulation of cellular clock time. Significant differences observed between male and female samples underscore the role of sex in the modulation of circadian signaling and MR-dependent pro-inflammatory phenotype in myeloid cells. Cardiac macrophage-specific bulk RNAseq and scRNAseq datasets verified MR-dependent regulation of many temporally induced genes in immune cell subsets, whereas FACS analysis showed that immune cell populations were mostly unchanged, and that IL-1β expression is highest in myeloid cells consistent with MyMRKO regulating IL-1β in this population. Our findings demonstrate the dynamic influence of MR transcriptional control of circadian clock and inflammatory pathways in myeloid cells, highlighting potential sex-based differences and offering insights into potential mechanisms underpinning MR modulation of myeloid cell phenotype.NEW & NOTEWORTHY Mineralocorticoid receptor (MR) signaling dynamically regulates the circadian clock and inflammatory gene expression in myeloid cells. Using myeloid-specific MR knockout mice, we identified disrupted time-of-day expression of core clock and inflammatory genes, with sex-based differences in response. These findings reveal novel MR-circadian clock interactions in immune cells and suggest a time- and sex-dependent mechanism by which MR shapes macrophage phenotype and potentially cardiac inflammation.

Inorganic Biomaterials Inducing Scaffolds Pre-Neuralization for Infarcted Myocardium Repair

Neural networks are found to play an important role in monitoring and coordinating cardiac physiological activities. However, the clinical use of neuroregulatory strategies for repairing infarcted myocardium, such as vagus nerve stimulation and pharmacological activation, confronts the challenges of managing stimulation signals and potential drug side effects. In this study, an innovative myocardial infarction repair strategy by creating a "pre-neuralized" scaffold that combines strontium silicate microparticles with neural stem cells (NSCs) is introduced. Strontium silicate promotes NSCs differentiation, resulting in a scaffold enriched with mature neurons. This scaffold exhibits neuroregulatory capabilities that enhance the maturation and synchronized contraction of cardiomyocytes, facilitating myocardial repair and improving cardiac function in vivo. The findings indicate that the pre-neuralized scaffold aids myocardial recovery by modulating genes linked to circadian rhythm, underscoring the strategic benefit of neural-induced regulation in tissue repair. In conclusion, this study presents a promising approach to repairing infarcted myocardium using inorganic biomaterial-induced scaffolds with neuromodulatory properties from the perspective of systemically physiological regulation. This work may offer a new perspective for addressing complex tissue and organ injuries.

Decoding the Liver-Heart Axis in Cardiometabolic Diseases

The liver and heart are closely interconnected organs, and their bidirectional interaction plays a central role in cardiometabolic disease. In this review, we summarize current evidence linking liver dysfunction-particularly metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, and cirrhosis-with an increased risk of heart failure and other cardiovascular diseases. We discuss how these liver conditions contribute to cardiac remodeling, systemic inflammation, and hemodynamic stress and how cardiac dysfunction in turn impairs liver perfusion and promotes hepatic injury. Particular attention is given to the molecular mediators of liver-heart communication, including hepatokines and cardiokines, as well as the emerging role of advanced research methodologies, including omics integration, proximity labeling, and organ-on-chip platforms, that are redefining our understanding of interorgan cross talk. By integrating mechanistic insights with translational tools, this review aims to support the development of multiorgan therapeutic strategies for cardiometabolic disease.

The Pro-Apoptotic Effect of Glucose Restriction in NSCLC via AMPK-Regulated Circadian Clock Gene Bmal1

The circadian clock is a crucial regulator of mammalian physiology, controlling daily oscillations in key biological processes, such as cell proliferation, apoptosis, and DNA damage repair. Disruption of circadian rhythms has been identified as a significant risk factor for cancer development and progression, yet the specific molecular mechanisms linking circadian dysfunction to cancer remain poorly understood. Recent studies have increasingly focused on the role of diet in modulating circadian rhythms, highlighting the potential for dietary interventions in cancer management. However, how dietary factors like glucose restriction interact with circadian rhythms to influence cancer cell behavior remains an open question. Here, we investigate the mechanisms underlying glucose restriction-induced apoptosis in non-small cell lung cancer (NSCLC) cells, with a focus on the role of circadian clock genes. Analysis of the GEPIA database revealed that the circadian gene Bmal1 is highly expressed in normal tissues and associated with better prognosis in lung adenocarcinoma patients. In NSCLC cells, Bmal1 expression correlated with proapoptotic gene activity. In a tumor xenograft model using severe combined immunodeficiency (SCID) mice, a glucose-restricted (ketogenic) diet significantly delayed tumor growth and increased the expression of Bmal1 and proapoptotic genes. These findings suggest that glucose restriction promotes apoptosis in NSCLC cells through a Bmal1-mediated pathway, providing novel insights into the intersection between circadian regulation and cancer biology. Targeting core circadian clock genes like Bmal1 may represent a promising therapeutic strategy for managing lung cancer, broadening our understanding of how circadian rhythms can be harnessed for cancer prevention and treatment.

Exploring the nexus: Sleep disorders, circadian dysregulation, and Alzheimer's disease

We reviewed the connections among Alzheimer's disease (AD), sleep deprivation, and circadian rhythm disorders. Evidence is mounting that disrupted sleep and abnormal circadian rhythms are not merely symptoms of AD, but are also involved in accelerating the disease. Amyloid-beta (Aβ) accumulates, a feature of AD, and worsens with sleep deprivation because glymphatic withdrawal is required to clear toxic proteins from the brain. In addition, disturbances in circadian rhythm can contribute to the induction of neuroinflammation and oxidative stress, thereby accelerating neurodegenerative processes. While these interactions are bidirectional, Alzheimer's pathology further disrupts sleep and circadian function in a vicious cycle that worsens cognitive decline, which is emphasized in the review. The evidence that targeting sleep and circadian mechanisms may serve as therapeutic strategies for AD was strengthened by this study through the analysis of the molecular and physiological pathways. Further work on this nexus could help unravel the neurobiological mechanisms common to the onset of Alzheimer's and disrupted sleep and circadian regulation, which could result in earlier intervention to slow or prevent the onset of the disease.

Circadian rhythm and aryl hydrocarbon receptor crosstalk in bone marrow adipose tissue and implications in leukemia

Leukemic cells modulate the bone marrow microenvironment to enhance their survival. Lipolysis in bone marrow adipose tissue (BMAT) has emerged as a critical factor supporting leukemic cell survival, yet understanding its primary role in leukemia development remains limited. Fanconi anemia (FA), characterized by a predisposition to acute myeloid leukemia (AML) and hypersensitivity to environmental toxins, is a transitional model for studying leukemic transformation. İntegrated multi-omics analyses were conducted on BMAT-derived mesenchymal stem/stromal cells (MSCs) from healthy donors (HD), AML, and FA patients. These analyses revealed intricate interactions among genes, metabolites, and lipids. Particularly noteworthy were the effects observed following the inhibition of aryl hydrocarbon receptor (AhR) signaling by StemRegenin1 (SR1). BMAT-MSCs showed increased expression of epithelial-mesenchymal transition (EMT) genes in FA and AML, suggesting a potential shift towards cancer-associated fibroblasts in the dysregulated marrow microenvironment. Identification of potential circadian rhythm biomarkers (NPAS2, PER2, BHLHE40, PER3, CIART) in BMAT-MSCs indicates a link between related lipid metabolism genes (e.g., PTGS1, PIK3R1) and SR1 treatment, implicating them in lipolysis processes. Dysregulation of circadian rhythm-related genes (CIART, BHLHE40, NPAS2) in AML BMAT-MSCs, along with changes in circulating lipid metabolites like palmitate suggests their role in shaping the leukemia microenvironment. Upregulation of FABP5 and CD36 suggests a novel molecular mechanism involving FABP5 in AhR-mediated circadian regulation and identifies CD36 as a potential partner for FABP5 in BMAT-MSCs. Overall, this study unveils the interplay between AhR signaling, circadian rhythm, and the leukemia microenvironment in BMAT-MSCs, offering new insights into leukemia pathogenesis and therapeutic opportunities.

Antihypertensive Medication Timing and Cardiovascular Events and Death: The BedMed Randomized Clinical Trial

Importance

Whether administration of blood pressure medications at bedtime instead of in the morning reduces cardiovascular risk is unknown, as findings from large clinical trials have not been consistent. There is also concern that bedtime antihypertensive use could induce glaucoma-related visual loss or other hypotensive/ischemic adverse effects.

Objective

To determine the effect of bedtime vs morning administration of antihypertensive medications on major cardiovascular events and death.

Design, Setting, and Participants

Multicenter, open-label, pragmatic randomized clinical trial with blinded end-point assessment and recruitment via 436 primary care clinicians across 5 Canadian provinces inviting their community-dwelling adult patients with hypertension taking at least 1 once-daily antihypertensive medication. Participants were recruited from March 31, 2017, to May 26, 2022, with final follow-up on December 22, 2023.

Interventions

Participants were randomized in a 1:1 ratio to using all once-daily antihypertensive medications either at bedtime (intervention group; n = 1677) or in the morning (control group; n = 1680).

Main Outcomes and Measures

The primary outcome was time to first occurrence of all-cause death or hospitalization/emergency department (ED) visit for stroke, acute coronary syndrome, or heart failure. All-cause unplanned hospitalizations/ED visits, and visual, cognitive, and fall- and/or fracture-related safety outcomes were also assessed.

Results

A total of 3357 adults (56.4% female; median age, 67 years; 53.7% taking monotherapy) were randomized and followed up for a median of 4.6 years in each treatment group. The composite primary outcome event occurred at a rate of 2.3 per 100 patient-years in the bedtime group and 2.4 per 100 patient-years in the morning group (adjusted hazard ratio, 0.96; 95% CI, 0.77-1.19; P = .70). Individual components of the primary outcome, all-cause hospitalizations/ED visits, and safety outcomes did not differ between groups. In particular, there was no difference in falls or fractures, new glaucoma diagnoses, or 18-month cognitive decline.

Conclusions and Relevance

Among adults with hypertension in primary care, bedtime administration of antihypertensive medications was safe but did not reduce cardiovascular risk. Antihypertensive medication administration time did not affect the risks and benefits of blood pressure-lowering medication and instead should be guided by patient preferences.

Trial Registration

ClinicalTrials.gov Identifier: NCT02990663.

A mechanism of global gene expression regulation is disrupted by multiple disease states and drug treatments

Conventional expression studies quantify messenger RNA (mRNA) transcript levels gene-by-gene. We recently showed that protein expression is modulated at a global scale by amino acid availability, suggesting that mRNA expression levels might be equivalently affected. Through re-analysis of public transcriptomic datasets, it was confirmed that nucleobase supply interacts with the specific demands of mRNA A + U:C + G sequence composition to shape a global profile of expression, which can be quantified as a gradient of average expression change by average composition change. In mammals, each separate organ and cell-type displays a distinct baseline profile of global expression. These profiles can shift dynamically across the circadian day and the menstrual cycle. They are also significantly distorted by viral infection, multiple complex genetic disorders (including Alzheimer's disease, schizophrenia, and autoimmune disorders), and after treatment with 115 of the 597 chemical entities analysed. These included known toxins and nucleobase analogues, but also many commonly prescribed medications such as antibiotics and proton pump inhibitors, thus revealing a new mechanism of drug action and side-effect. As well as key roles in disease susceptibility, mRNAs with extreme compositions are significantly over-represented in gene ontologies such as transcription and cell division, making these processes particularly sensitive to swings in global expression. This may permit efficient, en bloc transcriptional reprogramming of cell state through simple adjustment of nucleobase proportion and supply. It is also proposed that this mechanism helped mitigate the loss of essential amino acid synthesis in higher organisms. In summary, global expression regulation is invisible to conventional transcriptomic analysis, but its measurement allows a useful distinction between active, promoter-mediated gene expression changes and passive, cell state-dependent transcriptional competence. Linking cell metabolism directly to gene expression offers an entirely new perspective on evolution, disease aetiopathology (including gene x environment - GxE - interactions), and the nature of the pharmacological response.

A network of pro-inflammatory genes repressed by clock signalling in bronchial epithelium

Background

Circadian rhythms are biological cycles that regulate various physiological processes, including immune responses, tissue repair and oxidative stress. Previous studies indicated a role for distorted circadian signalling in COPD.

Methods

In this study, we performed an unbiased analysis of the gene network that coexpressed with circadian clock signalling in COPD using weighted gene coexpression network analysis on RNA sequencing data from bronchial brushes of COPD patients.

Results

We found that a large network of pro-inflammatory genes, including CXCL8, IL1B, IL1A, CSF1 and TGFB1, was inversely correlated with the expression of core clock genes in bronchial brushes of COPD patients. In contrast, genes that positively coexpressed with circadian clock signalling associated with ciliated cell differentiation. Furthermore, we found that both circadian clock genes and their coexpressed genes were differentially expressed in lung tissues of COPD patients compared with healthy smokers.

Conclusions

Our results provide an unbiased and comprehensive analysis of the gene expression network coexpressed with circadian clock signalling in bronchial epithelium. Our findings suggest an association between circadian clock signalling and enhanced inflammatory gene expression in COPD patients.

Circadian Biology in Obstructive Sleep Apnea-Associated Cardiovascular Disease

A dysregulated circadian system is independently associated with both Obstructive Sleep Apnea (OSA) and cardiovascular disease (CVD). OSA and CVD coexistence is often seen in patients with prolonged untreated OSA. However, the role of circadian dysregulation in their relationship is unclear. Half of the human genes, associated biological pathways, and physiological functions exhibit circadian rhythms, including blood pressure and heart rate regulation. Mechanisms related to circadian dysregulation and heart function are potentially involved in the coexistence of OSA and CVD. In this article, we provide a comprehensive overview of circadian dysregulation in OSA and associated CVD. We also discuss feasible animal models and new avenues for future research to understand their relationship. Oxygen-sensing pathways, inflammation, dysregulation of cardiovascular processes, oxidative stress, metabolic regulation, hormone signaling, and epigenetics are potential clock-regulated mechanisms connecting OSA and CVD.

Spatiotemporal Control Over Circadian Rhythms With Light

Circadian rhythms are endogenous biological oscillators that synchronize internal physiological processes and behaviors with external environmental changes, sustaining homeostasis and health. Disruption of circadian rhythms leads to numerous diseases, including cardiovascular and metabolic diseases, cancer, diabetes, and neurological disorders. Despite the potential to restore healthy rhythms in the organism, pharmacological chronotherapy lacks spatial and temporal resolution. Addressing this challenge, chrono-photopharmacology, the approach that employs small molecules with light-controlled activity, enables the modulation of circadian rhythms when and where needed. Two approaches-relying on irreversible and reversible drug activation-have been proposed for this purpose. These methodologies are based on photoremovable protecting groups and photoswitches, respectively. Designing photoresponsive bioactive molecules requires meticulous structural optimization to obtain the desired chemical and photophysical properties, and the design principles, detailed guidelines and challenges are summarized here. In this review, we also analyze all the known circadian modulators responsive to light and dissect the rationale following their construction and application to control circadian biology from the protein level to living organisms. Finally, we present the strength of a reversible approach in allowing the modulation of the circadian period and the phase.

Genetic disruption of the circadian gene Bmal1 in the intestinal epithelium reduces colonic inflammation

Disruption of the circadian clock is associated with the development of inflammatory bowel disease (IBD), but the underlying mechanisms remain unclear. Here, we observe that mice in the early active phase (Zeitgeber time 12, ZT12) of the circadian clock are more tolerant to dextran sodium sulfate (DSS)-induced colitis, compared to those in the early resting phase (ZT0). The expression of the circadian gene Bmal1 peaks in the early resting phase and declines in the early active phase. Bmal1 knockout in the intestinal epithelium reduces DSS-induced inflammatory symptoms. Mechanistically, BMAL1 promotes apoptosis by binding to apoptosis-related genes, including Bax, p53, and Bak1, and promotes their expression. Intriguingly, we observe circadian apoptotic rhythms in the homeostatic intestinal epithelium, while Bmal1 deletion reduces cell apoptosis. Consistently, reducing Bmal1 expression by the REV-ERBα agonist SR9009 has the best therapeutic efficacy against DSS-induced colitis at ZT0. Collectively, our data demonstrate that the Bmal1-centered circadian clock is involved in intestinal injury repair.

Circadian clock disruption promotes retinal photoreceptor degeneration

Daily rhythms are a central hallmark of vision, in particular by adapting retinal physiology and light response to the day-night cycle. These cyclic processes are regulated by retinal circadian clocks, molecular machineries regulating gene expression across the 24-h cycle. Although hundreds of genes associated with genetic retinal disorders have been identified, no direct link has been established with the clock. Hence, we investigated the hypothesis that a poorly functioning circadian clock aggravates retinal photoreceptor disease. We performed this study in the P23H rhodopsin-mutated mouse model (P23H Rho) that mimics one major cause of human autosomal dominant retinitis pigmentosa. We also used the rod-specific knockout (rod-Bmal1KO) of Bmal1, a key clock component. More specifically, we used either heterozygous P23H Rho mice or rod-Bmal1KO alone, as well as double mutants of these strains and control mice. We showed by structural (histology, immunohistochemistry) and functional (electroretinography: ERG) analyses that the retinitis pigmentosa phenotype is exacerbated in the double mutant line compared to the P23H Rho mutation alone. Indeed, we observed marked ERG amplitude reduction and more photoreceptor cell loss in double mutants with respect to simple P23H Rho mutants. These observations were further corroborated by transcriptome analysis revealing major gene expression differences between these genotypes. In this data, we identified unique gene expression sets implicating neurogenesis, phototransduction cascade, and metabolism, associated with enhanced photoreceptor degeneration. Thus, our results establish a link between clock dysfunction and retinal degeneration and suggest underlying molecular mechanisms, together providing new concepts for understanding and managing blinding diseases.

Regulation of cyclophosphamide induced hepatotoxicity by REV-ERBα modifiers

INTRODUCTION

Cyclophosphamide (CPA) is a widely used broad-spectrum antitumor drug with severe hepatotoxicity. Finding an effective way to mitigate the hepatotoxicity caused by CPA is a challenge in its clinical application.

METHODS

In Rev-erbα knockout and wild-type mice, hepatotoxicity was evaluated by ALT, AST, and histopathological scores 4-h post dose of CPA (i.p. 300 mg/kg). CYP2B10 expression and pharmacokinetic behavior of CPA were also detected. SR9009 (i.p. 10 mg/kg) and Berberine (BBR, i.p. 50 mg/kg) were pre-administered to mice. Then, the measurements were carried out following the same procedures as previous. The regulation effects of SR9009 and BBR on CYP2B10 were validated using Hepa-1c1c7 cells.

RESULTS

Firstly, REV-ERBα negatively regulated CPA-induced hepatotoxicity by altering the expression of CYP2B10 and CPA pharmacokinetics. Secondly, REV-ERBα agonists, SR9009 and BBR, increased REV-ERBα expression and alleviated hepatic toxicity of CPA. Furthermore, both SR9009 and BBR reduced expression of CYP2B10 and REV-ERBα target gene Bmal1 both in vivo and in vitro.

CONCLUSIONS

REV-ERBα agonists can significantly attenuate the hepatotoxicity of CPA by regulating CYP2B10. The discovery of REV-ERBα as novel regulator for CYP2B10 will help to establish new targets to improve drug efficacy or reduce toxicity.

Mini review: Bidirectional Regulation of Circadian Rhythm by Suprachiasmatic Nucleus and Nuclear Receptors in Female Mammals

The anterior region of the hypothalamus accommodates a bilateral structure called the suprachiasmatic nucleus (SCN), which controls, modulates, and perpetuates the homeostasis of circadian rhythm and sleep hormone release. These SCN have a predominance over multitudinous peripheral tissues like the uterus, liver, intestine, pancreas, endocrine system, immune system, reproductive system, and cardiovascular system. This peripheral clock acts as a pacemaker for circadian rhythm timing, which regulates crucial metabolic pathways and organizes numerous activities in the female reproductive network of mammals. The circadian CLOCK genes are expressed in various reproductive organs. The CLOCK, BMAL1, CRY, and PER genes harmonize the balance and manifestation of nuclear receptors (NRs) expression, and the other way round, NRs regulate these circadian genes. Several NRs, in particular estrogen, progesterone, androgen, and PPARs, nurture the ovary and uterus. Bidirectional coordination between SCN and NRs maintains the circadian rhythm of the hypothalamic-pituitary-gonadal (HPG) axis of the female reproductive organs.

Opportunities for Precision Dosing of Cytotoxic Drugs in Non-Small Cell Lung Cancer: Bridging the Gap in Precision Medicine

Precision dosing of classical cytotoxic drugs in oncology remains underdeveloped, especially in treating non-small cell lung cancer (NSCLC). Despite advancements in targeted therapy and immunotherapy, classical cytotoxic agents continue to play a critical role in NSCLC treatment. However, the current body surface area (BSA)-based dosing of these agents fails to adequately address interindividual variability in pharmacokinetics. By better considering patient characteristics, treatment outcomes can be improved, reducing risks of under-exposure and over-exposure. This narrative review explores opportunities for precision dosing for key cytotoxic agents used in NSCLC treatment: cisplatin, carboplatin, pemetrexed, docetaxel, (nab-)paclitaxel, gemcitabine, and vinorelbine. A comprehensive review of regulatory reports and an extensive literature search were conducted to evaluate current dosing practices, pharmacokinetics, pharmacodynamics, and exposure-response relationships. Our findings highlight promising developments in precision dosing, although the number of directly implementable strategies remains limited. The most compelling evidence supports using the biomarker cystatin C for more precise carboplatin dosing and adopting weekly dosing schedules for docetaxel, paclitaxel, and nab-paclitaxel. Additionally, we recommend direct implementation of therapeutic drug monitoring (TDM)-guided dosing for paclitaxel. This review stresses the urgent need to reassess conventional dosing paradigms for classical cytotoxic agents to better align with the principles of the precision dosing framework. Our recommendations show the potential of precision dosing to improve NSCLC treatment, addressing gaps in the current dosing of classical cytotoxic drugs. Given the large NSCLC patient population, optimising the dosing of these agents could significantly improve treatment outcomes and reduce toxicity for many patients.

Circadian rhythm gene cryptochrome 2 (Cry2) interacts with lipid metabolism to promote vascular aging

BACKGROUND

Vascular aging is the basis of many chronic diseases of the aged, such as hypertension, coronary heart disease and stroke.

OBJECTIVE

This study aims to deepen our understanding of the pathological mechanisms of vascular aging by combining multiple big data research methods, and reveal potential therapeutic targets and biomarkers.

METHODS

WGCNA method was used to integrate the aortic transcriptome data of multiple age stages, and extract the key module and key pathway. The gene of aortic rhythm was integrated by JTK algorithm. Correlation calculation was performed for core gene and associated pathways. Finally, the expression of the core gene and their interaction with the associated pathways were verified in cell senescence.

RESULTS

WGCNA showed that circadian rhythm is the key pathway of vascular aging, and circadian rhythm and metabolism interact to promote the occurrence of vascular aging. Cry2 has been identified as the most critical core rhythm gene. Lipid metabolism is the most Cry2-related subpathway, among which phospholipid metabolism and Serac1 have the strongest and most significant correlation with Cry2. Cry2 is mainly distributed in endothelial cells in both young and senescent blood vessels, and affects five lipid-related metabolic processes including lipid transport during endothelial senescence.

CONCLUSION

This study suggests that circadian rhythm and Cry2 may be potential targets of vascular aging, and further studies on their interaction with lipid metabolism will provide effective strategies for the prevention and treatment of age-related vascular diseases.

Daily proteome variations highlight sustained metabolic activity in cone cells of Nrl knockout mice

Vision is a highly rhythmic function adapted to daily changes in light intensity. Rhythms disruption is known to compromise retinal health and visual function. This study investigates expression patterns of cone proteins over the 24-h daily cycle in order to understand the molecular bases of cone cyclic physiology. Cones were isolated by vibratome-sectioning from Nrl knockout mice at four time points across the 24-h LD (Light-Dark) cycle and protein extracts were quantified by label-free LC-MS/MS. The resulting protein data was then submitted to MetaCycle analysis to identify proteins with rhythmic expression patterns and associated functions. Cyclic profiles were further validated by SWATH-MS analysis. A total of 1208 proteins were identified. Rhythmic expression patterns were found for 319 proteins, categorized into four clusters based on intensity variation. SWATH-MS analysis validated the approach. Functional enrichment analysis revealed proteins critical for photoreceptor function, including those involved in phototransduction, oxidative phosphorylation, RNA processing, proteostasis, transport, synaptic function and cilia biogenesis. These findings provide a unique dataset of rhythmic cone proteins, potentially crucial for elucidating cone cell physiology and visual function. This knowledge can empower future research on preventing and treating vision impairment.

Circadian clock features define novel subtypes among breast cancer cells and shape drug sensitivity

The circadian clock regulates key physiological processes, including cellular responses to DNA damage. Circadian-based therapeutic strategies optimize treatment timing to enhance drug efficacy and minimize side effects, offering potential for precision cancer treatment. However, applying these strategies in cancer remains limited due to a lack of understanding of the clock's function across cancer types and incomplete insights into how the circadian clock affects drug responses. To address this, we conducted deep circadian phenotyping across a panel of breast cancer cell lines. Observing diverse circadian dynamics, we characterized metrics to assess circadian rhythm strength and stability in vitro. This led to the identification of four distinct circadian-based phenotypes among 14 breast cancer cell models: functional, weak, unstable, and dysfunctional clocks. Furthermore, we demonstrate that the circadian clock plays a critical role in shaping pharmacological responses to various anti-cancer drugs and we identify circadian features descriptive of drug sensitivity. Collectively, our findings establish a foundation for implementing circadian-based treatment strategies in breast cancer, leveraging clock phenotypes and drug sensitivity patterns to optimize therapeutic outcomes.

Parasite and vector circadian clocks mediate efficient malaria transmission

Malaria transmission begins when Anopheles mosquitos deposit saliva and Plasmodium parasites during a bloodmeal. As Anopheles mosquitos are nocturnal, we investigated whether their salivary glands are under circadian control, anticipating bloodmeals and modulating parasite biology for host encounters. Here we show that approximately half of the mosquito salivary gland transcriptome, particularly genes essential for efficient bloodmeals such as anti-blood clotting factors, exhibits circadian expression. Furthermore, measuring haemoglobin levels, we demonstrate that mosquitos prefer to feed and ingest more blood at nighttime. Notably, we show a substantial subset of the salivary-gland-resident parasite transcriptome cycling throughout the day, indicating that this stage is not transcriptionally quiescent. Among the sporozoite genes undergoing rhythmic expression are those involved in parasite motility, potentially modulating the ability to initiate infection at different times of day. Our findings suggest a circadian tripartite relationship between the vector, parasite and mammalian host that together modulates malaria transmission.

A wrinkle in timers: evolutionary rewiring of conserved biological timekeepers

Biological timing mechanisms are intrinsic to all organisms, orchestrating the temporal coordination of biological events through complex genetic networks. Circadian rhythms and developmental timers utilize distinct timekeeping mechanisms. This review summarizes the molecular basis for circadian rhythms in mammals and Drosophila, and recent work leveraging these clocks to understand temporal regulation in Caenorhabditis elegans development. We describe the evolutionary connections between distinct timing mechanisms and discuss recent insights into the rewiring of core clock components in development. By integrating findings from circadian and developmental studies with biochemical and structural analyses of conserved components, we aim to illuminate the molecular basis of nematode timing mechanisms and highlight broader insights into biological timing across species.

Circadian clockwork controls the balance between mitochondrial turnover and dynamics: What is life … without time marking?

Circadian rhythms driven by biological clocks regulate physiological processes in all living organisms by anticipating daily geophysical changes, thus enhancing environmental adaptation. Time-resolved serial multi-omic analyses in vivo, ex vivo, and in synchronized cell cultures have revealed rhythmic changes in the transcriptome, proteome, and metabolome, involving up to 50 % of the mammalian genome. Mitochondrial oxidative metabolism is central to cellular bioenergetics, and many nuclear genes encoding mitochondrial proteins exhibit both circadian and ultradian oscillatory expression. However, studies on mitochondrial DNA (mtDNA) gene expression remain incomplete. Using a well-established in vitro synchronization protocol, we investigated the time-resolved expression of mtDNA genes coding for respiratory chain complex subunits, revealing a rhythmic profile dependent on BMAL1, the master circadian clock transcription factor. Additionally, the expression of genes coding for key mitochondrial biogenesis transcription factors, PGC1a, NRF1, and TFAM, showed BMAL1-dependent circadian oscillations. Notably, LC3-II, involved in mitophagy, displayed a similar in-phase circadian expression, thereby maintaining stable respiratory chain complex levels. Moreover, we found that simultaneous mitochondrial biogenesis and degradation occur in a coordinated manner with cycles in organelle dynamics, leading to rhythmic changes in mitochondrial fission and fusion. This study provides new insights into circadian clock regulation of mitochondrial turnover, emphasizing the importance of temporal regulation in cellular metabolism. Understanding these mechanisms opens potential therapeutic avenues for targeting mitochondrial dysfunctions and related metabolic disorders.

Circadian clock communication during homeostasis and ageing

Maintaining homeostasis is essential for continued health, and the progressive decay of homeostatic processes is a hallmark of ageing. Daily environmental rhythms threaten homeostasis, and circadian clocks have evolved to execute physiological processes in a manner that anticipates, and thus mitigates, their effects on the organism. Clocks are active in almost all cell types; their rhythmicity and functional output are determined by a combination of tissue-intrinsic and systemic inputs. Numerous inputs for a specific tissue are produced by the activity of circadian clocks of other tissues or cell types, generating a form of crosstalk known as clock communication. In mammals, the central clock in the hypothalamus integrates signals from external light-dark cycles to align peripheral clocks elsewhere in the body. This regulation is complemented by a tissue-specific milieu of external, systemic and niche inputs that modulate and cooperate with the cellular circadian clock machinery of a tissue to tailor its functional output. These mechanisms of clock communication decay during ageing, and growing evidence suggests that this decline might drive ageing-related morbidities. Dietary, behavioural and pharmacological interventions may offer the possibility to overcome these changes and in turn improve healthspan.

Curculigoside upregulates BMAL1 to decrease nucleus pulposus cell apoptosis by inhibiting the JAK/STAT3 pathway

BACKGROUND

Intervertebral disc degeneration (IVDD) is a natural process that occurs with aging and is the main cause of low back pain. Basic helix-loop-helix ARNT-like 1 (BMAL1) plays key roles in the pathogenesis of many diseases. The present study investigates the role of curculigoside (CUR), which has been reported to be a potential anti-apoptotic compound in other diseases.

METHODS

Dysregulated genes were identified by RNA sequencing (RNA-seq). Western blotting (WB), immunohistochemistry, immunofluorescence (IF) staining, and real-time fluorescent quantitative polymerase chain reaction were used to detect BMAL1 expression in 25 human intervertebral disc specimens (male: female =13:12), tissues from BMAL1-knockout mice and from an IVDD mouse model. The regulatory effects of CUR and BMAL1 in nucleus pulposus (NP) cells after Small Interfering RNA (siRNA) transfection were examined by flow cytometry, IF staining and WB. The therapeutic effect of intraperitoneal CUR injection was also evaluated in mice.

RESULTS

BMAL1 expression was negatively correlated with IVDD severity and was significantly lower in degenerative NP cells. After BMAL1 knockdown using siRNA, the apoptosis rate of degenerative NP cells was significantly higher, while transfection with a lentivirus overexpressing BMAL1 exerted the opposite effect. Bioinformatics analysis revealed that BMAL1 is regulated by the JAK-STAT3 pathway, and CUR upregulated BMAL1 expression by inhibiting STAT3 phosphorylation, subsequently alleviating NP cell apoptosis and increasing extracellular matrix (ECM) components., thus alleviating IVDD.

CONCLUSIONS

CUR can inhibit apoptosis and improve the ECM by upregulating BMAL1 expression, which is reduced in IVDD. This study provides a therapeutic strategy to alleviate apoptosis associated with inflammation-induced IVDD.

Corneal Sensory Nerve Injury Disrupts Lacrimal Gland Function by Altering Circadian Rhythms in Mice

Purpose

To investigate the impact of corneal sensory nerve injury on lacrimal gland function, focusing on mechanisms involving the superior salivatory nucleus (SSN), circadian rhythm disruption, immune microenvironment alterations, and the potential for neural regeneration.

Methods

A murine model of corneal sensory nerve injury was used to assess lacrimal gland function, with tear secretion measured using the phenol red thread test. Transcriptomic analysis of lacrimal glands examined circadian rhythm and immune-related gene expression. Basic fibroblast growth factor (bFGF) was used to promote corneal nerve regeneration, and its effects on tear secretion and nerve repair were evaluated.

Results

Corneal nerve injury resulted in a 35% reduction in tear secretion and significantly impaired SSN activity, as evidenced by a 31% decrease in c-FOS-positive neurons in choline acetyltransferase (ChAT)-expressing neurons. Transcriptomic analysis revealed significant downregulation of immune-related pathways, including Toll-like receptor (TLR), NOD-like receptor (NLR), and T-cell receptor signaling. Circadian rhythm gene expression exhibited phase shifts, with a 2.13-hour delay in peak expression and a substantial change in the number and types of rhythmic genes, which were enriched in different signaling pathways. The bFGF treatment restored tear secretion by 22% and promoted nerve regeneration, although nerve fiber density remained 74% lower than that of controls.

Conclusions

Corneal sensory nerve injury disrupts both central and peripheral circadian clock functions in the lacrimal gland, leading to reduced tear secretion and immune dysregulation. These findings highlight the novel role of circadian rhythms and neural-immune interactions in lacrimal gland dysfunction. Neural regeneration strategies, such as bFGF, offer therapeutic potential for dry eye syndrome, providing new directions for clinical intervention.

Bmal1-Mediated Circadian MELK Expression Potentiates MELK Inhibitor Chronotherapy for Esophageal Cancer

Esophageal squamous cell carcinoma (ESCC) remains a global health challenge. Circadian clock and maternal embryonic leucine zipper kinase (MELK) play a key role in tumorigenesis. However, a link between circadian clock dysregulation and MELK function in the occurrence and development of ESCC remains elusive. Here, In the in vivo and in vitro systems, we found for the first time that MELK exhibits pronounced circadian rhythms expression in mice esophageal tissue, xenograft model, and human ESCC cells. The diurnal differences expression between peak (ZT0) and trough (ZT12) points in normal esophageal tissue is nearly 10-fold. Circadian expression of MELK in ESCC cells was regulated by Bmal1 through binding to the MELK promoter. Supporting this, the levels of MELK were increased significantly in patients with ESCC and were accompanied by altered expression of core clock genes, especially, since Bmal1 is prominently upregulated. Most importantly, Bmal1-deleted eliminated the rhythmic expression of MELK, whereas the knockdown of other core genes had no effect on MELK expression. Furthermore, in nude mice with transplanted tumors, the anticancer effect of OTS167 at ZT0 administration is twice that of ZT12. Implications: Our findings suggest that MELK represents a therapeutic target, and can as a regulator of circadian control ESCC growth, with these findings advance our understanding of the clinical potential of chronotherapy and the importance of time-based MELK inhibition in cancer treatment.

Plastic chemicals disrupt molecular circadian rhythms via adenosine 1 receptor in vitro

The adenosine 1 receptor (A1R) is a G protein-coupled receptor that transduces signals to regulate sleep-wake cycles and circadian rhythms. Plastic products contain thousands of chemicals, known to disrupt physiological function. Recent research has demonstrated that some of these chemicals are also A1R agonists, however, the extent to which such activation propagates downstream and results in cellular alterations remains unknown. Thus, we investigate whether chemicals extracted from polyurethane (PUR) and polyvinyl chloride (PVC) plastics disrupt circadian rhythms via agonism of A1R. We confirm that plastic chemicals in both plastics activate A1R and inhibit intracellular cAMP in U2OS cells. Notably, this inhibition is comparable to that induced by the highly specific A1R agonist 2'-MeCCPA. To assess circadian disruption, we quantify temporal expression patterns of the clock genes PER2 and CRY2 at 4-h intervals over 48 h. Here, exposure to plastic chemicals shifts the phase in the oscillatory expression cycles of both clock genes by 9-17 min. Importantly, these effects are dose-dependent and reversible when A1R is inhibited by a pharmacological antagonist. This demonstrates that plastic chemicals can disrupt circadian processes by interfering with A1R signaling and suggests a novel mechanism by which these and other chemicals may contribute to non-communicable diseases.

Rhythm is essential: Unraveling the relation between the circadian clock and cancer

Physiological processes such as the sleep-wake cycle, metabolism, hormone secretion, neurotransmitter release, sensory capabilities, and a variety of behaviors, including sleep, are controlled by a circadian rhythm adapted to 24-hour day-night periodicity. Disruption of circadian rhythm may lead to the risks of numerous diseases, including cancers. Several epidemiological and clinical data reveal a connection between the disruption of circadian rhythms and cancer. On the contrary, oncogenic processes may suppress the homeostatic balance imposed by the circadian clock. The integration of circadian biology into cancer research offers new options for making cancer treatment more effective, and the pharmacological modulation of core clock genes is a new approach in cancer therapy. This review highlights the role of the circadian clock in tumorigenesis, how clock disruption alters the tumor microenvironment, and discusses how pharmacological modulation of circadian clock genes can lead to new therapeutic options.

The mutual impacts of stem cells and sleep: opportunities for improved stem cell therapy

Sleep is an indispensable physiological function regulated by circadian rhythms, which influence the biological pathways and overall health of the body. Sleep is crucial for the maintenance and restoration of bodily systems, and disturbances can lead to various sleep disorders, which can impair both mental and physical health. Treatment options for these disorders encompass lifestyle modifications, psychotherapy, medications, and therapies such as light therapy and surgery. Not only sleep deprivation has a significant impact on essential organs, but it also influences various types of stem cells in the body. In this review, we explore the connection between sleep and various types of stem cells, highlighting how circadian rhythms regulate stem cell activities that are vital for tissue regeneration and homeostasis. Disruptions in sleep can hinder stem cell self-renewal, homing, proliferation, function, and differentiation, thereby affecting tissue regeneration and overall health. We also discuss how transplantation of stem cells and their products may help improve sleep disorders, how sleep quality affects stem cell behavior, and the implications for stem cell therapies. Notably, while certain stem cell transplantations can disrupt sleep, enhancing sleep quality may improve the efficacy of these therapies. Finally, stem cells can be utilized to model sleep disorders, offering valuable insights into their underlying mechanisms.

Long-term sub-erythemal UVB exposure does not impact circadian rhythms in mice under standard and rotating shift light conditions

The International Agency for Research on Cancer (IARC) stated that circadian disruption is a potential carcinogen. However, the impact of environmental carcinogens, including sub-erythemal doses of UVB exposure, on circadian rhythms remains unclear. We evaluated the impact of long-term rotating shift, loss of Per1/2 genes, and chronic UVB exposure on the circadian rhythms of SKH-1 mice for up to 7 months. Real-time locomotion and circadian gene expression were measured in these animals. Mice under rotating shift exhibited a longer period of activity of up to 25.20 h, while those under standard light conditions had a clear 24-h rhythm. mPer1/mPer2 mice, conversely, displayed a shortened period of activity of 23.61 h. Interestingly, chronic UVB exposure had no impact on activity rhythms, though it induced skin tumors in all mice. Rotating shift and loss of mPer1/mPer2 led to circadian dysregulation of all core clock genes, with a notable phase difference in Cry1. These findings provide novel insights into environmental and genetic influences on circadian rhythms.

Research progress in modulating the auditory system by the cochlear circadian clock system in response to noise exposure

The circadian clock is an endogenous system evolved to adapt to environmental changes. Recent studies confirmed that the cochlea exhibits circadian oscillations regulating auditory function. These oscillations are linked to brain-derived neurotrophic factor and glucocorticoid levels. Circadian rhythms influence cochlear sensitivity to noise by regulating the secretion of brain-derived neurotrophic factors and glucocorticoids. This study explores the regulatory mechanism of the circadian clock system, its impact on the auditory system, and its potential role in noise-induced hearing loss. Understanding the regulatory mechanisms of circadian rhythms in auditory function will provide new ideas for developing treatments for noise-induced hearing loss.

Gut Microbiome-Produced Bile Acid Metabolite Lengthens Circadian Period in Host Intestinal Cells

Host circadian signaling, feeding, and the gut microbiome are tightly interconnected. Changes in the gut microbial community can affect the expression of core clock genes, but the specific metabolites and molecular mechanisms that mediate this relationship remain largely unknown. Here, we sought to identify gut microbial metabolites that impact circadian signaling. Through a phenotypic screen of a focused library of gut microbial metabolites, we identified a bile acid metabolite, lithocholic acid (LCA), as a circadian modulator. LCA lengthened the circadian period of core clock gene hPer2 transcription in a dose-responsive manner in human colonic cells. We found evidence that LCA modulates the casein kinase 1 δ/ε (CK1δ/ε)-protein phosphatase 1 (PP1) feedback loop and stabilizes core clock protein cryptochrome 2 (CRY2). Furthermore, we showed that LCA feeding alters circadian transcription in mouse distal ileum and colon. Taken together, our work identifies LCA as a molecular link between host circadian biology and the microbiome. Because bile acids are secreted in response to feeding, our work provides potential mechanistic insight into the molecular nature of the food-entrainable oscillator by which peripheral clocks adapt to the timing of food intake. Given the association between circadian rhythm, feeding, and metabolic disease, our insights may offer a new avenue for modulating host health.

The circadian rhythm as therapeutic target in inflammatory bowel disease

The primary objectives of the management of patients with inflammatory bowel disease (IBD) are to prevent IBD flares, prevent/delay disease progression and improve patients' quality of life. To this end, one needs to identify risk factor(s) associated with flare-ups and disease progression. We posit that disruption of circadian rhythms is one of the key factors that is associated with risk of flare-up and disease progression. This hypothesis is based on published studies that show: (1) The circadian rhythm regulates many biological processes including multiple IBD-relevant biological processes that are critical in inflammatory/immune processes such as environment/microbe interaction, microbe/host interaction, intestinal barrier integrity and mucosal immunity-all central in the pathogenesis of IBD, and (2) Circadian machinery is the primary tool for the host to interact with the environment. Circadian misalignment results in a loss of preparedness of the host to respond and adjust to the environmental changes that could make the host more vulnerable to IBD flare-ups. In this review, we first provide an overview of circadian rhythms and its role in healthy and disease states. Then we present data to support our hypothesis that: (1) IBD patients have disrupted circadian rhythms ("social jet lag") and (2) circadian misalignment and associated disrupted sleep decreases the resiliency of IBD patients resulting in microbiota dysbiosis, more disrupted intestinal barrier integrity and a more aggressive disease phenotype. We also show that circadian-directed interventions have a potential to mitigate the deleterious impact of disrupted circadian and improve IBD disease course.

Designing and Evaluating Circadian Experiments on Mouse Skin

All skin layers and cutaneous appendages harbor a robust circadian clock, whose phase is under the influence of light through the central clock in the suprachiasmatic nucleus. The skin clock coordinates fundamental biological processes, including metabolism and stem cell activation. It also prominently modulates activity of skin-resident immune cells and the inflammatory response. Numerous diurnally regulated genes in the skin have been implicated in skin diseases in GWASs. Therefore, the mouse skin is a powerful model for understanding the diverse roles of circadian biology in maintaining tissue health and the initiation and propagation of disease states. When planning experiments to study the circadian biology of mouse skin, multiple technical and biological factors must be carefully considered. In this paper, we provide comprehensive guidance on the general circadian experimental design and associated housing for the mice. We highlight the importance of aligning sample collection with the desired hair cycle stage and animal age. We introduce methods to disrupt the clock in the skin, including altering light and feeding schedules as well as using transgenic mouse models. Finally, we discuss the use of transcriptomic data, both bulk and single cell, for circadian studies.

The main sources of molecular organization in the cell. Atlas of self-organized and self-regulated dynamic biostructures

One of the most important goals of contemporary biology is to understand the principles of the molecular order underlying the complex dynamic architecture of cells. Here, we present an overview of the main driving forces involved in the cellular molecular complexity and in the emergent functional dynamic structures, spanning from the most basic molecular organization levels to the complex emergent integrative systemic behaviors. First, we address the molecular information processing which is essential in many complex fundamental mechanisms such as the epigenetic memory, alternative splicing, regulation of transcriptional system, and the adequate self-regulatory adaptation to the extracellular environment. Next, we approach the biochemical self-organization, which is central to understand the emergency of metabolic rhythms, circadian oscillations, and spatial traveling waves. Such a complex behavior is also fundamental to understand the temporal compartmentalization of the cellular metabolism and the dynamic regulation of many physiological activities. Numerous examples of biochemical self-organization are considered here, which show that practically all the main physiological processes in the cell exhibit this type of dynamic molecular organization. Finally, we focus on the biochemical self-assembly which, at a primary level of organization, is a basic but important mechanism for the order in the cell allowing biomolecules in a disorganized state to form complex aggregates necessary for a plethora of essential structures and physiological functions. In total, more than 500 references have been compiled in this review. Due to these main sources of order, systemic functional structures emerge in the cell, driving the metabolic functionality towards the biological complexity.

Circadian rhythm, microglia-mediated neuroinflammation, and Alzheimer's disease

Microglia, the brain's resident macrophages, are key mediators of neuroinflammation, responding to immune pathogens and toxins. They play a crucial role in clearing cellular debris, regulating synaptic plasticity, and phagocytosing amyloid-β (Aβ) plaques in Alzheimer's disease (AD). Recent studies indicate that microglia not only exhibit intrinsic circadian rhythms but are also regulated by circadian clock genes, influencing specific functions such as phagocytosis and the modulation of neuroinflammation. Disruption of the circadian rhythm is closely associated with AD pathology. In this review, we will provide an overview of how circadian rhythms regulate microglia-mediated neuroinflammation in the progression of AD, focusing on the pathway from the central nervous system (CNS) and the peripheral immune system. We also discuss potential therapeutic targets, including hormone modulation, lifestyle interventions, and anti-inflammatory therapies, aimed at maintaining brain health in AD. This will shed light on the involvement of circadian rhythm in AD and explore new avenues for AD treatment.

A Compensated Clock: Temperature and Nutritional Compensation Mechanisms Across Circadian Systems

Circadian rhythms are ∼24-h biological oscillations that enable organisms to anticipate daily environmental cycles, so that they may designate appropriate day/night functions that align with these changes. The molecular clock in animals and fungi consists of a transcription-translation feedback loop, the plant clock is comprised of multiple interlocking feedback-loops, and the cyanobacterial clock is driven by a phosphorylation cycle involving three main proteins. Despite the divergent core clock mechanisms across these systems, all circadian clocks are able to buffer period length against changes in the ambient growth environment, such as temperature and nutrients. This defining capability, termed compensation, is critical to proper timekeeping, yet the underlying mechanism(s) remain elusive. Here we examine the known players in, and the current models for, compensation across five circadian systems. While compensation models across these systems are not yet unified, common themes exist across them, including regulation via temperature-dependent changes in post-translational modifications.

Circadian Clock Disruption and Growth of Kidney Cysts in Autosomal Dominant Polycystic Kidney Disease

Key Points

Lack of Bmal1 , a circadian clock protein in renal collecting ducts disrupted the clock and increased cyst growth and fibrosis in an autosomal dominant polycystic kidney disease mouse model. Bmal1 gene deletion increased cell proliferation by increasing lipogenesis in kidney cells. Thus, circadian clock disruption could be a risk factor for accelerated disease progression in patients with autosomal dominant polycystic kidney disease.

Background

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in the PKD1 and PKD2 genes and often progresses to kidney failure. ADPKD progression is not uniform among patients, suggesting that factors secondary to the PKD1/2 gene mutation could regulate the rate of disease progression. Here, we tested the effect of circadian clock disruption on ADPKD progression. Circadian rhythms are regulated by cell-autonomous circadian clocks composed of clock proteins. BMAL1 is a core constituent of the circadian clock.

Methods

To disrupt the circadian clock, we deleted Bmal1 gene in the renal collecting ducts of the Pkd1 RC/RC (RC/RC) mouse model of ADPKD (RC/RC;Bmal1 f/f;Pkhd1 cre, called double knockout [DKO] mice) and in Pkd1 knockout mouse inner medullary collecting duct cells (Pkd1Bmal1 KO mouse renal inner medullary collecting duct cells). Only male mice were used.

Results

Human nephrectomy ADPKD kidneys showed altered clock gene expression when compared with normal control human kidneys. When compared with RC/RC kidneys, DKO kidneys showed significantly altered clock gene expression, increased cyst growth, cell proliferation, apoptosis, and fibrosis. DKO kidneys also showed increased lipogenesis and cholesterol synthesis–related gene expression and increased tissue triglyceride levels compared with RC/RC kidneys. Similarly, in vitro , Pkd1Bmal1 KO cells showed altered clock genes, increased lipogenesis and cholesterol synthesis–related genes, and reduced fatty acid oxidation–related gene expression compared with Pkd1KO cells. The Pkd1Bmal1 KO cells showed increased cell proliferation compared with Pkd1KO cells, which was rescued by pharmacological inhibition of lipogenesis.

Conclusions

Renal collecting duct–specific Bmal1 gene deletion disrupted the circadian clock and triggered accelerated ADPKD progression by altering lipid metabolism–related gene expression.

Circadian rhythms in stem cells and their therapeutic potential

Circadian rhythms are present in almost all cells, but their existence in stem cells has remains not well established. Circadian clock appears to be closely associated with differentiated mature cells and rarely detected in immature embryonic stem cells. Recent evidence reveals the presence of circadian genes and rhythmic physiologic activities in stem cells as well as stem cell-derived extracellular vesicle (EV) characteristics. The circadian clock entails diverse physiologic and pathological mechanisms underlying cell fate. Integration of circadian rhythm to clinical applications, such as chronotherapy, chrono-biomarker, and environment modification, may facilitate therapeutic outcomes of stem cell-based regenerative medicine. Understanding circadian rhythms in stem cells can optimize stem cell-based therapies by determining the best times for harvesting and administering stem cells, thereby enhancing therapeutic efficacy. Further research into the circadian properties of stem cells will refine stem cell-based therapies, contributing to advancements in regenerative medicine.

Changes in Mitochondrial Transcriptional Rhythms and Depression-like Behavior in the Hippocampus of IL-33-Overexpressing Mice

Neuroinflammation is involved in the development of depression and may induce depression-like behaviors by affecting metabolism through interactions with circadian rhythms. As the hub of metabolism, mitochondria are regulated by various types of metabolism and release signals that regulate cellular functions. In this study, we performed transcriptomic analysis of the hippocampus of IL-33-overexpressing mice to provide new ideas to explore the pathogenesis of inflammation-mediated depression at the transcriptional level. Male C57BL/6J mice and IL-33-overexpressing mice were subjected to behavioral tests. The hippocampus was extracted during the light or dark period, and differential gene expression analysis was conducted using RNA sequencing. Differential gene enrichment analysis was performed, as well as multilayered analysis of mitochondrial transcriptional rhythms by integrating the regulatory networks and Mito 3.0 database. The results were further verified using RT-qPCR. IL-33-overexpressing mice exhibited depressive behaviors associated with rhythmic disorders and shortened circadian cycles. Differential KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed that the top 20 pathways with the lowest p-values included mood-related, immune-related, and circadian rhythm-related pathways. Differential gene GO (Gene Ontology) enrichment analysis showed that 20 of the top 30 pathways with the lowest p-values were related to metabolism. Transcriptome data from IL-33-overexpressing mice showed that the mitochondrial-encoded subunit of the oxidative respiratory complex showed predominantly increased expression during the light period. Metabolic disorders and disrupted mitochondrial transcriptional rhythm were also observed. Weighted gene correlation network analysis showed that the circadian cycle is associated with depression-like behavior disorders. Network analysis showed that circadian-related genes were enriched in mitochondrial pathways related to metabolism and oxidative phosphorylation. Multilayer analysis of mitochondrial transcriptional rhythms using the mitochondrial database Mito 3.0 revealed that mitochondrial dynamics and surveillance pathways were the most enriched. The depressive behavior in mice caused by long-term IL-33 stimulation may be related to changes in the transcriptional rhythms of metabolism-related genes and the interaction between mitochondria and clock genes. This suggests that mitochondrial transcriptional rhythms are central to the pathogenesis of microinflammation-induced depression, further supporting the potential of mitochondria as a target for the prevention and treatment of depression.

Long-lasting sex-specific alteration in left ventricular cardiac transcriptome following gamma and simGCRsim radiation

Space irradiation (IR) is an important health risk for deep-space missions. We reported heart failure with preserved ejection fraction like cardiac phenotype 660-days following exposure to a single-dose of a simplified galactic cosmic ray simulation (simGCRsim) only in males with functional and structural impairment in left ventricular (LV) function. This sex-based dichotomy prompted us to investigate sex-specific changes in the LV transcriptome in three-month-old male and female mice exposed to 137Cs-γ- or simGCRsim-IR. Non-IR male and female (10 each) mice served as controls. LVs were collected at 440/660- and 440/550-days post-IR, male and female, respectively. RNA sequencing, differential gene expression, and functional annotation were performed on tissues from 5 mice/group. Sex and post-IR time points had the greatest influence on gene expression, surpassing the IR-type effects. SimGCRsim-IR showed more persistent transcriptome changes than γ-IR. We suggest that the single IR effects can persist up to 550-660 days, with overwhelmingly sex-biased responses at individual gene expression level.

Melatonin-Loaded Hydrogel Modulates Circadian Rhythms and Alleviates Oxidative Stress and Inflammation to Promote Wound Healing

Circadian rhythm disruption, commonly caused by factors such as jet lag and shift work, is increasingly recognized as a critical factor impairing wound healing. Although melatonin is known to regulate circadian rhythms and has potential in wound repair, its clinical application is limited by low bioavailability. To address these challenges, we developed an alginate-based dual-network hydrogel as a delivery system for melatonin, ensuring its stable and sustained release at the wound site. This approach enhances the efficacy of melatonin in modulating the wound healing process. We investigated the effects of circadian rhythm disruption on the wound microenvironment under the influence of the melatonin-loaded hydrogel with a focus on its biocompatibility, hemostatic properties, and antioxidant response functions. Additionally, we elucidated the mechanisms by which the melatonin-loaded hydrogel system promotes wound healing. Our findings provide insights into the relationship between circadian rhythm disruption and wound healing, offering a promising strategy for the management of chronic wounds associated with circadian rhythm disorders.

Diurnal variation in skeletal muscle mitochondrial function dictates time-of-day-dependent exercise capacity

Exercise impinges on almost all physiological processes at an organismal level and is a potent intervention to treat various diseases. Exercise performance is well established to display diurnal rhythm, peaking during the late active phase. However, the underlying molecular/metabolic factors and mitochondrial energetics that possibly dictate time-of-day exercise capacity remain unknown. Here, we have unraveled the importance of diurnal variation in mitochondrial functions as a determinant of skeletal muscle exercise performance. Our results show that exercise-induced muscle metabolome and mitochondrial energetics are distinct at ZT3 and ZT15. Importantly, we have elucidated key diurnal differences in mitochondrial functions that are well correlated with disparate time-of-day-dependent exercise capacity. Providing causal mechanistic evidence, we illustrate that loss of Sirtuin4 (SIRT4), a well-known mitochondrial regulator, abrogates mitochondrial diurnal variation and consequently abolishes time-of-day-dependent muscle output. Therefore, our findings unequivocally demonstrate the pivotal role of baseline skeletal muscle mitochondrial functions in dictating diurnal exercise capacity.

Changes in the immunohistochemical expression of nephrin protein in renal corpuscle of rats in response to sleep disturbance

Sleep is an essential health requirement; human body needs sufficient amount and quality of sleep to ensure its health. Sleep disturbance led to deterioration in renal functions. This study aimed to asses effect of sleep disturbance on nephrin protein in renal corpuscle. A sample of thirty adult male albino rats, subjected to sleep disturbance by light, divided into three groups; control group with normal sleep rhythm of 12-12 h dark- light phases, group A: subjected to interruption of sleep by light at three intervals, group B: rats were exposed to a reduction in sleep time by continuous light stimulation for 7 h. Animals were sacrificed by euthanasia, their kidneys were dissected and prepared for paraffin, sections stained for Nephrin protein, and the immunohistochemical intensity was quantified by Aperio Image Scope analysis software. This study showed variations in the effect of sleep disturbance patterns by light exposure on nephrin protein expression in renal corpuscles; in the control group a strong patchy distribution of Nephrine in the peripheral region of the glomerulus, group A showed a significant reduction compared to the control group, and group B a weak expression of nephrin protein in the glomerulus, with significant changes between group B and group A, but no significant changes between group B and control. These changes reflect that sleep disturbance affects the structural integrity of the slit diaphragm and nephrin protein expression, which is considered a novel protein for the slit diaphragm structural integrity, and a sign of podocyte injury.

Circadian Disruption and the Risk of Developing Obesity

PURPOSE OF THE REVIEW

This review summarizes recent evidence for a role of the clock in adipose tissue physiology and the impact of circadian desynchrony on the development of obesity.

RECENT FINDINGS

Circadian disruptions due to shift work, late time eating and nighttime light exposure are associated with obesity and its metabolic and cardiovascular consequences. Studies in mice harboring tissue-specific gain/loss of function mutations in clock genes revealed that the circadian clock acts on multiple pathways to control adipogenesis, lipogenesis/lipolysis and thermogenesis. Time-restricted eating (TRE), aligning feeding with the active period to restore clock function, represents a promising strategy to curb obesity. While TRE has shown clear benefits, especially in participants at higher cardiometabolic risk, current studies are limited in size and duration. Larger, well-controlled studies are warranted to conclusively assess the effects of TRE in relation to the metabolic status and gender. Field studies in shift-workers, comparing permanent night shift versus rotating shifts, are also necessary to identify the optimal time window for TRE.