Circadian Regulation Research Articles

The Anti-Elixir Triad: Non-Synced Circadian Rhythm, Gut Dysbiosis and Telomeric Damage.

Aging is an inevitable life process which is accelerated by lifestyle and environmental factors. It is an irreversible accretion of molecular and cellular damage associated with changes in the body composition and deterioration in physiological functions. Each cell (other than stem cells), reaches the limit of its ability to replicate, known as cellular or replicative senescence and consequently, the organs lose their physiological functions resulting in overall impairment. Other factors that promote aging include smoking, alcohol, UV rays, sleep habits, food, stress, sedentary life style and genetic abnormalities. These stress factors, can alter our endogenous clock (the circadian rhythm) and the microbial commensals. As a result of effect of these stressors, the microorganisms that generally support human physiological processes become baleful. The disturbance of natural physiology instigates many age-related pathologies, such as cardiovascular diseases, chronic obstructive pulmonary disorder, cerebrovascular diseases, opportunistic infections, high blood pressure, cancer, diabetes, kidney diseases, dementia, and Alzheimer's disease. The present review covers the three most essential processes of the circadian clock; the circadian gene mechanism and regulation, the mitotic clock (which plays a vital role in the telomere's attrition) and gut microbiota and their metabolome that drive aging and lead to age-related pathologies. In conclusion, maintaining a synchronized circadian rhythm, a healthy gut microbiome and telomere integrity is essential for mitigating the effects of aging and promoting longevity. The interplay among these factors underscores the importance of lifestyle choices in enhancing overall health and lifespan.

Blood Pressure Regulation in Post-COVID POTS: Beyond Sinus Tachycardia.

Postural orthostatic tachycardia syndrome (POTS) is a frequently diagnosed cardiovascular disorder after COVID-19 infection. POTS is characterized by the presence of excessive sinus tachycardia on standing without a fall in blood pressure (BP). We investigated the BP profile using 24-hour ambulatory BP monitoring in patients with new-onset POTS after COVID-19 compared with prepandemic population-based controls. We performed a case-control study in 100 patients (mean age, 40.0±12.9 years; 85% women) with verified post-COVID-19 new-onset POTS diagnosed by a positive head-up tilt testing versus 100 controls from a population-based cohort with a negative active standing test, no history of syncope, POTS, or endocrine disease (mean age, 42.3±14.0 years; 78% women). Twenty-four-hour BP profile was assessed for circadian BP variation including hypotensive systolic BP (SBP) episodes (<80, <90, and <100 mm Hg). Patients with post-COVID-19 POTS had significantly higher nighttime SBP, but not daytime SBP, and more daytime SBP hypotensive episodes compared with controls. Nondipping (34% versus 19%; P<0.001) and reverse dipping patterns (9% versus 0%; P<0.001) were more frequent in post-COVID-19 POTS. In the logistic regression, patients with post-COVID-19 POTS had significantly higher mean 24-hour SBP (odds ratio, 1.08 [95% CI, 1.04-1.11]; P<0.001) and nighttime SBP (odds ratio, 1.07 [95% CI, 1.04-1.10]; P<0.001), independent of age and sex. Patients with post-COVID-19 POTS demonstrate higher mean 24-hour and nighttime SBP and show disruptions of circadian BP rhythm regulation compared with population-based controls, as well as more daytime hypotensive episodes. Future studies are needed to test whether patients with post-COVID-19 POTS may benefit from tailored BP therapy.

CNSC-01. PEDIATRIC GLIOMAS EXPRESS CIRCADIAN GENES AND DEMONSTRATE CIRCADIAN REGULATION OF TEMOZOLOMIDE SENSITIVITY

Abstract INTRODUCTION Pediatric high-grade gliomas (pHGG) are highly invasive brain tumors with dismal survival rates, prompting the need for innovative therapeutic strategies. Previous research in adult glioblastoma patients revealed a correlation between the timing of Temozolomide administration and patient survival. There has, however, been limited exploration into circadian gene expression in pediatric gliomas. In this study, we investigate whether pHGGs exhibit rhythmic expression of circadian genes and whether the timing of drug administration influences Temozolomide sensitivity. METHODS A bioinformatics approach, immunocytochemistry and immunoblotting were used to assess key circadian genes in low- and high-grade gliomas. We then used timed qPCR to assess rhythmic expression in BMAL1 and REV-ERBα, two key circadian genes, across 48 hours in our pHGG cells following dexamethasone cell synchronization. Lastly, we used CyQuant Proliferation Assays to examine the effects of Temozolomide applied at peaks versus troughs in BMAL1 expression. RESULTS Using data from PedcBioPortal, we found significantly higher expression of BMAL1 in pHGGs compared to pLGGs (0.349 + 1.05 vs 0.0545 + 0.666, p &amp;lt; 0.001). We identified cellular localization of BMAL1 and REV-ERBα in pHGGs along with rhythmic expression of BMAL1 and REV-ERBα in our three pHGGs primary cell cultures across 48 hours (JTK_CYCLE, p &amp;lt; 0.005). Lastly, we demonstrated a chronotherapeutic response to Temozolomide in two of our pHGG cell lines, with significantly decreased proliferation when treatment occurred at trough versus peak BMAL1 expression (p &amp;lt; 0.01). CONCLUSION In this study, we found that circadian genes BMAL1 and REV-ERBα are expressed in pHGGs and expression patterns differ between pHGGs versus pLGGs. Circadian gene expression is rhythmic in pHGGs, and pHGGs can have differential Temozolomide-sensitivity based on circadian cycles. These findings suggest that circadian timing of chemotherapy may influence the efficacy of treatment, and next steps will be to explore the mechanisms underlying circadian regulation of Temozolomide sensitivity.

Circadian desynchrony in early life leads to enduring autistic-like behavioral changes in adulthood.

Circadian rhythm regulates a variety of biological processes in almost all living organisms. Modern lifestyles, e.g. transmeridian travel, night shift, light at night, etc., frequently disrupt people's regular sleep-wake cycles and create a misalignment (circadian desynchrony) between the natural environment and the endogenous body clock, and between different circadian oscillators within the body. The long-term consequences of circadian desynchrony on neurodevelopment and adult behavior remain elusive. Increasing clinical evidence supports a correlation between the disruption of the circadian system and neurodevelopmental disorders, such as autism spectrum disorders. Despite clinical correlations, experimental evidence is yet to establish a link between circadian disturbance in early life and adult behavioral changes. Here, using a "short day" (SD) mouse model, in which mice were exposed to an 8 h/8 h light/dark (LD) cycle mimicking a "shift work" schedule from gestation day 1 to postnatal day 21, we performed a battery of behavioral tests to assess changes in adult behaviors, including sociability, affective behaviors, stereotypy, cognition and locomotor functions. In contrast to the control mice kept in a 12 h/12 h LD cycle, the adult SD mice entrained to the 8 h/8 h LD cycle, but their free running rhythms remained normal in constant darkness. Interestingly, however, the SD mice displayed diminished sociability, a reduced preference for social novelty, excessive repetitive behaviors, and compromised cognitive functions, all of which resemble characteristics of autism-like behavioral alterations. In addition, the SD mice exhibited significant anxiety- and depressive-like behaviors and impaired motor functions. By western blotting and immunostaining analyses, hyperactivation of the mTORC1/S6K1 pathway was detected in multiple forebrain regions of SD mice. These findings underscore the enduring impact of early-life circadian disruption on neurochemical signaling and behavioral patterns into adulthood, highlighting a pivotal role for circadian regulation in neurodevelopment.

Serum iron and transferrin saturation variation are circadian regulated and linked to the harmonic circadian oscillations of erythropoiesis and hepatic Tfrc expression in mice.

Serum iron has long been thought to exhibit diurnal variation and is subsequently considered an unreliable biomarker of systemic iron status. Circadian regulation (endogenous ~24-h periodic oscillation of a biologic function) governs many critical physiologic processes. It is unknown whether serum iron levels are regulated by circadian machinery; likewise, the circadian nature of key players of iron homeostasis is unstudied. Here we show that serum iron, transferrin saturation (TSAT), hepatic transferrin receptor (TFR1) gene (Tfrc) expression, and erythropoietic activity exhibit circadian rhythms. Daily oscillations of serum iron, TSAT, hepatic Tfrc expression, and erythropoietic activity are maintained in mice housed in constant darkness, where oscillation reflects an endogenous circadian period. Oscillations of serum iron, TSAT, hepatic Tfrc, and erythropoietic activity were ablated when circadian machinery was disrupted in Bmal1 knockout mice. Interestingly, we find that circadian oscillations of erythropoietic activity and hepatic Tfrc expression are maintained in opposing phase, likely allowing for optimized usage and storage of serum iron whilst maintaining adequate serum levels and TSAT. This study provides the first confirmatory evidence that serum iron is circadian regulated, discerns circadian rhythms of TSAT, a widely used clinical marker of iron status, and uncovers liver-specific circadian regulation of TFR1, a major player in cellular iron uptake.

Short-term exercise counteracts accelerated ageing impacts on physical performance and liver health in mice.

Senescence impairs liver physiology, mitochondrial function and circadian regulation, resulting in systemic metabolic dysregulation. Given the limited research on the effects of combined exercise on an ageing liver, this study aimed to evaluate its impact on liver metabolism, circadian rhythms and mitochondrial function in senescence-accelerated mouse-prone 8 (SAMP8) and senescence-accelerated mouse-resistant 1 (SAMR1) mice. Histological, reverse transcription quantitative polymerase chain reaction (RT-qPCR) and immunoblotting analyses were conducted, supplemented by transcriptomic data sets and AML12 hepatocyte studies. Sedentary SAMP8 mice exhibited decreased muscle strength, reduced mitochondrial complex I levels and increased lipid droplet accumulation. In contrast, combined exercise mitigated muscle strength loss, upregulated proteins involved in mitochondrial complexes (CIII, CIV, CV) and increased Bmal1 messenger RNA (mRNA) expression in the liver. These molecular adaptations are associated with healthier liver phenotypes and may influence metabolic function and cellular longevity. Notably, elevated lipid content in aged mice was reduced post-exercise, indicating liver benefits even after a relatively short intervention. The combined exercise regimen did not improve aerobic capacity, likely due to the low volume and brief duration of running. Moreover, no significant effects were observed in SAMR1 mice, possibly because the training intensity was insufficient for younger, healthier animals. These findings underscore the potential of combined strength and endurance exercise to attenuate age-related liver dysfunction, particularly in ageing populations.

Sleep disorders in cerebrotendinous xanthomatosis: A case series

Cerebrotendinous xanthomatosis (CTX) is a rare genetic disorder characterized by a variety of neurological and systemic symptoms, including cerebellar ataxia, cataracts, tendon xanthomas, and polyneuropathy. This study aimed to investigate sleep patterns and disorders in four patients diagnosed with cerebrotendinous xanthomatosis. All participants reported significant sleep disturbances, and objective assessments confirmed the presence of insomnia, excessive daytime sleepiness, obstructive sleep apnea, and periodic limb movements. Notably, this is the first study to incorporate sleep assessments into the clinical management of CTX patients, which may be crucial for improving their quality of life. Further research is warranted to deepen our understanding of the potential impact of cholestanol deposits on regions of the central nervous system involved in sleep and circadian rhythm regulation.

Transcriptome Sequencing-Based Screening of Key Melatonin-Related Genes in Ischemic Stroke.

Ischemic stroke (IS) is a complex syndrome of neurological deficits due to stenosis or occlusion of the carotid and vertebral arteries for which there is still no effective treatment. Melatonin, a hormone secreted by the pineal gland, has multiple biological effects, such as antioxidant and anti-inflammatory properties, circadian rhythm regulation, and tissue regeneration, demonstrating potential applications in the treatment of IS. The aim of this study was to investigate key melatonin-regulated genes associated with IS using transcriptome sequencing and bioinformatics analyses and to explore their potential mechanisms of action in the disease process. We obtained gene expression data related to ischemic stroke (IS) from the Gene Expression Omnibus (GEO) database and identified candidate genes using machine learning algorithms. We then assessed the predictive power of these genes using PPI network analysis and diagnostic models. Finally, a series of enrichment analyses identified four key genes: ADM, PTGS2, MMP9, and VCAN. In addition, we determined the mRNA levels of these four key genes in an IS rat model using qPCR and found that all of these genes were significantly upregulated in the IS model compared to the control group, which is consistent with the results of previous analyses. Meanwhile, these genes have biological functions such as regulating vascular tone, participating in the inflammatory response, influencing tissue remodeling, and regulating cell adhesion and proliferation, playing key roles in the pathogenesis of IS. Therefore, we suggest that these four key genes may serve as prospective biomarkers for IS and help predict the risk of developing IS. In conclusion, this study elucidates for the first time the potential role of melatonin in the pathogenesis of IS and lays the foundation for in-depth studies on the functions of these key genes in the pathophysiology of IS and their potential applications in clinical diagnosis and treatment.

Circadian Regulation of Lipid Metabolism during Pregnancy.

A cluster of metabolic changes occur to provide energy for fetal growth and development during pregnancy. There is a burgeoning body of research highlighting the pivotal role of circadian rhythms in the pathogenesis of metabolic disorders and lipid homeostasis in mammals. Perturbations of the circadian system and lipid metabolism during gestation might be responsible for a variety of adverse reproductive outcomes comprising miscarriage, gestational diabetes mellitus, and preeclampsia. Growing studies have confirmed that resynchronizing circadian rhythms might alleviate metabolic disturbance. However, there is no clear evidence regarding the specific mechanisms by which the diurnal rhythm regulates lipid metabolism during pregnancy. In this review, we summarize previous knowledge on the strong interaction among the circadian clock, lipid metabolism, and pregnancy. Analyzing the circadian clock genes will improve our understanding of how circadian rhythms are implicated in complex lipid metabolic disorders during pregnancy. Exploring the potential of resynchronizing these circadian rhythms to disrupt abnormal lipid metabolism could also result in a breakthrough in reducing adverse pregnancy outcomes.

Influence of Acute Inflammation on the Expression of Clock Genes in the Ovine Pars Tuberalis Under Different Photoperiodic Conditions.

The pars tuberalis (PT) plays an important role in the photoperiodic regulation of the secretory activity of the pituitary gland. Additionally, PT secretory activity may be influenced by the animal's immune status. The melatonin signal processing in PT cells occurs through the presence of melatonin receptors and the expression of molecular clock genes. This study aimed to define the effects of acute inflammation induced by intravenous administration of lipopolysaccharide (LPS) on the expression of clock genes in the PT of ewes under different photoperiodic conditions. Two analogous experiments were conducted in different photoperiods: short-day and long-day. Both experiments included 24 sheep divided into two groups: day (n = 12) and night (n = 12), further subdivided into a control group (n = 6) and a group treated with LPS (n = 6) at a dose of 400 ng/kg. Under short-day conditions, the expression of clock circadian regulator, basic helix-loop-helix ARNT like 1, cryptochrome circadian regulator (CRY) 1, 2, and casein kinase 1 epsilon genes was lower during inflammation. LPS injection increased expression of the period circadian regulator 1 gene during the night. Under long-day conditions, CRY1 mRNA level was lower during the night, while diurnal CRY2 mRNA expression was decreased after LPS injection. Our results showed that inflammation disturbed the expression of molecular clock genes in the PT; however, this influence was partly dependent on photoperiod conditions.

House sparrows do not show a diel rhythm in double-strand DNA damage in erythrocytes.

DNA damage can be caused by a number of intrinsic and extrinsic factors. A recent study showed that free-living house sparrows (Passer domesticus) have higher DNA damage in the summer than the winter across five different tissues. This result was consistent when house sparrows were brought into captivity and exposed to comparable light cycles, with all other variables held constant. These results generated two hypotheses: (1) seasonal variation in DNA damage is related to circadian regulation and (2) seasonal variation in DNA damage is related to the total number of active hours. To investigate these hypotheses, we first quantified erythrocyte DNA damage in wild-caught house sparrows held in captivity on a 12L:12D light cycle at six points during the day to assess a diel or circadian rhythm but did not find one. We then performed a resonance experiment, in which birds experienced unnatural light cycles, and compared DNA damage in birds held on 6L:6D and 4.5L:7.5D resonance light cycles with their natural counterparts, 12L:12D and 9L:15D, respectively. We assessed corticosterone levels and DNA damage in blood before and after the resonance light cycles and DNA damage in abdominal fat, hippocampus, hypothalamus, and liver after the resonance light cycles. While our second experiment was not able to effectively test our hypotheses, we were able to demonstrate some interesting patterns. Throughout the resonance experiment, baseline corticosterone and testes size increased, consistent with the birds being photostimulated and preparing to breed. Surprisingly, the direction of change of DNA damage throughout the resonance photoperiod differed with tissue, which is not consistent with patterns during the breeding season in the wild. Our data indicate a potential uncoupling of the breeding physiology with the effect on DNA damage due to exposure to a resonance light cycle, which the birds may have interpreted as a skeleton photoperiod. Finally, though we were unable to fully disentangle the dynamics underlying seasonal DNA damage, we show that the previously documented patterns are not simply due to diel changes or the total amount of light exposure within a 24-hour period.

Melatonin as an inducer of Th17 cell differentiation: new mechanisms

Cells of the immune system are sensitive to the action of melatonin, and the most obvious target of the hormone is the Th17 T helper subset: in addition to two high-affinity membrane receptors for melatonin, MT1 and MT2, these cells express a nuclear receptor, RORα. Among the secondary messengers involved in the transmission of signals from melatonin receptors, proteins of the sirtuin family are currently of particular interest. It is known that in non-tumor cells, sirtuin 1 (SIRT1) not only increases its expression in response to melatonin, but is also involved in the implementation of melatonin effects, as indicated by inhibitory assays using a specific SIRT1 blocker or corresponding siRNA/shRNA. This relates to the regulation of circadian oscillators, as well as the anti-inflammatory, antioxidant and anti-apoptotic effects of melatonin. Further mechanisms of SIRT1 activity in the cell include transcriptional and posttranscriptional regulation of gene expression through deacetylation of histones and non-histone proteins, and the apparent target of SIRT1 is the transcription factor RORα. It is this factor that mediates classical melatonin/SIRT1-dependent transcriptional control of key circadian regulators, the genes of which have ROR-binding sequences in their promoters. These data raise questions about the functions of SIRT1 in other cells expressing RORα, in particular in Th17 T helper cells, for which it is one of two key differentiation factors, along with RORγt. And if for RORα such a connection still remains hypothetical, for RORγt it has been convincingly demonstrated in studies both in vivo and in vitro: it has been shown that SIRT1 directly binds to RORγt and stimulates the development of Th17 cells, and blockade of sirtuin suppresses the differentiation of these cells in normal and prevents the development of Th17-associated pathology in mice. Summarizing these data, we can confidently predict the existence of a new mechanism for the regulation of the T helper Th17 population by melatonin, through the activation of sirtuin SIRT1, and this mechanism must be taken into account when interpreting data on the immunoregulatory activity of melatonin.

BiP Proteins from Symbiodiniaceae: A “Shocking” Story

More than four decades ago, the discovery of a companion protein of immunoglobulins in myeloma cells and soon after, of their ability to associate with heavy chains, made the term immunoglobulin binding protein (BiP) emerge, prompting a tremendous amount of effort to understand their versatile cellular functions. BiPs belong to the heat shock protein (Hsp) 70 family and are crucial for protein folding and cellular stress responses. While extensively studied in model organisms such as Chlamydomonas, their roles in dinoflagellates, especially in photosynthetic Symbiodiniaceae, remain largely underexplored. Given the importance of Symbiodiniaceae-cnidarian symbiosis, critical for the sustaining of coral reef ecosystems, understanding the contribution of Hsps to stress resilience is essential; however, most studies have focused on Hsps in general but none on BiPs. Moreover, despite the critical role of light in the physiology of these organisms, research on light effects on BiPs from Symbiodiniaceae has also been limited. This review synthesizes the current knowledge from the literature and sequence data, which reveals a high degree of BiP conservation at the gene, protein, and structural levels in Symbiodiniaceae and other dinoflagellates. Additionally, we show the existence of a potential link between circadian clocks and BiP regulation, which would add another level of regulatory complexity. The evolutionary relationship among dinoflagellates overall suggests conserved functions and regulatory mechanisms, albeit expecting confirmation by experimental validation. Finally, our analysis also highlights the significant knowledge gap and underscores the need for further studies focusing on gene and protein regulation, promoter architecture, and structural conservation of Symbiodiniaceae and dinoglagellate BiPs in general. These will deepen our understanding of the role of BiPs in the Symbiodiniaceae-cnidarian interactions and dinoflagellate physiology.

The Circadian Brain and Cognition.

Circadian rhythms are inherent to living organisms from single cells to humans and operate on a genetically determined cycle of approximately 24hours. These endogenous rhythms are aligned with the external light/dark cycle of the Earth's rotation and offer the advantage of anticipating environmental changes. Circadian rhythms act directly on human cognition and indirectly through their fundamental influence on sleep/wake cycles. The strength of the circadian regulation of performance depends on the accumulated sleep debt and the cognitive domain, and it has been suggested to involve the activation of ascending arousal systems and their interaction with attention and other cognitive processes. In addition, attention-related cortical responses show extensive circadian rhythms, the phases of which vary across brain regions. This review discusses the impact of the circadian system on sleep/wake regulation and cognitive performance. It further addresses the health implications of circadian disruption, particularly in relation to mental and neurological disorders.

PRC2-EZH1 contributes to circadian gene expression by orchestrating chromatin states and RNA polymerase II complex stability.

Circadian rhythmicity of gene expression is a conserved feature of cell physiology. This involves fine-tuning between transcriptional and post-transcriptional mechanisms and strongly depends on the metabolic state of the cell. Together these processes guarantee an adaptive plasticity of tissue-specific genetic programs. However, it is unclear how the epigenome and RNA Pol II rhythmicity are integrated. Here we show that the PcG protein EZH1 has a gateway bridging function in postmitotic skeletal muscle cells. On the one hand, the circadian clock master regulator BMAL1 directly controls oscillatory behavior and periodic assembly of core components of the PRC2-EZH1 complex. On the other hand, EZH1 is essential for circadian gene expression at alternate Zeitgeber times, through stabilization of RNA Polymerase II preinitiation complexes, thereby controlling nascent transcription. Collectively, our data show that PRC2-EZH1 regulates circadian transcription both negatively and positively by modulating chromatin states and basal transcription complex stability.

The clock-associated LUX ARRHYTHMO regulates high-affinity nitrate transport in Arabidopsis roots.

The circadian clock organizes physiological processes in plants to occur at specific times of the day, optimizing efficient use of resources. Nitrate is a crucial inorganic nitrogen source for agricultural systems to sustain crop productivity. However, because nitrate fertilization has a negative impact on the environment, it is important to carefully manage nitrate levels. Understanding crop biological rhythms can lead to more ecologically friendly agricultural practices. Gating responses through the circadian clock could be a strategy to enhance root nitrate uptake and to limit nitrate runoff. In Arabidopsis, the NITRATE TRANSPORTER 2.1 (NRT2.1) gene encodes a key component of the high-affinity nitrate transporter system. Our study reveals that NRT2.1 exhibits a rhythmic expression pattern, with daytime increases and nighttime decreases. The NRT2.1 promoter activity remains rhythmic under constant light, indicating a circadian regulation. The clock-associated transcription factor LUX ARRHYTHMO (LUX) binds to the NRT2.1 promoter in vivo. Loss-of-function of LUX leads to increased NRT2.1 transcript levels and root nitrate uptake at dusk. This supports LUX acting as a transcriptional repressor and modulating NRT2.1 expression in a time-dependent manner. Furthermore, applying nitrate at different times of the day results in varying magnitudes of the transcriptional response in nitrate-regulated genes. We also demonstrate that a defect in the high-affinity nitrate transport system feeds back to the central oscillator by modifying the LUX promoter activity. In conclusion, this study uncovers a molecular pathway connecting the root nitrate uptake and circadian clock, with potential agro-chronobiological applications.

Circadian rhythms of macrophages are altered by the acidic tumor microenvironment

Tumor-associated macrophages (TAMs) are prime therapeutic targets due to their pro-tumorigenic functions, but varying efficacy of macrophage-targeting therapies highlights our incomplete understanding of how macrophages are regulated within the tumor microenvironment (TME). The circadian clock is a key regulator of macrophage function, but how circadian rhythms of macrophages are influenced by the TME remains unknown. Here, we show that conditions associated with the TME such as polarizing stimuli, acidic pH, and lactate can alter circadian rhythms in macrophages. While cyclic AMP (cAMP) has been reported to play a role in macrophage response to acidic pH, our results indicate pH-driven changes in circadian rhythms are not mediated solely by cAMP signaling. Remarkably, circadian disorder of TAMs was revealed by clock correlation distance analysis. Our data suggest that heterogeneity in circadian rhythms within the TAM population level may underlie this circadian disorder. Finally, we report that circadian regulation of macrophages suppresses tumor growth in a murine model of pancreatic cancer. Our work demonstrates a novel mechanism by which the TME influences macrophage biology through modulation of circadian rhythms.

Dual-Approach Co-expression Analysis Framework (D-CAF) Enables Identification of Novel Circadian Regulation From Multi-Omic Timeseries Data.

The circadian clock is a central driver of many biological and behavioral processes, regulating the levels of many genes and proteins, termed clock controlled genes and proteins (CCGs/CCPs), to impart biological timing at the molecular level. While transcriptomic and proteomic data has been analyzed to find potential CCGs and CCPs, multi-omic modeling of circadian data, which has the potential to enhance the understanding of circadian control of biological timing, remains relatively rare due to several methodological hurdles. To address this gap, a Dual-approach Co-expression Analysis Framework (D-CAF) was created to perform perturbation-robust co-expression analysis on time-series measurements of both transcripts and proteins. Applying this D-CAF framework to previously gathered transcriptomic and proteomic data from mouse macrophages gathered over circadian time, we identified small, highly significant clusters of oscillating transcripts and proteins in the unweighted similarity matrices and larger, less significant clusters of of oscillating transcripts and proteins using the weighted similarity network. Functional enrichment analysis of these clusters identified novel immunological response pathways that appear to be under circadian control. Overall, our findings suggest that D-CAF is a tool that can be used by the circadian community to integrate multi-omic circadian data to improve our understanding of the mechanisms of circadian regulation of molecular processes.

PER3 promoter hypermethylation correlates to the progression of pan-cancer

BackgroundMalignant cells exhibit reduced period circadian regulator 3 (PER3) expression. However, the underlying mechanisms of variations in PER3 expression in cancers and the specific function of PER3 in tumor progression remain poorly understood.ResultsWe explored multiple public databases, conducted bioinformatics analyses, and performed in vitro and in vivo experiments for validation. We found PER3 expression was decreased in most types of cancers, and PER3 downregulation was associated with a poor prognosis in 8 types of cancer. PER3 promoter methylation levels were increased in 11 types of cancer. Promoter hypermethylation (CpG islands [CGIs] cg12258811 and cg14204433) correlated with decreased PER3 expression in six cancers (breast invasive carcinoma, colon adenocarcinoma, head and neck squamous cell carcinoma, kidney renal papillary cell carcinoma [KIRP], lung adenocarcinoma [LUAD], and uterine corpus endometrial carcinoma). CGI cg12258811 hypermethylation was associated with reduced survival time and advanced cancer stages. Moreover, the bisulfite pyrosequencing assay confirmed CGI cg12258811 hypermethylation and its negative correlation with PER3 expression. In vitro and in vivo experiments demonstrated that PER3 inhibited KIRP and LUAD progression. Decitabine enhanced PER3 expression and inhibited KIRP cell functions by reducing promoter (cg12258811) methylation level.ConclusionsOur findings advanced the mechanistic understanding of variations in PER3 expression in cancers and confirmed the tumor-associated function of PER3 hypermethylation and downregulation.

Screening and identification of key biomarkers associated with endometriosis using bioinformatics and next-generation sequencing data analysis

BackgroundEndometriosis is a common cause of endometrial-type mucosa outside the uterine cavity with symptoms such as painful periods, chronic pelvic pain, pain with intercourse and infertility. However, the early diagnosis of endometriosis is still restricted. The purpose of this investigation is to identify and validate the key biomarkers of endometriosis.MethodsNext-generation sequencing dataset GSE243039 was obtained from the Gene Expression Omnibus database, and differentially expressed genes (DEGs) between endometriosis and normal control samples were identified. After screening of DEGs, gene ontology (GO) and REACTOME pathway enrichment analyses were performed. Furthermore, a protein–protein interaction (PPI) network was constructed and modules were analyzed using the Human Integrated Protein–Protein Interaction rEference database and Cytoscape software, and hub genes were identified. Subsequently, a network between miRNAs and hub genes, and network between TFs and hub genes were constructed using the miRNet and NetworkAnalyst tool, and possible key miRNAs and TFs were predicted. Finally, receiver operating characteristic curve analysis was used to validate the hub genes.ResultsA total of 958 DEGs, including 479 upregulated genes and 479 downregulated genes, were screened between endometriosis and normal control samples. GO and REACTOME pathway enrichment analyses of the 958 DEGs showed that they were mainly involved in multicellular organismal process, developmental process, signaling by GPCR and muscle contraction. Further analysis of the PPI network and modules identified 10 hub genes, including vcam1, snca, prkcb, adrb2, foxq1, mdfi, actbl2, prkd1, dapk1 and actc1. Possible target miRNAs, including hsa-mir-3143 and hsa-mir-2110, and target TFs, including tcf3 (transcription factor 3) and clock (clock circadian regulator), were predicted by constructing a miRNA-hub gene regulatory network and TF-hub gene regulatory network.ConclusionsThis investigation used bioinformatics techniques to explore the potential and novel biomarkers. These biomarkers might provide new ideas and methods for the early diagnosis, treatment and monitoring of endometriosis.