Hypoxia-inducible factor-1α in myocardial infarction

Hypoxia-inducible factor 1 (HIF1) has a crucial function in the regulation of oxygen levels in mammalian cells, especially under hypoxic conditions. Its importance in cardiovascular diseases, particularly in cardiac ischemia, is because of its ability to alleviate cardiac dysfunction. The oxygen-responsive subunit, HIF1α, plays a crucial role in this process, as it has been shown to have cardioprotective effects in myocardial infarction through regulating the expression of genes affecting cellular survival, angiogenesis, and metabolism. Furthermore, HIF1α expression induced reperfusion in the ischemic skeletal muscle, and hypoxic skin wounds in diabetic animal models showed reduced HIF1α expression. Increased expression of HIF1α has been shown to reduce apoptosis and oxidative stress in cardiomyocytes during acute myocardial infarction. Genetic variations in HIF1α have also been found to correlate with altered responses to ischemic cardiovascular disease. In addition, a link has been established between the circadian rhythm and hypoxic molecular signaling pathways, with HIF1α functioning as an oxygen sensor and circadian genes such as period circadian regulator 2 responding to changes in light. This editorial analyzes the relationship between HIF1α and the circadian rhythm and highlights its significance in myocardial adaptation to hypoxia. Understanding the changes in molecular signaling pathways associated with diseases, specifically cardiovascular diseases, provides the opportunity for innovative therapeutic interventions, especially in low-oxygen environments such as myocardial infarction.

The role of circadian clock genes in colorectal carcinoma: Novel insights into regulatory mechanism and implications in clinical therapy

Colorectal cancer (CRC) is a lethal malignancy with limited treatment strategies. Accumulating evidence indicates that CRC tumorigenesis, progression and metastasis are intimately associated with circadian clock, an inherent 24-h cycle oscillation of biochemical, physiological functions in almost every eukaryote. In the present review, we summarize the altered expression level of circadian genes in CRC and the prognosis associated with gene abundance switch. We illustrate the function and potential mechanisms of circadian genes in CRC pathogenesis and progression. Moreover, circadian based-therapeutic strategies including chronotherapy, therapeutics targeting potential circadian components, and melatonin treatment in CRC are also highlighted.

Influence of sleep disruption on inflammatory bowel disease and changes in circadian rhythm genes

According to clinical investigations, sleep disruption (SD) can influence the immune system and cause inflammatory bowel disease (IBD). However, the detailed effects of sleep on IBD development and progression have not been clarified. Here, we used dextran sulfate sodium (DSS) to induce colitis in mice, and then interfered with SD (day-time 8:00 a.m. to 5:00 p.m.) to explore the influence of sleep on colitis by analyzing colon length, mouse body weight, disease activity index (DAI) score, pathology detection, and infiltration of inflammatory cells with LCA immunohistochemistry analysis. Next, we detected the mRNA levels of circadian genes and related inflammatory factors, including Bmal1, CLOCK, Cry1, Cry2, Per1, Per2, Timeless, Rev-erbα, TNF-α, IL-6, and IFN-γ. Additionally, we conducted a sleep survey in IBD patients and collected colon lesion sites to detect the mRNA levels of those eight circadian genes and three inflammatory factors. We found that SD promoted the body weight decrease, increased inflammation as shown with pathological staining of the DSS animal model, and increased expression of the clock gene Cry2 in DSS-induced colitis mice. In IBD patients with active disease, the mRNA level of circadian genes Bmal1, Cry1, Cry2, and Rev-erbα in inflammatory tissues decreased significantly compared with non-inflammatory tissues.

A role for the circadian transcription factor NPAS2 in the progressive loss of non-rapid eye movement sleep and increased arousal during fentanyl withdrawal in male mice

RATIONALE

Synthetic opioids like fentanyl are contributing to the rise in rates of opioid use disorder and drug overdose deaths. Sleep dysfunction and circadian rhythm disruption may worsen during opioid withdrawal and persist during abstinence. Severe and persistent sleep and circadian alterations are putative factors in opioid craving and relapse. However, very little is known about the impact of fentanyl on sleep architecture and sleep-wake cycles, particularly opioid withdrawal. Further, circadian rhythms regulate sleep-wake cycles, and the circadian transcription factor, neuronal PAS domain 2 (NPAS2) is involved in the modulation of sleep architecture and drug reward. Here, we investigate the role of NPAS2 in fentanyl-induced sleep alterations.

OBJECTIVES

To determine the effect of fentanyl administration and withdrawal on sleep architecture, and the role of NPAS2 as a factor in fentanyl-induced sleep changes.

METHODS

Electroencephalography (EEG) and electromyography (EMG) was used to measure non-rapid eye movement sleep (NREMS) and rapid eye movement sleep (REMS) at baseline and following acute and chronic fentanyl administration in wild-type and NPAS2-deficient male mice.

RESULTS

Acute and chronic administration of fentanyl led to increased wake and arousal in both wild-type and NPAS2-deficient mice, an effect that was more pronounced in NPAS2-deficient mice. Chronic fentanyl administration led to decreased NREMS, which persisted during withdrawal, progressively decreasing from day 1 to 4 of withdrawal. The impact of fentanyl on NREMS and arousal was more pronounced in NPAS2-deficient mice.

CONCLUSIONS

Chronic fentanyl disrupts NREMS, leading to a progressive loss of NREMS during subsequent days of withdrawal. Loss of NPAS2 exacerbates the impact of fentanyl on sleep and wake, revealing a potential role for the circadian transcription factor in opioid-induced sleep changes.

Investigating the genetic pathways of insomnia in Autism Spectrum Disorder

BACKGROUND

Sleep problems are common in children with autism spectrum disorder (autism). There is sparse research to date to examine whether insomnia in people with autism is related to autism genetics or insomnia genetics. Moreover, there is a lack of research examining whether circadian-rhythm related genes share potential pathways with autism.

AIMS

To address this research gap, we tested whether polygenic scores of insomnia or autism are related to risk of insomnia in people with autism, and whether the circadian genes are associated with insomnia in people with autism.

METHODS AND PROCEDURES

We tested these questions using the phenotypically and genotypically rich MSSNG dataset (N = 1049) as well as incorporating in the analyses data from the Vanderbilt University Biobank (BioVU) (N = 349).

OUTCOMES AND RESULTS

In our meta-analyzed sample, there was no evidence of associations between the polygenic scores (PGS) for insomnia and a clinical diagnosis of insomnia, or between the PGS of autism and insomnia. We also did not find evidence of a greater burden of rare and disruptive variation in the melatonin and circadian genes in individuals with autism and insomnia compared to individuals with autism without insomnia.

CONCLUSIONS AND IMPLICATIONS

Overall, we did not find evidence for strong effects of genetic scores influencing sleep in people with autism, however, we cannot rule out the possibility that smaller genetic effects may play a role in sleep problems. Our study indicated the need for a larger collection of data on sleep problems and sleep quality among people with autism.

A Pattern to Link Adenosine Signaling, Circadian System, and Potential Final Common Pathway in the Pathogenesis of Major Depressive Disorder

Several studies have reported separate roles of adenosine receptors and circadian clockwork in major depressive disorder. While less evidence exists for regulation of the circadian clock by adenosine signaling, a small number of studies have linked the adenosinergic system, the molecular circadian clock, and mood regulation. In this article, we review relevant advances and propose that adenosine receptor signaling, including canonical and other alternative downstream cellular pathways, regulates circadian gene expression, which in turn may underlie the pathogenesis of mood disorders. Moreover, we summarize the convergent point of these signaling pathways and put forward a pattern by which Homer1a expression, regulated by both cAMP-response element binding protein (CREB) and circadian clock genes, may be the final common pathogenetic mechanism in depression.

DNA methylation of circadian genes and markers of cardiometabolic risk in female hospital workers: An exploratory study

Night shift work has been linked to increased risk of cardiovascular disease (CVD); however, the underlying mechanisms remain unclear. A compelling yet understudied mechanism involves differential DNA methylation of circadian genes. To investigate the relevance of this mechanism, we conducted an exploratory cross-sectional study of 74 female hospital personnel (38 day workers, 36 night shift workers). Sociodemographic, lifestyle, and health characteristics as well as shift work status and history were determined through self-report. Fasting blood samples were collected to measure markers of cardiometabolic risk and DNA was extracted to measure DNA methylation of 1150 cytosine-guanine (CpG) sites across 22 circadian genes. Associations between methylation levels at individual CpG sites (β-values) and markers of cardiometabolic risk were analyzed while considering effect modification by shift work status. The false discovery rate was applied to account for multiple comparisons (q ≤ 0.20). Two CpG sites [cg06758649 (CRY1) and cg06899802 (CSNK1A1)] were differentially associated with waist circumference and body mass index by shift work status, and eight CpG sites [cg26103512 (CSNK1D), cg03941313 (CSNK1E), cg18217763 (CSNK1E), cg16682686 (DEC1), cg12061096 (RORA), cg10133825 (RORA), cg19652148 (RORA), and cg22904654 (RORA)] were differentially associated with LDL cholesterol concentration by shift work status (all q ≤ 0.20). Our findings suggest that the relationship between DNA methylation of circadian genes and cardiometabolic risk differs by day and night shift worker status, which may contribute to mechanisms of increased risk of CVD observed among night shift workers.

PredCRG: A computational method for recognition of plant circadian genes by employing support vector machine with Laplace kernel

BACKGROUND

Circadian rhythms regulate several physiological and developmental processes of plants. Hence, the identification of genes with the underlying circadian rhythmic features is pivotal. Though computational methods have been developed for the identification of circadian genes, all these methods are based on gene expression datasets. In other words, we failed to search any sequence-based model, and that motivated us to deploy the present computational method to identify the proteins encoded by the circadian genes.

RESULTS

Support vector machine (SVM) with seven kernels, i.e., linear, polynomial, radial, sigmoid, hyperbolic, Bessel and Laplace was utilized for prediction by employing compositional, transitional and physico-chemical features. Higher accuracy of 62.48% was achieved with the Laplace kernel, following the fivefold cross- validation approach. The developed model further secured 62.96% accuracy with an independent dataset. The SVM also outperformed other state-of-art machine learning algorithms, i.e., Random Forest, Bagging, AdaBoost, XGBoost and LASSO. We also performed proteome-wide identification of circadian proteins in two cereal crops namely, Oryza sativa and Sorghum bicolor, followed by the functional annotation of the predicted circadian proteins with Gene Ontology (GO) terms.

CONCLUSIONS

To the best of our knowledge, this is the first computational method to identify the circadian genes with the sequence data. Based on the proposed method, we have developed an R-package PredCRG ( https://cran.r-project.org/web/packages/PredCRG/index.html ) for the scientific community for proteome-wide identification of circadian genes. The present study supplements the existing computational methods as well as wet-lab experiments for the recognition of circadian genes.

Thyrotroph embryonic factor polymorphism predicts faster progression of Parkinson's disease in a longitudinal study

The thyrotroph embryonic factor gene is a circadian clock-controlled gene. The rs738499 polymorphism of this gene has been suggested to be associated with depression and sleep disturbance in Parkinson's disease in previous cross-sectional studies. We aimed to investigate whether this single nucleotide polymorphism is associated with the progression rates of various motor and non-motor symptoms in patients with Parkinson's disease. We recruited 186 patients with Parkinson's disease for a longitudinal study. Motor and non-motor symptoms were assessed at baseline and follow-up, and 170 Parkinson's disease patients completed the clinical evaluation twice with an average follow-up period of 3.3 ± 1.1 years. A stepwise linear regression model was used to validate factors associated with Parkinson's disease symptoms' annual progression rates. Faster annual worsening rates of sleep quality and Hoehn-Yahr stage were found in carriers with the homozygous dominant (TT). After adjustment for related clinical factors, the rs738499 polymorphism showed a contribution of 3.1% to the annual decline rate on the Parkinson's Disease Sleep Scale score and a contribution of 5.5% to the annual increase rate of the Hoehn-Yahr stage. Additionally, anxiety and axial symptoms predicted the progression of sleep disturbances and motor staging. The TT genotype of rs738499 might be a potential predictor of rapid deterioration in sleep quality and Hoehn-Yahr stage in patients with Parkinson's disease and may advance the understanding of the genetic contributions to Parkinson's disease.

Association analysis between chronic obstructive pulmonary disease and polymorphisms in circadian genes

Background

Circadian genes have been suggested to play an important role in lung pathology. However, it remains unknown whether polymorphisms of these genes are associated with chronic obstructive pulmonary disease (COPD). Here, we aimed to investigate the association of circadian genes polymorphisms with COPD in a case-control study of 477 COPD patient and 323 control Han Chinese persons.

Methods

Genotyping assays were carried out for nine single nucleotide polymorphisms (SNPs) from five circadian genes (PER3, CLOCK, RORB, BMAL1 and CRY2) that were previously identified in lung pathology. Age, sex, BMI and smoking status and comorbidities were recorded for all subjects.

Results

No significant association was found in all SNP sites in overall subjects and no significant difference was found in age, sex, smoking status stratification analysis.

Discussion

The findings of this investigation indicated the effect of circadian genes polymorphisms on COPD susceptibility may only be small and possibly dependent on the subject factors, such as age and sex.

Light-resetting impact on behavior and the central circadian clock in two vole species (genus: Lasiopodomys)

The behavioral circadian rhythms of subterranean rodents show intra- and interspecies diversity in terms of adaptation to dark underground environments, but the endogenous molecular mechanism of rhythm regulation in the suprachiasmatic nuclei (SCN) is stable to many species. In this study, we sought to determine the rhythms of behavior and central molecular regulatory mechanisms in the SCN of the subterranean Mandarin voles (Lasiopodomys mandarinus) compared with a related aboveground species, Brandt's voles (Lasiopodomys brandtii). Both species were reared under a 12 L:12 D cycle or in continuous darkness for 4 weeks. The pattern of wheel-running activity was similar in both species and had a periodicity of almost 24 h regardless of rearing conditions. However, the intensity of daily activity in Brandt's voles decreased markedly in darkness, while there was no significant difference in activity intensity in mandarin voles under different light regimes. In both vole species, all tested genes in the SCN showed significant time-dependent expression regardless of rearing conditions, and the expression levels of most genes did not differ significantly between different species and conditions. However, the peak phase shift in gene expression differed between the two species. In conclusion, behavioral patterns in mandarin and Brandt's voles were regulated by a stable molecular endogenous biological clock. The observed differences in activity intensity and phase shift suggest that different mechanisms regulate circadian rhythms in different living environments.

Microarray Data Normalization and Robust Detection of Rhythmic Features

Data derived from microarray technologies are generally subject to various sources of noise and accordingly the raw data are pre-processed before formally analysed. Data normalization is a key pre-processing step when dealing with microarray experiments, such as circadian gene-expressions, since it removes systematic variations across arrays. A wide variety of normalization methods are available in the literature. However, from our experience in the study of rhythmic expression patterns in oscillatory systems (e.g. cell-cycle, circadian clock), the choice of the normalization method may substantially impair the identification of rhythmic genes. Hence, the identification of a gene as rhythmic could be just as an artefact of how the data were normalized. Yet, gene rhythmicity detection is crucial in modern toxicological and pharmacological studies, thus a procedure to truly identify rhythmic genes that are robust to the choice of a normalization method is required.To perform the task of detecting rhythmic features, we propose a rhythmicity measure based on bootstrap methodology to robustly identify rhythmic genes in oscillatory systems. Although our methodology can be extended to any high-throughput experiment, in this chapter, we illustrate how to apply it to a publicly available circadian clock microarray gene-expression data and give full details (both statistical and computational) so that the methodology can be used in an easy way. We will show that the choice of normalization method has very little effect on the proposed methodology since the results derived from the bootstrap-based rhythmicity measure are highly rank correlated for any pair of normalization methods considered. This suggests, on the one hand, that the rhythmicity measure proposed is robust to the choice of the normalization method, and on the other hand, that gene rhythmicity detected using this measure is potentially not a mere artefact of the normalization method used. In this way the researcher using this methodology will be protected against the possible effect of different normalizations, as the conclusions obtained will not depend so strongly on them. Additionally, the described bootstrap methodology can also be employed as a tool to simulate gene-expression participating in an oscillatory system from a reference data set.

Circadian clock pathway genes associated with colorectal cancer risk and prognosis

Circadian clock genes influence biological processes and may be involved in tumorigenesis. We systematically evaluated genetic variants in the circadian clock pathway genes associated with colorectal cancer risk and survival. We evaluated the association of 119 single nucleotide polymorphisms (SNPs) in 27 circadian clock pathway genes with the risk of colorectal cancer in a case-control study (1150 cases and 1342 controls). The false discovery rate (FDR) method was applied to correct for multiple comparisons. Gene-based analysis was performed by the sequence kernel association test (SKAT). Cox proportional hazards regression was used to calculate the effects of SNPs on the overall survival of patients. We identified that compared to those with the G allele, individuals with the rs76436997 A allele in RORA had a significant 1.33-fold increased risk of colorectal cancer (P = 3.83 × 10^- 4). Specifically, the GA/AA genotypes were related to an enhanced risk of colorectal cancer compared with that associated with the GG genotype, which was more common in patients with well and moderately differentiated tumors and Dukes A/B stages. The SNP rs76436997 significantly increased the overall survival time of colorectal cancer patients (P = 0.044). Furthermore, RNA-seq data showed that the mRNA levels of RORA were significantly lower in colorectal tumors than the paired normal tissues. Gene-based analysis revealed a significant association between RORA and colorectal cancer risk. These findings highlight the important roles of genetic variations in circadian clock pathway genes play in colorectal cancer risk and suggest that RORA is potentially related to colorectal carcinogenesis.

Epigenetic Basis of Circadian Rhythm Disruption in Cancer

Self-sustained and synchronized to environmental stimuli, circadian clocks are under genetic and epigenetic regulation. Recent findings have greatly increased our understanding of epigenetic plasticity governed by circadian clock. Thus, the link between circadian clock and epigenetic machinery is reciprocal. Circadian clock can affect epigenetic features including genomic DNA methylation, noncoding RNA, mainly miRNA expression, and histone modifications resulted in their 24-h rhythms. Concomitantly, these epigenetic events can directly modulate cyclic system of transcription and translation of core circadian genes and indirectly clock output genes. Significant findings interlocking circadian clock, epigenetics, and cancer have been revealed, particularly in breast, colorectal, and blood cancers. Aberrant methylation of circadian gene promoter regions and miRNA expression affected circadian gene expression, together with 24-h expression oscillation pace have been frequently observed.

Identification of human circadian genes based on time course gene expression profiles by using a deep learning method

Circadian genes express periodically in an approximate 24-h period and the identification and study of these genes can provide deep understanding of the circadian control which plays significant roles in human health. Although many circadian gene identification algorithms have been developed, large numbers of false positives and low coverage are still major problems in this field. In this study we constructed a novel computational framework for circadian gene identification using deep neural networks (DNN) - a deep learning algorithm which can represent the raw form of data patterns without imposing assumptions on the expression distribution. Firstly, we transformed time-course gene expression data into categorical-state data to denote the changing trend of gene expression. Two distinct expression patterns emerged after clustering of the state data for circadian genes from our manually created learning dataset. DNN was then applied to discriminate the aperiodic genes and the two subtypes of periodic genes. In order to assess the performance of DNN, four commonly used machine learning methods including k-nearest neighbors, logistic regression, naïve Bayes, and support vector machines were used for comparison. The results show that the DNN model achieves the best balanced precision and recall. Next, we conducted large scale circadian gene detection using the trained DNN model for the remaining transcription profiles. Comparing with JTK_CYCLE and a study performed by Möller-Levet et al. (doi: https://doi.org/10.1073/pnas.1217154110), we identified 1132 novel periodic genes. Through the functional analysis of these novel circadian genes, we found that the GTPase superfamily exhibits distinct circadian expression patterns and may provide a molecular switch of circadian control of the functioning of the immune system in human blood. Our study provides novel insights into both the circadian gene identification field and the study of complex circadian-driven biological control. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.

Circadian gene methylation in rotating-shift nurses: a cross-sectional study

Investigating the methylation status of the circadian genes may contribute to a better understanding of the shift work-related circadian disruption in individuals exposed to artificial light at night. In the present study, we determined the methylation status of the circadian genes associated with a shift work pattern among nurses and midwives participating in a cross-sectional study in Lodz, Poland. Quantitative methylation polymerase chain reaction assays were used to assess promoter CpG methylation in PER1, PER2, PER3, CRY1, CRY2, BMAL1, CLOCK, and NPAS2 in genomic DNA from whole blood of 347 women having a rotating-shift work schedule and 363 women working days only. The percentage of methylated reference (PMR) was assessed using fluorescent probes for PER1, PER2, PER3, CRY1, and NPAS2, and the percentage of gene methylation, as the methylation index (MI), using two sets of primers for BMAL1, CLOCK, and CRY2. We tested the possible association between current and lifetime rotating night-shift work characteristics and circadian gene methylation by using proportional odds regression model with blood DNA methylation, categorized into tertiles, and adjusted for age, current smoking status, folate intake and blood collection time. The findings indicated that CpG methylation in PER2 promoter was significantly decreased (P < 0.004) among nurses and midwives currently working rotating shifts, as compared with day-working nurses and midwives. The lower percentage of PER2 methylation was associated with a higher monthly frequency of current night duties (2-7 night shifts, and eight or more night shifts per month) (P = 0.012) and was associated at borderline significance (P = 0.092) with the lifetime duration of shift work (>10 ≤ 20 years and >20 ≤ 43 years of rotating-shift work) among nurses and midwives (N = 710). Moreover, women with a longer lifetime duration of shift work presented a lower status of PER1 methylation (P = 0.040) than did the women with up to 10 years of rotating-shift work. Long lifetime duration of shift work (> 10 years) among current rotating night-shift workers (N =  347) was associated with BMAL1 hypomethylation (P = 0.013). Among eight of the investigated circadian genes, only PER1, PER2, and BMAL1 showed differential methylation attributable to the rotating-shift work of nurses and midwives. The findings on blood-based DNA methylation in the circadian genes may provide a better insight into the mechanistic principles underlying the possible health effects of night-shift work but these should be verified in further studies recruiting larger populations of shift workers.

Cryptochrome-1 Gene Expression is a Reliable Prognostic Indicator in Egyptian Patients with Chronic Lymphocytic Leukemia: A Prospective Cohort Study

Objective

Traditional prognostic factors have proved insufficient to account for heterogeneity in the clinical behavior of chronic lymphocytic leukemia (CLL). Cryptochrome-1 (CRY-1) is a circadian clock gene essential in maintaining the circadian rhythm and regulating cell proliferation. We evaluated CRY-1 gene expression in CLL and addressed its putative role as a prognostic indicator for the clinical course of CLL.

Materials and Methods

A total of 100 CLL patients at diagnosis were studied for CRY-1 gene expression by real-time reverse-transcription polymerase chain reaction and were followed for assessment of time to first treatment (TFT).

Results

CRY-1 was expressed in 94% of the CLL patients at diagnosis. The median CRY-1 relative gene expression level (0.006) stratified patients into high and low expression groups. Forty of 100 (40%) CLL patients showed high CRY-1, 54/100 (54%) showed low CRY-1, and 6/100 (6%) had undetectable CRY-1 gene expression. High CRY-1 gene expression was concordant with CD38⁺, Zap-70⁺, and double CD38⁺Zap-70⁺ expression; unfavorable/intermediate cytogenetics; unmutated immunoglobulin heavy-chain variable-region gene; and diffuse marrow infiltration. The high CRY-1 gene expression patient group exhibited shorter TFT than the patients with low CRY-1 gene expression. A Cox proportional hazard regression model identified CRY-1 gene expression to be independently predictive for TFT.

Conclusion

CRY-1 is differentially expressed among CLL patients, stratifying them into low-risk and high-risk groups. CRY-1 gene expression could constitute a reliable prognostic indicator for CLL progression, complementing the role of standard well-established prognostic factors. CRY-1 gene expression could be employed as a prognostic indicator for disease progression during the initial prognostic work-up and follow-up for CLL patients.

Circadian gene variants and breast cancer

The endogenous and self-sustained circadian rhythm generated and maintained in suprachiasmatic nucleus and peripheral tissues can coordinate various molecular, biochemical and physiological processes in living organisms resulting in the adaptation to environmental cues, e.g. light. Multifactorial breast cancer etiology also involves circadian gene alterations, especially among individuals exposed to light at night. Indeed, shift work that causes circadian disruption has been classified by the International Agency for Research on Cancer as a probable human carcinogen, group 2A. Thus it seems extremely important to recognize specific susceptible gene variants among around 20 candidate circadian genes that may be linked with breast cancer etiology. The aim of this review was to evaluate recent data investigating a putative link between circadian gene polymorphisms and breast cancer risk. We summarize fifteen epidemiological studies, including five studies on shift work that have indicated BMAL1, BMAL2, CLOCK, NPAS2, CRY1, CRY2, PER1, PER3 and TIMELESS as a candidate breast cancer risk variants.

Comparisons of chromosome Y-substituted mouse strains reveal that the male-specific chromosome modulates the effects of androgens on cardiac functions

Background

The C57BL/6J.Y^A/J mouse strain is a chromosome-substituted line where the original male-specific portion of chromosome Y (MSY) from C57BL/6J mice was substituted for that from A/J mice. In hearts from male C57BL/6J.Y^A/J and C57BL/6J mice, orchidectomy (ORX) affected in a strictly strain-specific fashion the expression a subset of genes showing enrichment for functional categories, including that of circadian rhythms and cardiac contractility. We further tested whether: (1) there were strain-specific differences in cardiac circadian rhythms; (2) strain-dependent differences in the effects of ORX on contractility genes translated into differences in cardiac functions; and (3) differential contractility responses occurred preferentially at times when circadian rhythms also showed strain-specific differences.

Methods

In hearts from the two above strains, we (1) profiled the expression levels of 15 circadian genes at 4-h intervals across a 24 h period; (2) tested the effects of either ORX or androgen replacement on expression of cardiac contractility genes, and that of ORX on myocardial functional reserve; and (3) verified whether the effects of MSY variants on cardiac contractility-related responses showed synchronicity with differences in circadian rhythms.

Results

Among the 15 tested circadian genes, a subset of them were affected by strain (and thus the genetic origin of MSY), which interacted with the amplitude of their peak of maximal expression at 2:00 PM. At that same time-point, ORX decreased (and androgen supplementation increased) the expression of three contractility-related genes, and decreased myocardial relaxation reserve in C57BL/6J.Y^A/J, but not in C57BL/6J mice. These effects were not detected at 10:00 AM, i.e., at another time-point when circadian genes showed no strain-specific differences.

Conclusions

The results indicate that in mice, androgens have activational effects on cardiac circadian rhythms, contractile gene expression, and myocardial functional reserve. All effects occurred preferentially at the same time of the day, but varied as a function of the genetic origin of MSY. Androgens may therefore be necessary but not sufficient to impart male-specific characteristics to some particular cardiac functions, with genetic material from MSY being one other necessary factor to fully define their range of actions.

Electronic supplementary material

The online version of this article (doi:10.1186/s13293-016-0116-4) contains supplementary material, which is available to authorized users.

[Seasons, circadian rhythms, sleep and suicidal behaviors vulnerability]

INTRODUCTION

Suicidal behaviors are common in the general population and are so a major public health problem. In order to improve suicide prevention and to reduce the mortality by suicide, it appears essential to better identify suicide risk factors. Seasonality, circadian rhythms and sleep abnormalities have been already associated with numerous psychiatric disorders. This review aimed to characterize the associations between seasonality, circadian rhythms, sleep and suicidal behaviors including suicide attempts and completed suicides.

METHODS

We conducted a literature search between 1973 and 2015 in PubMed databases using the following terms: ("suicide" OR "suicidality" OR "suicide attempts" OR "suicidal behavior") AND ("circadian rhythms" OR "seasons" OR "sleep").

RESULTS

Many studies confirm a specific seasonality for suicide with a higher peak of suicides in spring for both sex and a lower peak in autumn especially for women. This distribution seems to correlate with depressive symptoms (especially for the autumn peak), gender and different types of suicide. Regarding gender and type of suicide differences, males more commonly commit violent suicide with a higher rate of suicides in spring. Suicide behaviors appear to be influenced by climatic and biological factors like sunshine, daylight cycles, temperature, air pollutants, viruses, parasites and aeroallergens. Circadian variations exist in suicide rates depending on age with a morning peak for elder and an evening peak for youth. In addition, completed suicide peak in early morning whereas suicide attempts peak rather in later afternoon. Several biomarkers dysregulation like melatonin, serotonin and cortisol may be implicated in suicide circadian variations. Furthermore, specific sleep disorders like insomnia, nightmares and sleep deprivation are common risk factors of suicide and possibly independently of the presence of depressive symptoms. Finally, the efficacy of chronotherapeutics (such as luminotherapy, dark therapy, sleep deprivation and melatonin drugs) has been suggested in the reduction of suicidal behaviors.

CONCLUSION

The suicide seasonality is very well documented showing a main peak in spring and another one in autumn. A suicide circadian distribution also exists depending of the suicidal behavior intensity and of the age. Numerous sleep disorders are also suicide risk factors and can be treated with chronotherapeutics. A better identification of seasonality, circadian rhythms and sleep abnormalities in suicidal behaviors could allow a better prevention in suicidal attempts and a reduction in death by suicide.

Circadian gene variants influence sleep and the sleep electroencephalogram in humans

The sleep electroencephalogram (EEG) is highly heritable in humans and yet little is known about the genetic basis of inter-individual differences in sleep architecture. The aim of this study was to identify associations between candidate circadian gene variants and the polysomnogram, recorded under highly controlled laboratory conditions during a baseline, overnight, 8 h sleep opportunity. A candidate gene approach was employed to analyze single-nucleotide polymorphisms from five circadian-related genes in a two-phase analysis of 84 healthy young adults (28 F; 23.21 ± 2.97 years) of European ancestry. A common variant in Period2 (PER2) was associated with 20 min less slow-wave sleep (SWS) in carriers of the minor allele than in noncarriers, representing a 22% reduction in SWS duration. Moreover, spectral analysis in a subset of participants (n = 37) showed the same PER2 polymorphism was associated with reduced EEG power density in the low delta range (0.25-1.0 Hz) during non-REM sleep and lower slow-wave activity (0.75-4.5 Hz) in the early part of the sleep episode. These results indicate the involvement of PER2 in the homeostatic process of sleep. Additionally, a rare variant in Melatonin Receptor 1B was associated with longer REM sleep latency, with minor allele carriers exhibiting an average of 65 min (87%) longer latency from sleep onset to REM sleep, compared to noncarriers. These findings suggest that circadian-related genes can modulate sleep architecture and the sleep EEG, including specific parameters previously implicated in the homeostatic regulation of sleep.

Photoperiod regulates growth of male accessory glands through juvenile hormone signaling in the linden bug, Pyrrhocoris apterus

Adult reproductive diapause is characterized by lower behavioral activity, ceased reproduction and absence of juvenile hormone (JH). The role of JH receptor Methoprene-tolerant (Met) in female reproduction is well established; however, its function in male reproductive development and behavior is unclear. In the bean bug, Riptortus pedestris, circadian genes are essential for mediating photoperiodically-dependent growth of the male accessory glands (MAGs). The present study explores the role of circadian genes and JH receptor in male diapause in the linden bug, Pyrrhocoris apterus. These data indicate that circadian factors Clock, Cycle and Cry2 are responsible for photoperiod measurement, whereas Met and its partner protein Taiman participate in JH reception. Surprisingly, knockdown of the JH receptor neither lowered locomotor activity nor reduced mating behavior of males. These data suggest existence of a parallel, JH-independent or JH-upstream photoperiodic regulation of reproductive behavior.

Circadian Genes in Breast Cancer

Exploring the putative impact of circadian rhythms is a relatively novel approach to illuminating hormone-related female breast cancer etiology and prognosis. One of several proposed mechanisms underlying breast cancer risk among individuals exposed to light at night involves circadian gene alterations. Although in vitro and animal studies indicate a key role of circadian genes in breast tumor suppression, there is a paucity of data on the role of circadian genes in human breast cancer. This review summarizes recent findings of circadian gene expression and DNA methylation profile from human breast cancer studies in relation to hormonal status, clinicopathological features of tumors, and exposure to night shift work. The major findings from human studies indicate that expression of circadian genes is deregulated in breast cancer. Breast cancer etiology and prognosis-associated PERs, CRYs, CLOCK downregulation, and TIMELESS upregulation may be related to relevant gene methylation in tumor tissue. Alterations and desynchronization of molecular clock machinery found on genetic and epigenetic level were observed in more aggressive breast cancer tumors and those lacking estrogen receptors.

Nightshift work and genome-wide DNA methylation

The negative health effects of shift work, including carcinogenesis, may be mediated by changes in DNA methylation, particularly in the circadian genes. Using the Infinium HumanMethylation450 Bead Array (Illumina, San Diego, CA), we compared genome-wide methylation between 65 actively working dayshift workers and 59 actively working nightshift workers in the healthcare industry. A total of 473 800 loci, including 391 loci across the 12 core circadian genes, were analyzed to identify methylation markers associated with shift work status using linear regression models adjusted for gender, age, body mass index, race, smoking status and leukocyte cell profile as measured by flow cytometry. Analyses at the level of gene, CpG island and gene region were also conducted. To account for multiple comparisons, we controlled the false discovery rate (FDR ≤0.05). Significant differences between nightshift and dayshift workers were found at 16 135 of 473 800 loci, across 3769 of 20 164 genes, across 7173 of 22 721 CpG islands and across 5508 of 51 843 gene regions. For each significant loci, gene, CpG island or gene region, average methylation was consistently found to be decreased among nightshift workers compared to dayshift workers. Twenty-one loci located in the circadian genes were also found to be significantly hypomethylated among nightshift workers. The largest differences were observed for three loci located in the gene body of PER3. A total of nine significant loci were found in the CSNK1E gene, most of which were located in a CpG island and near the transcription start site of the gene. Methylation changes in these circadian genes may lead to altered expression of these genes which has been associated with cancer in previous studies. Gene ontology enrichment analysis revealed that among the significantly hypomethylated genes, processes related to host defense and immunity were represented. Our results indicate that the health effects of shift work may be mediated by hypomethylation of a wide variety of genes, including those related to circadian rhythms. While these findings need to be followed-up among a considerably expanded group of shift workers, the data generated by this study supports the need for future targeted research into the potential impacts of shift work on specific carcinogenic mechanisms.

The relationships between clinical characteristics, alcohol and psychotropic exposure, and circadian gene expression in human postmortem samples of affective disorder and control subjects

Circadian abnormalities may be related to mood disorders. Circadian gene expression was measured in postmortem brain tissue from individuals with affective disorders and controls. Relationships between circadian gene expression, clinical characteristics, and alcohol and psychotropic medication use were noted. Further study is warranted to characterize these relationships.