Prediction of mammalian tissue-specific CLOCK-BMAL1 binding to E-box DNA motifs

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.

Circadian rhythm, hypoxia, and cellular senescence: From molecular mechanisms to targeted strategies

Cellular senescence precipitates a decline in physiological activities and metabolic functions, often accompanied by heightened inflammatory responses, diminished immune function, and impaired tissue and organ performance. Despite extensive research, the mechanisms underpinning cellular senescence remain incompletely elucidated. Emerging evidence implicates circadian rhythm and hypoxia as pivotal factors in cellular senescence. Circadian proteins are central to the molecular mechanism governing circadian rhythm, which regulates homeostasis throughout the body. These proteins mediate responses to hypoxic stress and influence the progression of cellular senescence, with protein Brain and muscle arnt-like 1 (BMAL1 or Arntl) playing a prominent role. Hypoxia-inducible factor-1α (HIF-1α), a key regulator of oxygen homeostasis within the cellular microenvironment, orchestrates the transcription of genes involved in various physiological processes. HIF-1α not only impacts normal circadian rhythm functions but also can induce or inhibit cellular senescence. Notably, HIF-1α may aberrantly interact with BMAL1, forming the HIF-1α-BMAL1 heterodimer, which can instigate multiple physiological dysfunctions. This heterodimer is hypothesized to modulate cellular senescence by affecting the molecular mechanism of circadian rhythm and hypoxia signaling pathways. In this review, we elucidate the intricate relationships among circadian rhythm, hypoxia, and cellular senescence. We synthesize diverse evidence to discuss their underlying mechanisms and identify novel therapeutic targets to address cellular senescence. Additionally, we discuss current challenges and suggest potential directions for future research. This work aims to deepen our understanding of the interplay between circadian rhythm, hypoxia, and cellular senescence, ultimately facilitating the development of therapeutic strategies for aging and related diseases.

Correlation of the expression of circadian-clock genes with the severity of obstructive sleep apnea in patients

This study investigates the connection of Obstructive Sleep Apnea (OSA) with the expression and daily oscillation patterns of core circadian clock genes and related genes. OSA, a sleep disorder characterized by repetitive airway occlusion leading to nocturnal arousals, sleep fragmentation, and intermittent hypoxemia (IH), shares sleep dysfunction as an overlapping phenotype with circadian clock genes. The research involved 40 subjects (30 OSA patients and 10 normal controls), categorized into four groups based on Polysomnography (PSG) results: normal, mild, moderate, and severe. Peripheral blood samples were collected twice from each participant in the evening before and the morning after PSG examination. Using real-time quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR), the study measured the expression levels of target genes in leukocytes. Results revealed changes in diurnal expression patterns of several genes (PER1, PER3, CRY1, BMAL1, CLOCK, HIF-1α, IL-1β, TNFα) in OSA groups compared to normal controls. While PER2, CRY2, and NPAS2 genes did not show diurnal patterns, their expression was significantly elevated in severe OSA. Notably, the expression levels of HIF-1α, IL-1β, and TNFα increased with OSA severity, consistent with the roles of IH and inflammation as clinical indicators in OSA. These findings not only demonstrate that circadian clock-related gene expression fluctuates with OSA but also provide potential molecular markers for early diagnosis and personalized treatment. By identifying biomarkers parallel to clinical indicators in OSA, this innovative study paves the way for future research and clinical applications in the field.

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.

The impact of circadian rhythms on retinal immunity

The eye is an immune-protected organ, which is driven by factors such as cytokines, chemicals, light, and mechanical stimuli. The circadian clock is an intrinsic timing mechanism that influences the immune activities, such as immune cell count and activity, as well as inflammatory responses. Recent studies have demonstrated that the eye also possesses an intrinsic circadian rhythm, and this rhythmic regulation participates in ocular immune modulation. In this review, we discuss the immunoregulatory mechanisms of the circadian clock within the eye, and reveal new perspectives for the prevention and treatment of ocular diseases.

Global mapping of BMAL1 protein-DNA interactions in human retinal Müller cells

The circadian clock, a conserved biologic timekeeping mechanism, is pivotal in orchestrating rhythmic physiologic processes. While extensively studied in the central clock, the involvement of BMAL1 in peripheral clocks, particularly in human Müller cells, remains underexplored. Müller cells, critical for retinal homeostasis, may unveil novel insights into circadian regulation. Employing ChIP-sequencing, we comprehensively mapped BMAL1 binding sites in human Müller cells. The analysis identified 275 reproducible peaks, with predominant distribution across promoters (26.6%), intronic (26.3%), and intergenic (22.1%) regions, with 80% of these confident peaks linked to protein-coding genes. Differential peak analysis revealed 89 unique genes significantly enriched with BMAL1 sites in their promoters, while functional enrichment of the associated genes indicated key biologic processes such as circadian regulation of gene expression, photoperiodism, and glucocorticoid receptor signaling pathway regulation. Motif analysis revealed a highly conserved 6-nucleotide motif, CACGTG, appearing in 89.09% of the peaks. Analysis of the binding sites across genomic regions highlighted the robust BMAL1 binding, further confirmed by qPCR validation of circadian targets such as G6PC3, CIART, PER1, and TXNIP, which are critical for Müller cell health, along with SHMT2 and MALAT1, which have emerged as novel genes that may have implications for Müller cell health. Our findings unveil the regulatory landscape of BMAL1 in Müller cells, contributing to a broader understanding of the clock-mediated mechanism in ocular tissues. These insights hold therapeutic potential for circadian-related retinal diseases, presenting avenues for chronotherapeutic interventions.

Circadian clock disruption and growth of kidney cysts in 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 DKO mice), and in Pkd1 knockout mouse inner medullary collecting duct cells ( Pkd1Bmal1 KO mIMCD3 cells). Only male mice were used.

Results

Human nephrectomy ADPKD kidneys and Pkd1 KO mIMCD3 cells showed reduced Bmal1 gene expression compared to normal controls. When compared to 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 to 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 to Pkd1KO cells. The Pkd1Bmal1 KO cells showed increased cell proliferation compared to Pkd1KO cells, which was rescued by pharmacological inhibition of lipogenesis.

Conclusion

Renal collecting duct specific Bmal1 gene deletion disrupts the circadian clock and triggers accelerated ADPKD progression by altering lipid metabolism-related gene expression.

Key points

Lack of BMAL1, a circadian clock protein in renal collecting ducts disrupted the clock and increased cyst growth and fibrosis in an ADPKD 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 ADPKD.

Blood DNA methylation in post-acute sequelae of COVID-19 (PASC): a prospective cohort study

BACKGROUND

DNA methylation integrates environmental signals with transcriptional programs. COVID-19 infection induces changes in the host methylome. While post-acute sequelae of COVID-19 (PASC) is a long-term complication of acute illness, its association with DNA methylation is unknown. No universal blood marker of PASC, superseding single organ dysfunctions, has yet been identified.

METHODS

In this single centre prospective cohort study, PASC, post-COVID without PASC, and healthy participants were enrolled to investigate their symptoms association with peripheral blood DNA methylation data generated with state-of-the-art whole genome sequencing. PASC-induced quality-of-life deterioration was scored with a validated instrument, SF-36. Analyses were conducted to identify potential functional roles of differentially methylated loci, and machine learning algorithms were used to resolve PASC severity.

FINDINGS

103 patients with PASC (22.3% male, 77.7% female), 15 patients with previous COVID-19 infection but no PASC (40.0% male, 60.0% female), and 27 healthy volunteers (48.1% male, 51.9% female) were enrolled. Whole genome methylation sequencing revealed 39 differentially methylated regions (DMRs) specific to PASC, each harbouring an average of 15 consecutive positions, that differentiate patients with PASC from the two control groups. Motif analyses of PASC-regulated DMRs identify binding domains for transcription factors regulating circadian rhythm and others. Some DMRs annotated to protein coding genes were associated with changes of RNA expression. Machine learning support vector algorithm and random forest hierarchical clustering reveal 28 unique differentially methylated positions (DMPs) in the genome discriminating patients with better and worse quality of life.

INTERPRETATION

Blood DNA methylation levels identify PASC, stratify PASC severity, and suggest that DNA motifs are targeted by circadian rhythm-regulating pathways in PASC.

FUNDING

This project has been funded by the following agencies: NIH-AI173035 (A. Jaitovich and R. Alisch); and NIH-AG066179 (R. Alisch).

Association between sarcopenia and sleep disorders: a cross-sectional population based study

Objective

Sleep disorders is a worldwide public health problem. We sought to examine the association between sarcopenia, a decline in skeletal muscle mass and function, and sleep disorders within the adult demographic of the United States during the period spanning 2011 to 2018.

Methods

Diagnosis of sarcopenia and sleep disorders was ascertained through appropriate calculations and a structured questionnaire. The primary correlation analysis was conducted using a weighted multivariate logistic regression model. Furthermore, to confirm the presence of a potential non-linear association between sarcopenia and sleep disorders, additional analyses were performed using multivariate logistic regression and restricted cubic spline (RCS) regression with dose-response curve analysis. Subgroup analyses were also conducted to explore the influence of relevant socio-demographic factors and other covariates.

Results

The final analysis encompassed 5,616 participants. Model 4, inclusive of all pertinent covariates, revealed a positive correlation between sarcopenia and sleep disorders, yielding an odds ratio (OR) of 1.732 (95% CI: 1.182-2.547; P = 0.002). Further analysis, utilizing the restricted cubic spline model, indicated a decreasing trend in sleep disorders as sarcopenia indices rose. Stratified analyses across diverse variables underscored the significant impact of sarcopenia on sleep disorders prevalence in several subgroups. Specifically, males, individuals aged 40 and above, non-Hispanic whites, those with high school education or equivalent, unmarried individuals, obese individuals (BMI ≥ 30), alcohol drinkers, former smokers, diabetics, and those engaging in less rigorous recreational activities exhibited a more pronounced association between sarcopenia and sleep disorders. The incidence of sleep disorders exhibited an upward trend as the incidence of sarcopenia declined among study participants.

Conclusions

In summary, our study provides evidence of an association between sarcopenia and the prevalence of sleep disorders, with a negative correlation observed between the sarcopenia index and the odds ratio of sleep disorders. These findings suggest that maintaining optimal muscle mass may have a beneficial impact on sleep-related issues. In terms of exploring the mechanisms underlying the relationship between sarcopenia and sleep disorders, more in-depth research is warranted to ascertain the definitive causal relationship.

Circadian immunity from bench to bedside: a practical guide

The immune system is built to counteract unpredictable threats, yet it relies on predictable cycles of activity to function properly. Daily rhythms in immune function are an expanding area of study, and many originate from a genetically based timekeeping mechanism known as the circadian clock. The challenge is how to harness these biological rhythms to improve medical interventions. Here, we review recent literature documenting how circadian clocks organize fundamental innate and adaptive immune activities, the immunologic consequences of circadian rhythm and sleep disruption, and persisting knowledge gaps in the field. We then consider the evidence linking circadian rhythms to vaccination, an important clinical realization of immune function. Finally, we discuss practical steps to translate circadian immunity to the patient's bedside.

Clock gene Per2 modulates epidermal tissue repair in vivo

Wound healing can be influenced by genes that control the circadian cycle, including Per2 and BMAL1, which coordinate the functions of several organs, including the skin. The aim of the study was to evaluate the role of PER2 during experimental skin wound healing. Two groups (control and Per2-KO), consisting of 14 male mice each, were anesthetized by inhalation, and two 6 mm wounds were created on their dorsal skin using a punch biopsy. A silicone ring was sutured around the wound perimeter to restrict contraction. The wound healing process was clinically measured daily (closure index) until complete wound repair. On Day 6, histomorphometric analysis was performed using the length and thickness of the epithelial migration tongue, in addition to counting vessels underlying the lesion by immunofluorescence assay and maturation of collagen fibers through picrosirius staining. Bromodeoxyuridine (BrdU) incorporation and quantification were performed using the subcutaneous injection technique 2 h before euthanasia and through immunohistochemical analysis of the proliferative index. In addition, the qualitative analysis of myofibroblasts and periostin distribution in connective tissue was performed by immunofluorescence. Statistically significant differences were observed in the healing time between the experimental groups (means: 15.5 days for control mice and 13.5 days for Per2-KO; p = 0.001). The accelerated healing observed in the Per2-KO group (p < 0.05) was accompanied by statistical differences in wound diameter and length of the migrating epithelial tongue (p = 0.01) compared to the control group. Regarding BrdU immunoreactivity, higher expression was observed in the intact epithelium of Per2-KO animals (p = 0.01), and this difference compared to control was also present, to a lesser extent, at the wound site (p = 0.03). Immunofluorescence in the connective tissue underlying the wound showed a higher angiogenic potential in the Per2-KO group in the intact tissue area and the wound region (p < 0.01), where increased expression of myofibroblasts was also observed. Qualitative analysis revealed the distribution of periostin protein and collagen fibers in the connective tissue underlying the wound, with greater organization and maturation during the analyzed period. Our research showed that the absence of the Per2 gene positively impacts the healing time of the skin in vivo. This acceleration depends on the increase of epithelial proliferative and angiogenic capacity of cells carrying the Per2 deletion.