BackgroundVariation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be influenced by extrinsic factors which modulate this rate of stem cell division. To date, no molecular mitotic clock has been developed to approximate the number of stem cell divisions in a tissue of an individual and which is correlated with cancer risk.ResultsHere, we integrate mathematical modeling with prior biological knowledge to construct a DNA methylation-based age-correlative model which approximates a mitotic clock in both normal and cancer tissue. By focusing on promoter CpG sites that localize to Polycomb group target genes that are unmethylated in 11 different fetal tissue types, we show that increases in DNA methylation at these sites defines a tick rate which correlates with the estimated rate of stem cell division in normal tissues. Using matched DNA methylation and RNA-seq data, we further show that it correlates with an expression-based mitotic index in cancer tissue. We demonstrate that this mitotic-like clock is universally accelerated in cancer, including pre-cancerous lesions, and that it is also accelerated in normal epithelial cells exposed to a major carcinogen.ConclusionsUnlike other epigenetic and mutational clocks or the telomere clock, the epigenetic clock proposed here provides a concrete example of a mitotic-like clock which is universally accelerated in cancer and precancerous lesions.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1064-3) contains supplementary material, which is available to authorized users.

Background: Intra-sample cellular heterogeneity presents numerous challenges to the identification of biomarkers in large Epigenome-Wide Association Studies (EWAS). While a number of reference-based deconvolution algorithms have emerged, their potential remains underexplored and a comparative evaluation of these algorithms beyond tissues such as blood is still lacking. Results: Here we present a novel framework for reference-based inference, which leverages cell-type specific DNAse Hypersensitive Site (DHS) information from the NIH Epigenomics Roadmap to construct an improved reference DNA methylation database. We show that this leads to a marginal but statistically significant improvement of cell-count estimates in whole blood as well as in mixtures involving epithelial cell-types. Using this framework we compare a widely used state-of-the-art reference-based algorithm (called constrained projection) to two non-constrained approaches including CIBERSORT and a method based on robust partial correlations. We conclude that the widely-used constrained projection technique may not always be optimal. Instead, we find that the method based on robust partial correlations is generally more robust across a range of different tissue types and for realistic noise levels. We call the combined algorithm which uses DHS data and robust partial correlations for inference, EpiDISH (Epigenetic Dissection of Intra-Sample Heterogeneity). Finally, we demonstrate the added value of EpiDISH in an EWAS of smoking.

An outstanding challenge of Epigenome-Wide Association Studies (EWAS) performed in complex tissues is the identification of the specific cell-type(s) responsible for the observed differential DNA methylation. Here, we present a novel statistical algorithm, called CellDMC, which is able to identify not only differentially methylated positions, but also the specific cell-type(s) driving the differential methylation. We provide extensive validation of CellDMC on in-silico mixtures of DNA methylation data generated with different technologies, as well as on real mixtures from epigenome-wide-association and cancer epigenome studies. We demonstrate how CellDMC can achieve over 90% sensitivity and specificity in scenarios where current state-of-the-art methods fail to identify differential methylation. By applying CellDMC to a smoking EWAS performed in buccal swabs, we identify differentially methylated positions occurring in the epithelial compartment, which we validate in smoking-related lung cancer. CellDMC may help towards the identification of causal DNA methylation alterations in disease.

The degree and variation of IC contamination in complex epithelial tissues is substantial. We provide a valuable resource and tool for assessing the epithelial purity and IC contamination of samples and for identifying differential methylation in such complex tissues.

We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new analysis pipeline. To facilitate access to the data, we provide the and R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio.

A major challenge faced by epigenome-wide association studies (EWAS) is cell-type heterogeneity. As many EWAS have already demonstrated, adjusting for changes in cell-type composition can be critical when analyzing and interpreting findings from such studies. Because of their importance, a great number of different statistical algorithms, which adjust for cell-type composition, have been proposed. Some of the methods are 'reference based' in that they require a priori defined reference DNA methylation profiles of cell types that are present in the tissue of interest, while other algorithms are 'reference free.' At present, however, it is unclear how best to adjust for cell-type heterogeneity, as this may also largely depend on the type of tissue and phenotype being considered. Here, we provide a critical review of the major existing algorithms for correcting cell-type composition in the context of Illumina Infinium Methylation Beadarrays, with the aim of providing useful recommendations to the EWAS community.

It is well-established that the DNA methylation landscape of normal cells undergoes a gradual modification with age, termed as 'epigenetic drift'. Here, we review the current state of knowledge of epigenetic drift and its potential role in cancer etiology. We propose a new terminology to help distinguish the different components of epigenetic drift, with the aim of clarifying the role of the epigenetic clock, mitotic clocks and active changes, which accumulate in response to environmental disease risk factors. We further highlight the growing evidence that epigenetic changes associated with cancer risk factors may play an important causal role in cancer development, and that monitoring these molecular changes in normal cells may offer novel risk prediction and disease prevention strategies.

Abstract:Soil erosion is a severe problem hindering sustainable agriculture on the Loess Plateau of China. Plot experiments were conducted under the natural rainfall condition during 1995-1997 at Wangdongguo and Aobao catchments in this region to evaluate the effects of various land use, cropping systems, land slopes and rainfall on runoff and sediment losses, as well as the differences in catchment responses. The experiments included various surface conditions ranging from bare soil to vegetated surfaces (maize, wheat residue, Robinia pseudoacacia L., Amorpha fruticosa L., Stipa capillata L., buckwheat and Astragarus adsurgens L.). The measurements were carried out on hill slopes with different gradients (i.e. 0°to 36°). These plots varied from 20 to 60 m in length. Results indicated that runoff and erosion in this region occurred mainly during summer storms. Summer runoff and sediment losses under cropping and other vegetation were significantly less than those from ploughed bare soil (i.e. without crop/plant or crop residue). There were fewer runoff and sediment losses with increasing canopy cover. Land slope had a major effect on runoff and sediment losses and this effect was markedly larger in the tillage plots than that in the natural grass and forest plots, although this effect was very small when the maximum rainfall intensity was larger than 58Ð8 mm/h or smaller than 2Ð4 mm/h. Sediment losses per unit area rose with increasing slope length for the same land slope and same land use. The effect of slope length on sediment losses was stronger on a bare soil plot than on a crop/plant plot. The runoff volume and sediment losses were both closely related to rainfall volume and maximum intensity, while runoff coefficient was mainly controlled by maximum rainfall intensity. Hortonian overland flow is the dominant runoff process in the region. The differences in runoff volume, runoff coefficient and sediment losses between the catchments are mainly controlled by the maximum rainfall intensity and infiltration characteristics. The Aobao catchment yielded much larger runoff volume, runoff coefficient and sediment than the Wangdongguo catchment.