Genome-wide association analyses of chronotype in 697,828 individuals provides insights into circadian rhythms.

Being a morning person is a behavioural indicator of a person's underlying circadian rhythm. Using genome-wide data from 697,828 UK Biobank and 23andMe participants we increase the number of genetic loci associated with being a morning person from 24 to 351. Using data from 85,760 individuals with activity-monitor derived measures of sleep timing we find that the chronotype loci associate with sleep timing: the mean sleep timing of the 5% of individuals carrying the most morningness alleles is 25 min earlier than the 5% carrying the fewest. The loci are enriched for genes involved in circadian regulation, cAMP, glutamate and insulin signalling pathways, and those expressed in the retina, hindbrain, hypothalamus, and pituitary. Using Mendelian Randomisation, we show that being a morning person is causally associated with better mental health but does not affect BMI or risk of Type 2 diabetes. This study offers insights into circadian biology and its links to disease in humans.

Genome-Wide and Abdominal MRI Data Provide Evidence That a Genetically Determined Favorable Adiposity Phenotype Is Characterized by Lower Ectopic Liver Fat and Lower Risk of Type 2 Diabetes, Heart Disease, and Hypertension.

Recent genetic studies have identified alleles associated with opposite effects on adiposity and risk of type 2 diabetes. We aimed to identify more of these variants and test the hypothesis that such favorable adiposity alleles are associated with higher subcutaneous fat and lower ectopic fat. We combined MRI data with genome-wide association studies of body fat percentage (%) and metabolic traits. We report 14 alleles, including 7 newly characterized alleles, associated with higher adiposity but a favorable metabolic profile. Consistent with previous studies, individuals carrying more favorable adiposity alleles had higher body fat % and higher BMI but lower risk of type 2 diabetes, heart disease, and hypertension. These individuals also had higher subcutaneous fat but lower liver fat and a lower visceral-to-subcutaneous adipose tissue ratio. Individual alleles associated with higher body fat % but lower liver fat and lower risk of type 2 diabetes included those in PPARG, GRB14, and IRS1, whereas the allele in ANKRD55 was paradoxically associated with higher visceral fat but lower risk of type 2 diabetes. Most identified favorable adiposity alleles are associated with higher subcutaneous and lower liver fat, a mechanism consistent with the beneficial effects of storing excess triglycerides in metabolically low-risk depots.

Identifying pathways modulating sleep duration: from genomics to transcriptomics.

Recognizing that insights into the modulation of sleep duration can emerge by exploring the functional relationships among genes, we used this strategy to explore the genome-wide association results for this trait. We detected two major signalling pathways (ion channels and the ERBB signalling family of tyrosine kinases) that could be replicated across independent GWA studies meta-analyses. To investigate the significance of these pathways for sleep modulation, we performed transcriptome analyses of short sleeping flies' heads (knockdown for the ABCC9 gene homolog; dSur). We found significant alterations in gene-expression in the short sleeping knockdowns versus controls flies, which correspond to pathways associated with sleep duration in our human studies. Most notably, the expression of Rho and EGFR (members of the ERBB signalling pathway) genes was down- and up-regulated, respectively, consistently with the established role of these genes for sleep consolidation in Drosophila. Using a disease multifactorial interaction network, we showed that many of the genes of the pathways indicated to be relevant for sleep duration had functional evidence of their involvement with sleep regulation, circadian rhythms, insulin secretion, gluconeogenesis and lipogenesis.

Type-2 diabetes-associated variants with cross-trait relevance: Post-GWAs strategies for biological function interpretation.

Genome-wide association studies (GWAs) for type 2 diabetes (T2D) have been successful in identifying many loci with robust association signals. Nevertheless, there is a clear need for post-GWAs strategies to understand mechanism of action and clinical relevance of these variants. The association of several comorbidities with T2D suggests a common etiology for these phenotypes and complicates the management of the disease. In this study, we focused on the genetics underlying these relationships, using systems genomics to identify genetic variation associated with T2D and 12 other traits. GWAs studies summary statistics for pairwise comparisons were obtained for glycemic traits, obesity, coronary artery disease, and lipids from large consortia GWAs meta-analyses. We used a network medicine approach to leverage experimental information about the identified genes and variants with cross traits effects for biological function interpretation. We identified a set of 38 genetic variants with cross traits effects that point to a main network of genes that should be relevant for T2D and its comorbidities. We prioritized the T2D associated genes based on the number of traits they showed association with and the experimental evidence showing their relation to the disease etiology. In this study, we demonstrated how systems genomics and network medicine approaches can shed light into GWAs discoveries, translating findings into a more therapeutically relevant context.

Genome-Wide Association Analyses in 128,266 Individuals Identifies New Morningness and Sleep Duration Loci.

Disrupted circadian rhythms and reduced sleep duration are associated with several human diseases, particularly obesity and type 2 diabetes, but until recently, little was known about the genetic factors influencing these heritable traits. We performed genome-wide association studies of self-reported chronotype (morning/evening person) and self-reported sleep duration in 128,266 white British individuals from the UK Biobank study. Sixteen variants were associated with chronotype (P<5x10-8), including variants near the known circadian rhythm genes RGS16 (1.21 odds of morningness, 95% CI [1.15, 1.27], P = 3x10-12) and PER2 (1.09 odds of morningness, 95% CI [1.06, 1.12], P = 4x10-10). The PER2 signal has previously been associated with iris function. We sought replication using self-reported data from 89,283 23andMe participants; thirteen of the chronotype signals remained associated at P<5x10-8 on meta-analysis and eleven of these reached P<0.05 in the same direction in the 23andMe study. We also replicated 9 additional variants identified when the 23andMe study was used as a discovery GWAS of chronotype (all P<0.05 and meta-analysis P<5x10-8). For sleep duration, we replicated one known signal in PAX8 (2.6 minutes per allele, 95% CI [1.9, 3.2], P = 5.7x10-16) and identified and replicated two novel associations at VRK2 (2.0 minutes per allele, 95% CI [1.3, 2.7], P = 1.2x10-9; and 1.6 minutes per allele, 95% CI [1.1, 2.2], P = 7.6x10-9). Although we found genetic correlation between chronotype and BMI (rG = 0.056, P = 0.05); undersleeping and BMI (rG = 0.147, P = 1x10-5) and oversleeping and BMI (rG = 0.097, P = 0.04), Mendelian Randomisation analyses, with limited power, provided no consistent evidence of causal associations between BMI or type 2 diabetes and chronotype or sleep duration. Our study brings the total number of loci associated with chronotype to 22 and with sleep duration to three, and provides new insights into the biology of sleep and circadian rhythms in humans.

Genetic variants in RBFOX3 are associated with sleep latency.

Time to fall asleep (sleep latency) is a major determinant of sleep quality. Chronic, long sleep latency is a major characteristic of sleep-onset insomnia and/or delayed sleep phase syndrome. In this study we aimed to discover common polymorphisms that contribute to the genetics of sleep latency. We performed a meta-analysis of genome-wide association studies (GWAS) including 2 572 737 single nucleotide polymorphisms (SNPs) established in seven European cohorts including 4242 individuals. We found a cluster of three highly correlated variants (rs9900428, rs9907432 and rs7211029) in the RNA-binding protein fox-1 homolog 3 gene (RBFOX3) associated with sleep latency (P-values=5.77 × 10(-08), 6.59 × 10(-)(08) and 9.17 × 10(-)(08)). These SNPs were replicated in up to 12 independent populations including 30 377 individuals (P-values=1.5 × 10(-)(02), 7.0 × 10(-)(03) and 2.5 × 10(-)(03); combined meta-analysis P-values=5.5 × 10(-07), 5.4 × 10(-07) and 1.0 × 10(-07)). A functional prediction of RBFOX3 based on co-expression with other genes shows that this gene is predominantly expressed in brain (P-value=1.4 × 10(-316)) and the central nervous system (P-value=7.5 × 10(-)(321)). The predicted function of RBFOX3 based on co-expression analysis with other genes shows that this gene is significantly involved in the release cycle of neurotransmitters including gamma-aminobutyric acid and various monoamines (P-values<2.9 × 10(-11)) that are crucial in triggering the onset of sleep. To conclude, in this first large-scale GWAS of sleep latency we report a novel association of variants in RBFOX3 gene. Further, a functional prediction of RBFOX3 supports the involvement of RBFOX3 with sleep latency.

Chronotype and sleep duration: the influence of season of assessment.

Little is known about human entrainment under natural conditions, partly due to the complexity of human behavior, torn between biological and social time and influenced by zeitgebers (light-dark cycles) that are progressively "polluted" (and thereby weakened) by artificial light. In addition, data about seasonal variations in sleep parameters are scarce. We, therefore, investigated seasonal variation in cross-sectional assessments of sleep/wake times of 9765 subjects from four European populations (EGCUT = Estonian Genome Centre, University of Tartu in Estonia; KORA = Cooperative Health Research in the Region of Augsburg in Germany; KORCULA = The Korcula study in Croatia; and ORCADES = The Orkney Complex Disease Study in Scotland). We identified time-of-year dependencies for the distribution of chronotype (phase of entrainment assessed as the mid-sleep time point on free days adjusted for sleep deficit of workdays) in cohorts from Estonia (EGCUT) and Germany (KORA). Our results indicate that season (defined as daylight saving time - DST and standard zonetime periods - SZT) specifications of photoperiod influence the distribution of chronotype (adjusted for age and sex). Second, in the largest investigated sample, from Estonia (EGCUT; N = 5878), we could detect that seasonal variation in weekly average sleep duration was dependent on individual chronotype. Later chronotypes in this cohort showed significant variation in their average sleep duration across the year, especially during DST (1 h advance in social time from the end of March to end of October), while earlier chronotypes did not. Later chronotypes not only slept less during the DST period but the average chronotype of the population assessed during this period was earlier than during the SZT (local time for a respective time zone) period. More in detail, hierarchical multiple regression analyses showed that, beyond season of assessment (DST or SZT), social jetlag (SJl; the discrepancy between the mid sleep on free and work days - which varied with age and sex) contributed to a greater extent to the variation in sleep duration than chronotype (after taking into account factors that are known to influence sleep duration, i.e. age, sex and body mass index). Variation in chronotype was also dependent on age, sex, season of assessment and SJl (which is highly correlated with chronotype - SJl was larger among later chronotypes). In summary, subjective assessments of sleep/wake times are very reliable to assess internal time and sleep duration (e.g. reproducing sleep duration and timing tendencies related to age and sex across the investigated populations), but season of assessment should be regarded as a potential confounder. We identified in this study photoperiod (seasonal adaptation) and SJl as two main factors influencing seasonal variation in chronotype and sleep duration. In conclusion, season of assessment, sex and age have an effect on epidemiological variation in sleep duration, chronotype and SJl, and should be included in studies investigating associations between these phenotypes and health parameters, and on the development of optimal prevention strategies.

Light and the human circadian clock.

The circadian clock can only reliably fulfil its function if it is stably entrained. Most clocks use the light-dark cycle as environmental signal (zeitgeber) for this active synchronisation. How we think about clock function and entrainment has been strongly influenced by the early concepts of the field's pioneers, and the astonishing finding that circadian rhythms continue a self-sustained oscillation in constant conditions has become central to our understanding of entrainment.Here, we argue that we have to rethink these initial circadian dogmas to fully understand the circadian programme and how it entrains. Light is also the prominent zeitgeber for the human clock, as has been shown experimentally in the laboratory and in large-scale epidemiological studies in real life, and we hypothesise that social zeitgebers act through light entrainment via behavioural feedback loops (zeitnehmer). We show that human entrainment can be investigated in detail outside of the laboratory, by using the many 'experimental' conditions provided by the real world, such as daylight savings time, the 'forced synchrony' imposed by the introduction of time zones, or the fact that humans increasingly create their own light environment. The conditions of human entrainment have changed drastically over the past 100 years and have led to an increasing discrepancy between biological and social time (social jetlag). The increasing evidence that social jetlag has detrimental consequences for health suggests that shift-work is only an extreme form of circadian misalignment, and that the majority of the population in the industrialised world suffers from a similarly 'forced synchrony'.

Social jetlag and obesity.

Obesity has reached crisis proportions in industrialized societies. Many factors converge to yield increased body mass index (BMI). Among these is sleep duration. The circadian clock controls sleep timing through the process of entrainment. Chronotype describes individual differences in sleep timing, and it is determined by genetic background, age, sex, and environment (e.g., light exposure). Social jetlag quantifies the discrepancy that often arises between circadian and social clocks, which results in chronic sleep loss. The circadian clock also regulates energy homeostasis, and its disruption-as with social jetlag-may contribute to weight-related pathologies. Here, we report the results from a large-scale epidemiological study, showing that, beyond sleep duration, social jetlag is associated with increased BMI. Our results demonstrate that living "against the clock" may be a factor contributing to the epidemic of obesity. This is of key importance in pending discussions on the implementation of Daylight Saving Time and on work or school times, which all contribute to the amount of social jetlag accrued by an individual. Our data suggest that improving the correspondence between biological and social clocks will contribute to the management of obesity.

Morningness-eveningness, use of stimulants, and minor psychiatric disorders among undergraduate students.

Morningness-eveningness dimension in humans have been indicated to influence social behavior and individual health. The aim of the present study was to investigate the association of the morningness-eveningness dimension with behavioral and health aspects in a sample of undergraduate students. We assessed demographic data; the Pittsburgh Sleep Quality Index was used to evaluate sleep quality; the Morningness/Eveningness Questionnaire to determine morningness-eveningness, and the Self-Reporting Questionnaire to assess minor psychiatric disorders. A total of 372 students (66.7% females), on average 21.6 years old, participated in this study. Among them, 92.2% did not smoke, 58.9% engaged in physical activities, and 19.7% were night-shift workers. In regard to morningness-eveningness, 55.9% of the participants were intermediate between evening (39.5%) and morning (4.6%) types. Poor sleep quality (OR = 1.89), minor psychiatric disorders (OR = 1.92), and tobacco consumption (OR = 3.65) predominated among evening types. Evening types were predominantly males (OR = 1.72). This study suggests that evening types are more vulnerable to sleep and psychiatric disturbances, and tend to smoke more than morning types.

CLOCK gene variants associate with sleep duration in two independent populations.

BACKGROUND: Sleep is an active and complex behavior, yet it has two straightforward properties-timing and duration. Clock genes are associated with dysfunctional timing of sleep, mood, and obesity disorders, which are commonly associated with sleep duration. METHODS: Sleep duration was assessed in Central Europe, Estonia, and South Tyrol (n approximately 77,000) with the Munich ChronoType Questionnaire. It showed a Gaussian distribution in all investigated populations after averaging over a standard workweek and normalization according to age and gender. A follow-up, two-stage design, linkage disequilibrium-based association study was conducted with subjects from South Tyrol (discovery sample; n = 283) and with short (< 7 hours) and long (> 8.5 hours) sleepers from Estonia (confirmation sample; n = 1011). One hundred ninety-four single nucleotide polymorphism markers covering 19 candidate clock genes were genotyped in the discovery sample, and two of the best association signals (analyzed by a linear regression model) were investigated in the confirmation sample. RESULTS: Single and multi-marker associations were found within a CLOCK gene intronic region (rs12649507 and rs11932595). In a meta-analysis between South Tyrol and Estonia association signals, rs12649507 (p = .0087) remained significant. Significance persisted only for the multiple-marker association signal of the rs12649507/rs11932595 haplotype GGAA with long sleep (p = .0015). CONCLUSIONS: We report an association between variants of the human CLOCK gene and sleep duration in two independent populations. This adds another putative function for CLOCK besides its possible involvement in circadian timing, depression, obesity, and personality.

Possible influence of BCHE locus of butyrylcholinesterase on stature and body mass index.

Butyrylcholinesterase activity has been shown to be positively associated with weight and body mass index (BMI). The present study was carried out to search for an association between variants of the BCHE gene and weight, stature, and BMI on the basis of means and variances compared between nonusual variants and their respective usual controls. Individuals bearing the atypical mutation (N = 52) did not differ from their usual phenotype controls (N = 104) in these parameters. The BCHE*U/BCHE*K individuals (N = 222) presented a significantly higher BMI variance than their BCHE*U/BCHE*U controls (N = 222, F = 1.40, P = 0.012). This higher BMI variance does not seem to be an isolated effect of the K mutation, but appears to be the result of an interaction between the K allele and the usual allele, since no such difference in variance was detected between BCHE*K/BCHE*K individuals (N = 23) and their BCHE*U/BCHE*U (N = 23) controls. These data may suggest a relation between variability in the BCHE locus itself and BMI. Individuals with the BCHE UF phenotype (N = 45) showed a significantly higher mean stature (about 3 cm more; P = 0.02) than their controls with the usual phenotype (N = 135). A role in cell proliferation has been proposed for BCHE, and since growth depends on the number of mitoses, it is not unexpected that variants of this enzyme may influence body stature in different ways. This study reports the first data on the relation of BCHE alleles to anthropometric characters.

Expression of acetylcholinesterase (AChE) and aryl acylamidase (AAA) during early zebrafish embryogenesis.

In zebrafish, the onset of acetylcholinesterase (AChE) expression was detected by RT-PCR at 4 hpf (hours post-fertilization). The aryl acylamidase (AAA) associated with AChE, a serotonin sensitive activity with unknown physiological function, was significantly higher than the esterase activity on zebrafish embryos homogenates at 4-12 h development (test-t = 3.523; d.f. = 4). Remarkably, the ratio of AAA/AChE activity decreased 210-fold from 4 to 144 h development, indicating a distinct embryonic role of AAA during early embryogenesis. The AAA activity was sensitive to eserine and serotonin, ensuring its association with AChE. This is the first report of AAA activity on fish, establishing zebrafish as a model to study AAA on development.

Variability of the paraoxonase gene (PON1) in Euro- and Afro-Brazilians.

The human high-density lipoprotein-associated paraoxonase (EC 3.1.1.2; PON1) plays a role in the hydrolysis of organophosphorus compounds and against the oxidative damage of low-density lipoprotein. In the present study, variants of PON1 (55 and 192) were investigated by PCR-RFLP and PCR-SSCA in Euro- (N = 101) and Afro-Brazilians (N = 70). The PON1*55 and PON1*192 allele frequencies were significantly different in these ethnic groups (p < 0.05 and p < 0.001, respectively). The genotype frequencies for PON1*55 (LL, LM, and MM) in Euro- and Afro-Brazilians were 33, 56, and 11% and 47, 49, and 4%, respectively. The genotype frequencies for PON1*192 were significantly different in Euro- and Afro-Brazilians (QQ, QR, RR: 48, 42, and 10% and 21, 52, and 27%, respectively; p < 0.001). The haplotype frequency distributions were also significantly different in Euro- (LQ = 30.20%; LR = 30.69%; and MQ = 39.11%) and Afro-Brazilians (LQ = 24.97%; LR = 46.46%; MQ = 22.18%; and MR = 6.39%; p < 0.001). Linkage disequilibrium (D) in relation to the maximum expected value was higher in Euro- (100%) than in Afro-Brazilians (58%). We suggest that the high linkage disequilibrium in Caucasians and Asians characterized by the absence or very low frequency of the MR haplotype is mainly due to genetic drift and possibly also to natural selection favoring the PON1*192Q allele or a variant in linkage disequilibrium with it. This seems to be the first study on the PON1 variability at the DNA level in South American samples and one of the few studies on individuals of mixed African origin.