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Evaluating the impact of sleep on genome-wide methylation levels in college students

ABSTRACT: Approximately 4 Î¼g of DNA was isolated from blood of each of 16 subjects using the Qiagen DNEasy Blood and Tissue Kit. Of the 16 samples, 8 were from group 1 (CESD-H/TST-H; 5 female, 3 male) and 8 were from group 2 (CESD-H/TST-L; 5 female, 3 male). All DNA samples were confirmed to be of high purity (A260/280: 1.7-2.0). Pooled samples were prepared for each group by combining approximately 75 ng of DNA from each of the eight subjects. These two samples were submitted to the Yale Genomics Core for epigenome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip, which measures the level of methylation Î² (a value ranging from 0 to 1, where 0 represents a completely unmethylated site and 1 a completely methylated site) at each of the 485,577 CpG sites on the array. Illuminaâs GenomeStudio software was used to calculate the degree of differential methylation by group for each CpG site on the array, and FDR-adjusted p-values (Q-values) were calculated for each site in order to adjust for multiple comparisons. CESD=depression score; TST=sleep score Blood-derived genomic DNA was isolated from 16 subjects; 8 each with high and low total sleep scores, respectively. DNA was pooled by group and genome-wide methylation profiling was performed.

ORGANISM(S): Homo sapiens

SUBMITTER: Yong Zhu

PROVIDER: E-GEOD-80559 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Evaluating the impact of sleep on genome-wide methylation levels in college students

Project description:Approximately 4 μg of DNA was isolated from blood of each of 16 subjects using the Qiagen DNEasy Blood and Tissue Kit. Of the 16 samples, 8 were from group 1 (CESD-H/TST-H; 5 female, 3 male) and 8 were from group 2 (CESD-H/TST-L; 5 female, 3 male). All DNA samples were confirmed to be of high purity (A260/280: 1.7-2.0). Pooled samples were prepared for each group by combining approximately 75 ng of DNA from each of the eight subjects. These two samples were submitted to the Yale Genomics Core for epigenome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip, which measures the level of methylation β (a value ranging from 0 to 1, where 0 represents a completely unmethylated site and 1 a completely methylated site) at each of the 485,577 CpG sites on the array. Illumina’s GenomeStudio software was used to calculate the degree of differential methylation by group for each CpG site on the array, and FDR-adjusted p-values (Q-values) were calculated for each site in order to adjust for multiple comparisons. CESD=depression score; TST=sleep score

2016-08-01 | GSE80559 | GEO

Epigenome analysis of peripheral blood mononuclear cell (PBMC) samples from obstructive sleep apnea patients and healthy subjects

Project description:Genome wide DNA methylation profiling of obstructive sleep apnea (OSA) patients and healthy subjects. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in peripheral blood mononuclear cell samples. Samples included 8 normal subjects and 16 patients with obstructive sleep apnea syndrome.

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Epigenome analysis of peripheral blood mononuclear cell (PBMC) samples from obstructive sleep apnea patients and healthy subjects

2015-12-31 | E-GEOD-61463 | biostudies-arrayexpress

Epigenomics of Total Acute Sleep Deprivation in Relation to Genome-wide DNA Methylation Profiles and RNA Expression

Project description:Despite an established link between sleep deprivation and epigenetic processes in humans, it remains unclear to what extent sleep deprivation modulates DNA methylation. We performed a within subject randomized blinded study with 16 healthy subjects to examine the effect of one night of total acute sleep deprivation (TSD) on the genome wide methylation profile in blood compared to normal sleep. Genome-wide differences in methylation between both conditions were assessed by applying a paired regression model that corrected for monocyte subpopulations (neutrophil/leukocyte ratio). Additionally, the correlations between the methylation of genes detected to be modulated by TSD and gene expression were examined in a separate, publicly available cohort of ten healthy male donors (E-GEOD-49065). Sleep deprivation significantly affected the DNA methylation profile both independently and in dependency of shifts in monocyte composition. Our study detected differential methylation of 269 probes. Notably, one CpG site was located 69bp upstream of ING5, which has been shown to be differentially expressed following sleep deprivation. Gene set enrichment analysis detected the Notch and Wnt signaling pathways to be enriched among the differentially methylated genes. These results provide evidence that total acute sleep deprivation alters the methylation profile in healthy human subjects. This is, to our knowledge, the first study that systematically investigated the impact of total acute sleep deprivation on genome-wide DNA methylation profiles in blood and related the epigenomic findings to the expression data.

2016-06-30 | E-MTAB-4664 | biostudies-arrayexpress

Circulating microRNA as potential diagnostic biomarkers for sleep disorder

Project description:Next Generation Sequencing (NGS) was carried out on subjects who visited an oriental medicine clinic due to recurrent sleep disturbance, and 40 individuals (17 male and 23 female) were set as the sleep diorder (SD) group based on their scores on the sleep distrurbance questionnaire of Pittsburgh sleep quality index (PSQI). The control group consisted of 40 healthy individuals (20 males and females each), as assessed by both subjective diagnosis and test for metabolic syndrome factors.Ten individuals (five males and females each) from the SD and the control group, respectively, were allocated for NGS analysis.

2021-07-07 | GSE165041 | GEO

DNA methylation profiling in blood of OSA patients and controls

Project description:Obstructive sleep apnea (OSA) is associated with increased risk for cardiovascular morbidity and mortality. Epidemiological and animal models studies generate hypotheses for innovative strategies in OSA management by interfering intermediates mechanisms associated with cardiovascular complications. In this study, we interrogated DNA methylation profiles in 16 polysomnographically evaluated OSA patients (Apnea Hypopnea Index, AHI > 30) and 8 controls (AHI<5 events/h sleep). Blood samples were collected at initial visit (V1) and a year later (V2). OSA patients received Continuous Positive Air Pressure (CPAP) therapy with high adherence (> 4 hours/night). Control individuals did not receive CPAP therapy. Genomic DNA was treated with sodium bisulfite. Converted DNA was analyzed using Illumina’s Infinium Human Methylation 450 BeadChip assay. DNA methylation profiles enabled the prospective evaluation of inflammatory and epigenetics mechanism involved in cardiovascular complication of OSA patients compared with non OSA subjects, as well as the variation of epigenetic profiles in OSA patients after one year of high-adherence CPAP therapy.

2022-11-04 | GSE190164 | GEO

The phase-shifting effect of bright light exposure on circadian rhythmicity in the human transcriptome

Project description:Eleven healthy human subjects were enrolled in a 6-day simulated shift work protocol. Blood samples were collected during the two 24-hour measurement periods. Blood samples were collected every 4 hours during both measurement periods. Subjects entered the lab on Day 1. At the start of Day 2, the first 24-hour measurement period was started. Subjects slept according to their habitual sleep/wake schedule, followed by a 16-hour constant posture procedure. On days 3-6, the sleep period was delayed by 10 hours. Participants in the control group were exposed to dim light throughout the waking periods; participants in the bright group were exposed to bright light (~6,000lux) for 8 hours during the waking period. Following the third night on this schedule, subjects underwent another 24-hour measurement period. During both measurement periods, blood samples were collected and PBMCs were isolated. mRNA was extracted, labelled, and hybridized to microarrays.

2019-02-14 | GSE122725 | GEO

Whole-genome sequencing of normal Singaporean volunteers

Project description:Sleep is associated with various health outcomes. Despite their growing adoption, the potential for consumer wearables to contribute sleep metrics to sleep-related biomedical research remains largely uncharacterized. Here we analyzed sleep tracking data, along with questionnaire responses and multi-modal phenotypic data generated from 482 normal volunteers. First, we compared wearable-derived and self-reported sleep metrics, particularly total sleep time (TST) and sleep efficiency (SE). We then identified demographic, socioeconomic and lifestyle factors associated with wearable-derived TST. Among others, male gender (β = -15.539, 95% confidence interval [CI] = -26.245 - -4.832, p = 0.005), older age (β = -0.493, CI = -0.941 - -0.044, p = 0.032) and manual labor (β = -26.856, CI = -49.715 - -3.997, p = 0.022) were associated with reduced TST, whereas alcohol consumption (β = 19.247, CI = 8.008 - 30.486, p = 8.54x10-04) was associated with increased TST. Multi-modal phenotypic data analysis showed that wearable-derived TST and SE were associated with various cardiovascular disease risk markers such as body mass index (β = -0.006, CI = -0.00 - -0.000, p = 0.040) and waist circumference (β = 0.001, CI = -0.015-0.017, p = 0.893), whereas self-reported measures were not. We then showed that insufficient sleep was associated with premature telomere attrition, using telomere length estimated using whole-genome sequencing (β = 1.275, CI = 0.187 - 2.363, p = 0.023) and quantitative PCR (β = 0.001, CI = 8.318x10-05 - 0.001, p = 0.028). Our study highlights the potential for sleep metrics from consumer wearables to provide novel insights into data generated from population cohort studies.

| EGAS00001004007 | EGA

Epigenomic profiling in visceral white adipose tissue of offspring of mice exposed to late gestational sleep fragmentation

Project description:Background: Late gestational sleep fragmentation (LG-SF) is one of the major perturbations associated with sleep apnea and other sleep disorders during pregnancy. Objectives: To investigate the effects of late LG-SF on the epigenome of visceral white adipose tissue (VWAT) in the offspring. Methods: Time-pregnant mice were exposed to LG-SF or control sleep (LG-SC) conditions during the last 6 days of gestation. We performed large-scale DNA methylation analyses using MeDIP coupled to microarrays (MeDIP-chip) in VWAT of 24-week-old LG-SF and LG-SC offspring (n=8 mice/group). Univariate multiple-testing adjusted statistical analyses were applied to identify differentially methylated regions (DMRs) between the groups. DMRs were mapped to their corresponding genes, and tested for potential overlaps with biological pathways and gene networks. Results: We detected 2148 DMRs between LG-SF and LG-SC groups (p< 0.0001, MAT algorithm). A large proportion of the DMR-associated genes have reported functions that are altered in obesity and metabolic syndrome. Overrepresented pathways and gene networks were related to metabolic regulation and inflammatory response. Conclusions: Our findings show a major role for epigenomic regulation of pathways associated to metabolic processes and inflammatory response in VWAT. Furthermore, LG-SF-induced epigenetic alterations appear to increase the susceptibility to obesity and metabolic syndrome in the offspring. 16 mouse VWAT samples were analyzed by MeDIP coupled to microarray analysis: Offspring of mothers exposed to late-gestational sleep fragmentation (n=8, LG-SF group) and offspring of mothers mouse exposed to normal sleep conditions (n=8, LG-SC group)

2015-04-02 | E-GEOD-63208 | biostudies-arrayexpress

Multi-omic signatures of sarcoidosis and progression in bronchoalveolar lavage cells [miRNA]

Project description:We profiled DNA methylation, mRNA expression, and miRNA expression from bronchoalveolar lavage cells obtained from 64 sarcoidosis subjects and 16 healthy controls.

2024-08-08 | GSE263451 | GEO

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