It is not yet known whether DNA methylation levels can be used to accurately predict age across a broad spectrum of human tissues and cell types, nor whether the resulting age prediction is a biologically meaningful measure. I developed a multi-tissue predictor of age that allows one to estimate the DNA methylation age of most tissues and cell types. The predictor, which is freely available, was developed using 8,000 samples from 82 Illumina DNA methylation array datasets, encompassing 51 healthy tissues and cell types. I found that DNA methylation age has the following properties: first, it is close to zero for embryonic and induced pluripotent stem cells; second, it correlates with cell passage number; third, it gives rise to a highly heritable measure of age acceleration; and, fourth, it is applicable to chimpanzee tissues. Analysis of 6,000 cancer samples from 32 datasets showed that all of the considered 20 cancer types exhibit significant age acceleration, with an average of 36 years. Low age-acceleration of cancer tissue is associated with a high number of somatic mutations and TP53 mutations, while mutations in steroid receptors greatly accelerate DNA methylation age in breast cancer. Finally, I characterize the 353 CpG sites that together form an aging clock in terms of chromatin states and tissue variance. I propose that DNA methylation age measures the cumulative effect of an epigenetic maintenance system. This novel epigenetic clock can be used to address a host of questions in developmental biology, cancer and aging research.

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DNA methylation age of human tissues and cell types

Background: There has been a long-standing need in biomedical research for a method that quantifies the normally mixed composition of leukocytes beyond what is possible by simple histological or flow cytometric assessments. The latter is restricted by the labile nature of protein epitopes, requirements for cell processing, and timely cell analysis. In a diverse array of diseases and following numerous immune-toxic exposures, leukocyte composition will critically inform the underlying immuno-biology to most chronic medical conditions. Emerging research demonstrates that DNA methylation is responsible for cellular differentiation, and when measured in whole peripheral blood, serves to distinguish cancer cases from controls. Results: Here we present a method, similar to regression calibration, for inferring changes in the distribution of white blood cells between different subpopulations (e.g. cases and controls) using DNA methylation signatures, in combination with a previously obtained external validation set consisting of signatures from purified leukocyte samples. We validate the fundamental idea in a cell mixture reconstruction experiment, then demonstrate our method on DNA methylation data sets from several studies, including data from a Head and Neck Squamous Cell Carcinoma (HNSCC) study and an ovarian cancer study. Our method produces results consistent with prior biological findings, thereby validating the approach. Conclusions: Our method, in combination with an appropriate external validation set, promises new opportunities for large-scale immunological studies of both disease states and noxious exposures.

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DNA methylation arrays as surrogate measures of cell mixture distribution

Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates

Sexual Behavior in the Human Male

This survey of sexual practices in the United States has been combed by the media for items of interest to the public: monogamous sex is much more widespread in this country than has been thought; infidelity is less frequent than presumed; vaginal intercourse is the defining experience of heterosexual behavior; watching one's partner undress is stimulating to many people; married couples have more sex than single people (unmarried, cohabiting couples have the most sex of all); the majority of couples experience sex twice a week to several times a month; 2.8% of men identify themselves as homosexual and 1.4% of women do so, but a higher percentage of people consider a same-gender experience to have some appeal; 75% of men always experience orgasm compared with 28.6% of women, but more nearly equal numbers of men and women declare themselves satisfied with their sexual experiences. The book is, in fact, a

The Social Organization of Sexuality: Sexual Practices in the United States

From the moment of conception, we begin to age. A decay of cellular structures, gene regulation, and DNA sequence ages cells and organisms. DNA methylation patterns change with increasing age and contribute to age related disease. Here we identify 88 sites in or near 80 genes for which the degree of cytosine methylation is significantly correlated with age in saliva of 34 male identical twin pairs between 21 and 55 years of age. Furthermore, we validated sites in the promoters of three genes and replicated our results in a general population sample of 31 males and 29 females between 18 and 70 years of age. The methylation of three sites—in the promoters of the EDARADD, TOM1L1, and NPTX2 genes—is linear with age over a range of five decades. Using just two cytosines from these loci, we built a regression model that explained 73% of the variance in age, and is able to predict the age of an individual with an average accuracy of 5.2 years. In forensic science, such a model could estimate the age of a person, based on a biological sample alone. Furthermore, a measurement of relevant sites in the genome could be a tool in routine medical screening to predict the risk of age-related diseases and to tailor interventions based on the epigenetic bio-age instead of the chronological age.

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Epigenetic Predictor of Age

The genetics of sex differences in brain and behavior.

This is the first report of a full genome scan of sexual orientation in men. A sample of 456 individuals from 146 families with two or more gay brothers was genotyped with 403 microsatellite markers at 10-cM intervals. Given that previously reported evidence of maternal loading of transmission of sexual orientation could indicate epigenetic factors acting on autosomal genes, maximum likelihood estimations (mlod) scores were calculated separated for maternal, paternal, and combined transmission. The highest mlod score was 3.45 at a position near D7S798 in 7q36 with approximately equivalent maternal and paternal contributions. The second highest mlod score of 1.96 was located near D8S505 in 8p12, again with equal maternal and paternal contributions. A maternal origin effect was found near marker D10S217 in 10q26, with a mlod score of 1.81 for maternal meioses and no paternal contribution. We did not find linkage to Xq28 in the full sample, but given the previously reported evidence of linkage in this region, we conducted supplemental analyses to clarify these findings. First, we re-analyzed our previously reported data and found a mlod of 6.47. We then re-analyzed our current data, after limiting the sample to those families previously reported, and found a mlod of 1.99. These Xq28 findings are discussed in detail. The results of this first genome screen for normal variation in the behavioral trait of sexual orientation in males should encourage efforts to replicate these findings in new samples with denser linkage maps in the suggested regions.

/pdf/a-genomewide-scan-of-male-sexual-orientation-3izerj6mlu.pdf

A genomewide scan of male sexual orientation

Activation of latent HIV-1 expression by the potent anti-tumor promoter 12-deoxyphorbol 13-phenylacetate.

Sex determination is the commitment of an organism toward male or female development. Traditionally, in mammals, sex determination is considered equivalent to gonadal determination. Since the presence or the absence of the testes ultimately determines the phenotype of the external genitalia, sex determination is typically seen as equivalent to testis determination. But what exactly does sex determine? The endpoint of sex determination is almost invariably seen as the reproductive structures, which represent the most obvious phenotypic difference between the sexes. One could argue that the most striking differences between males and females are not the anatomy of the genitals, but the size of the gametes-considerably larger in females than males. In fact, there could be many different endpoints to sex determination, leading to differences between the sexes: brain sexual differences, behavioral differences, and susceptibility to disease. The central dogma of sexual differentiation, stemming initially from the gonad-transfer experiments of Alfred Jost, is that sexual dimorphisms of all somatic tissues are dependent on the testicular secretion of the developing fetus. In this chapter, we will take the example of sex differences in brain and behavior as an endpoint of sex determination. We will argue that genetic factors play a role in sexually dimorphic traits such as the number of dopaminergic cells in the mesencephalon, aggression, and sexual orientation, independently from gonadal hormones.

Sven Bocklandt

Papers

Epigenetic Predictor of Age

The genetics of sex differences in brain and behavior.

A genomewide scan of male sexual orientation

Activation of latent HIV-1 expression by the potent anti-tumor promoter 12-deoxyphorbol 13-phenylacetate.

Sex Differences in Brain and Behavior: Hormones Versus Genes