Project description:Sex difference had been implicated in pathophysiology and prognosis of common diseases, such as acute lymphoblastic leukemia and coronary heart disease. It is well known that the disease phenotype is shaped by the interaction between the environment, genome, and epigenome. The environmental and the genetic components were extensively studied in the past. Unlike the formers, the role of epigenetics has only been recently investigated. To date, little has been known about differences in epigenetic makeup between the two sexes. Here we present a genome-wide study of sex-specific differences in DNA methylation in healthy individuals. We compared the methylation status of ~26,000 CpGs in the promoter of ~14,000 genes between age-matched males (n=12) and females (n=12). We identified 19 CpGs in 18 genes to have significant sex-specific methylation differences. Our finding was validated by a recent publication of Liu et al. 2010 where they found similar results (ie. 11 of their 12 CpGs overlapped with ours) using the same microarray platform. However, with further investigation we showed that the probes with sex-specific methylation differences displayed cross-reactive targets on the sex chromosomes. This data indicates that autosomal sex-specific methylation detected in this study and by Lui et al, 2010 using the Illumina array platform, is the result of technical artifacts or non-specificity of those microarray probes. Overall, our findings suggest that there is no sex-specific DNA methylation difference in human beyond the sex chromosomes using the Illumina Methylation 27 microarray. Genome-wide DNA methylation data of sodium-bisulfite converted-genomic DNA obtained from whole blood lymphocytes of 12 healthy males compared to that of 12 age-matched healthy females
Project description:Sex differences in lifespan are widespread across animal taxa, but their causes remain unresolved. Alterations to the epigenome are hypothesized to contribute to vertebrate aging, and DNA methylation-based aging clocks allow for quantitative estimation of biological aging trajectories. Here, we investigate the influence of age, sex, and their interaction on genome-wide DNA methylation patterns in the brown anole (Anolis sagrei), a lizard with pronounced female-biased survival and longevity. We develop a series of age predictor models and find that, contrary to our predictions, rates of epigenetic aging were not slower in female lizards. However, methylation states at loci acquiring age-associated changes appear to be more “youthful” in young females, suggesting that female DNA methylomes are preemptively fortified in early life in opposition to the direction of age-related drift. Collectively, our findings provide insights into epigenetic aging in reptiles and suggest that early-life epigenetic profiles may be more informative than rates of change over time for predicting sex biases in longevity.
Project description:Sex difference had been implicated in pathophysiology and prognosis of common diseases, such as acute lymphoblastic leukemia and coronary heart disease. It is well known that the disease phenotype is shaped by the interaction between the environment, genome, and epigenome. The environmental and the genetic components were extensively studied in the past. Unlike the formers, the role of epigenetics has only been recently investigated. To date, little has been known about differences in epigenetic makeup between the two sexes. Here we present a genome-wide study of sex-specific differences in DNA methylation in healthy individuals. We compared the methylation status of ~26,000 CpGs in the promoter of ~14,000 genes between age-matched males (n=12) and females (n=12). We identified 19 CpGs in 18 genes to have significant sex-specific methylation differences. Our finding was validated by a recent publication of Liu et al. 2010 where they found similar results (ie. 11 of their 12 CpGs overlapped with ours) using the same microarray platform. However, with further investigation we showed that the probes with sex-specific methylation differences displayed cross-reactive targets on the sex chromosomes. This data indicates that autosomal sex-specific methylation detected in this study and by Lui et al, 2010 using the Illumina array platform, is the result of technical artifacts or non-specificity of those microarray probes. Overall, our findings suggest that there is no sex-specific DNA methylation difference in human beyond the sex chromosomes using the Illumina Methylation 27 microarray.
Project description:Human DNA methylation Beadchip v1.2 was used to profile n=310 whole blood samples. The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of different ethnic groups. Here we focus on subjects older than 35. Groups include Tsimane Indians, Hispanics, and Caucasian samples. To measure DNA methylation age, we used the epigenetic clock software described in Horvath S (n=2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928.
Project description:Human DNA methylation Beadchip v1.2 was used to profile n=46 whole blood samples. The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of different ethnic groups. Here we focus on subjects younger than 35 years old. Groups include Tsimane Indians and Caucasian samples. To measure DNA methylation age, we used the epigenetic clock software described in Horvath S (n=2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928.
Project description:In this epigenome-wide association study (EWAS), we examined the associations between PCDD, PCDF, and PCB exposures and DNA methylation. Whole blood DNA methylation was measured using Illumina EPIC arrays (n=292). We modeled lipid-adjusted toxic equivalencies (TEQs) for: ΣDioxins (sum of 28 PCDDs, PCDFs, cPCBs, and mPCBs), PCDDs, PCDFs, cPCBs, and mPCBs using robust multivariable linear regression adjusting for age, race, sex, smoking, total lipids, and estimated percentages of six blood cell types.
Project description:Genome wide DNA methylation assays was conducted using the Illumina Infinium MethylationEPIC BeadArray technology (Methyl850K chip) that allows genome-wide DNA methylation analysis of 866,836 CpG sites. We included baseline and 2-year follow-up samples from 25 persons with mild cognitive impairment (cases) and 20 persons with cognitively normal (controls). Sample was balanced by age and sex.
Project description:Genome-wide DNA methylation profiling of blood samples from people living with HIV HIV-1 infection impacts biological ageing, and epigenetic clocks highlight epigenetic age acceleration in people with HIV. Despite evidence indicating sex differences in clinical, immunological, and virological measures, females have been underrepresented in most HIV epigenetic studies. Hence, we generated a more representative epigenetic dataset to examine sex differences in epigenetic ageing and relationships to clinical phenotypes.