The speed and resolution at which we can scour the genome for DNA methylation changes has improved immeasurably in the last 10years and the advent of the Illumina 450K BeadChip has made ...epigenome-wide association studies (EWAS) a reality. The resulting datasets are conveniently formatted to allow easy alignment of significant hits to genes and genetic features, however; methods that parse significant hits into discreet differentially methylated regions (DMRs) remain a challenge to implement. In this paper we present details of a novel DMR caller, the Probe Lasso: a flexible window based approach that gathers neighbouring significant-signals to define clear DMR boundaries for subsequent in-depth analysis. The method is implemented in the R package ChAMP (Morris et al., 2014) and returns sets of DMRs according to user-tuned levels of probe filtering (e.g., inclusion of sex chromosomes, polymorphisms) and probe-lasso size distribution. Using a sub-sample of colon cancer- and healthy colon-samples from TCGA we show that Probe Lasso shifts DMR calling away from just probe-dense regions, and calls a range of DMR sizes ranging from tens-of-bases to tens-of-kilobases in scale. Moreover, using TCGA data we show that Probe Lasso leverages more information from the array and highlights a potential role of hypomethylated transcription factor binding motifs not discoverable using a basic, fixed-window approach.
The Illumina Infinium HumanMethylation450 BeadChip is a new platform for high-throughput DNA methylation analysis. Several methods for normalization and processing of these data have been published ...recently. Here we present an integrated analysis pipeline offering a choice of the most popular normalization methods while also introducing new methods for calling differentially methylated regions and detecting copy number aberrations.
ChAMP is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at bioconductor.org
DNA methylation is an epigenetic mark that has a crucial role in many biological processes. To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome-wide ...analysis should be embraced. This in turn requires a technique that balances accuracy, genome coverage, resolution and cost, yet is low in DNA input in order to minimize the drain on precious samples. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) fulfils these criteria, combining MeDIP with massively parallel DNA sequencing. Here we report an improved protocol using 100-fold less genomic DNA than that commonly used. We show comparable results for specificity (>97%) and enrichment (>100-fold) over a wide range of DNA concentrations (5,000-50 ng) and demonstrate the utility of the protocol for the generation of methylomes from rare bone marrow cells using 160-300 ng of starting DNA. The protocol described here, i.e., DNA extraction to generation of MeDIP-seq library, can be completed within 3-5 d.
Epigenome-wide association studies (EWAS) provide an alternative approach for studying human disease through consideration of non-genetic variants such as altered DNA methylation. To advance the ...complex interpretation of EWAS, we developed eFORGE (http://eforge.cs.ucl.ac.uk/), a new standalone and web-based tool for the analysis and interpretation of EWAS data. eFORGE determines the cell type-specific regulatory component of a set of EWAS-identified differentially methylated positions. This is achieved by detecting enrichment of overlap with DNase I hypersensitive sites across 454 samples (tissues, primary cell types, and cell lines) from the ENCODE, Roadmap Epigenomics, and BLUEPRINT projects. Application of eFORGE to 20 publicly available EWAS datasets identified disease-relevant cell types for several common diseases, a stem cell-like signature in cancer, and demonstrated the ability to detect cell-composition effects for EWAS performed on heterogeneous tissues. Our approach bridges the gap between large-scale epigenomics data and EWAS-derived target selection to yield insight into disease etiology.
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•Development of a tool for the analysis and interpretation of EWAS data•Identification of cell type-specific signals in heterogeneous EWAS data•Identification of cell-composition effects in EWAS•Compilation of eFORGE catalog of 20 published EWAS
Breeze et al. develop a tool for the analysis and interpretation of EWAS data. The eFORGE tool identifies cell type-specific, disease-relevant signals in heterogeneous EWAS data and can also identify cell-composition effects. Explore consortium data at the Cell Press IHEC webportal at http://www.cell.com/consortium/IHEC.
There are numerous approaches to decipher a whole genome DNA methylation profile (“methylome”), each varying in cost, throughput and resolution. The gold standard of these methods, whole genome ...bisulfite-sequencing (BS-seq), involves treatment of DNA with sodium bisulfite combined with subsequent high throughput sequencing. Using BS-seq, we generated a single-base-resolution methylome in human peripheral blood mononuclear cells (in press). This BS-seq map was then used as the reference methylome to compare two alternative sequencing-based methylome assays (performed on the same donor of PBMCs): methylated DNA immunoprecipitation (MeDIP-seq) and methyl-binding protein (MBD-seq). In our analysis, we found that MeDIP-seq and MBD-seq are complementary strategies, with MeDIP-seq more sensitive to highly methylated, high-CpG densities and MDB-seq more sensitive to highly methylated, moderate-CpG densities. Taking into account the size of a mammalian genome and the current expense of sequencing, we feel 3gigabases (Gbp) 45bp paired-end MeDIP-seq or MBD-seq uniquely mapped reads is the minimum requirement and cost-effective strategy for methylome pattern analysis.
DNA methylation is an epigenetic mark that is indispensable for mammalian development and occurs at cytosine residues throughout the genome (the "methylome"). Approximately 70 % of all CpG ...dinucleotides are affected by DNA methylation, which serve to "lock in" chromatin states and thus transcriptional programs. The systemic and pervasive occurrence of DNA methylation throughout the genome defines cellular identity and therefore requires genome-wide assays to fully appreciate and discern differential patterns of methylation that influence aspects of phenotypic plasticity including susceptibility to common complex disease.One method that permits methylome analysis is methylated DNA immunoprecipitation (MeDIP) combined with next-generation sequencing (MeDIP-seq). MeDIP uses an antibody raised against 5-methylcytosine to capture methylated fragments of DNA, which are subsequently sequenced to envisage the methylome landscape. The advantageous cost versus coverage balance of MeDIP-seq has made it the method of choice to replace or complement array-based methods for population epigenetic studies. Here we detail nano-MeDIP-seq, which allows methylome analysis using nanogram quantities of starting material.
Shorter telomere length and poor sleep are more prevalent at older ages, but their relationship is uncertain. This study explored associations between sleep duration and telomere length in a sample ...of healthy middle and early old age people.
Participants were 434 men and women aged 63.3 years on average drawn from the Whitehall II cohort study. Sleep duration was measured by self-report.
There was a linear association between sleep duration and leukocyte telomere length in men but not in women (P = 0.035). Men reporting shorter sleep duration had shorter telomeres, independently of age, body mass index, smoking, educational attainment, current employment, cynical hostility scores and depressive symptoms. Telomeres were on average 6% shorter in men sleeping 5 hours or fewer compared with those sleeping more than 7 hours per night.
This study adds to the growing literature relating sleep duration with biomarkers of aging, and suggests that shortening of telomeres might reflect mechanisms through which short sleep contributes to pathological conditions in older men.
Objective: This study investigated the etiology of autistic-like traits in the general population and the etiological overlap between the three aspects of the triad of impairments (social ...impairments, communication impairments, restricted repetitive behaviors and interests) that together define autism spectrum disorders. Method: Parents of 3,400 8-year-old twin pairs from the Twins Early Development Study completed the Childhood Asperger Syndrome Test, a screening instrument for autism spectrum symptoms in mainstream samples. Genetic model-fitting of categorical and continuous data is reported. Results: High heritability was found for extreme autistic-like traits (0.64-0.92 for various cutoffs) and autistic-like traits as measured on a continuum (0.78-0.81), with no significant shared environmental influences. All three subscales were highly heritable but showed low covariation. In the genetic modeling, distinct genetic influences were identified for the three components. Conclusions: These results suggest the triad of impairments that define autism spectrum disorders is heterogeneous genetically. Molecular genetic research examining the three components separately may identify different causal pathways for the three components. The analyses give no indication that different genetic processes affect extreme autistic impairments and autistic impairments as measured on a continuum, but this can only be directly tested once genes are identified. (Contains 2 figures and 3 tables.)
The putative cannabinoid receptor GPR55 has been shown to play a tumor‐promoting role in various cancers, and is involved in many physiological and pathological processes of the gastrointestinal (GI) ...tract. While the cannabinoid receptor 1 (CB1) has been reported to suppress intestinal tumor growth, the role of GPR55 in the development of GI cancers is unclear. We, therefore, aimed at elucidating the role of GPR55 in colorectal cancer (CRC), the third most common cancer worldwide. Using azoxymethane (AOM)‐ and dextran sulfate sodium (DSS)‐driven CRC mouse models, we found that GPR55 plays a tumor‐promoting role that involves alterations of leukocyte populations, i.e. myeloid‐derived suppressor cells and T lymphocytes, within the tumor tissues. Concomitantly, expression levels of COX‐2 and STAT3 were reduced in tumor tissue of GPR55 knockout mice, indicating reduced presence of tumor‐promoting factors. By employing the experimental CRC models to CB1 knockout and CB1/GPR55 double knockout mice, we can further show that GPR55 plays an opposing role to CB1. We report that GPR55 and CB1 mRNA expression are differentially regulated in the experimental models and in a cohort of 86 CRC patients. Epigenetic methylation of CNR1 and GPR55 was also differentially regulated in human CRC tissue compared to control samples. Collectively, our data suggest that GPR55 and CB1 play differential roles in colon carcinogenesis where the former seems to act as oncogene and the latter as tumor suppressor.
What's new?
The cannabinoid receptor GPR55 may boost colon tumor growth, new results show. Earlier work has established the receptor's role in various cancers, but this study is the first to investigate its relationship to colorectal cancer. These authors observed that mice lacking GPR55 had a much lighter tumor burden than wild type mice, as well as lower levels of COX‐2 and STAT3, both of which help drive tumor growth. Knocking out GPR55 also bumped the infiltration of CD4+ and CD8+ T cells in the tumor microenvironment, suggesting that GPR55 aids cancer by arranging a friendlier leukocyte population around the tumor.
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