PMCC PMCC

Conseils de recherche
Les critères de recherche

Avancée
Résultats 1-25 (94)
 

Notices sélectionnées (0)
Aucune

Sélectionner un filtre

Revues
plus »
Année de publication
plus »
1.  Differentiation therapy for glioblastoma – too many obstacles? 
Molecular & Cellular Oncology  2015;3(2):e1124174.
ABSTRACT
The therapeutic potential of differentiation therapy for glioblastoma will depend on the robustness and stability of the differentiated state. We recently reported several obstacles to bone morphogenetic protein (BMP)-induced differentiation therapy. Improved understanding of the mechanisms that tumor cells use to escape differentiation commitment is urgently needed.
doi:10.1080/23723556.2015.1124174
PMCID: PMC4905420  PMID: 27308621
Astrocyte; BMP; differentiation; DNA methylation; epigenetics; Glioblastoma; neural stem cell; oligodendrocyte
2.  Increased DNA methylation variability in type 1 diabetes across three immune effector cell types 
Nature Communications  2016;7:13555.
The incidence of type 1 diabetes (T1D) has substantially increased over the past decade, suggesting a role for non-genetic factors such as epigenetic mechanisms in disease development. Here we present an epigenome-wide association study across 406,365 CpGs in 52 monozygotic twin pairs discordant for T1D in three immune effector cell types. We observe a substantial enrichment of differentially variable CpG positions (DVPs) in T1D twins when compared with their healthy co-twins and when compared with healthy, unrelated individuals. These T1D-associated DVPs are found to be temporally stable and enriched at gene regulatory elements. Integration with cell type-specific gene regulatory circuits highlight pathways involved in immune cell metabolism and the cell cycle, including mTOR signalling. Evidence from cord blood of newborns who progress to overt T1D suggests that the DVPs likely emerge after birth. Our findings, based on 772 methylomes, implicate epigenetic changes that could contribute to disease pathogenesis in T1D.
The incidence of type 1 diabetes is increasing, potentially implicating non-genetic factors. Here the authors conduct an epigenome-wide association study in disease-discordant twins and find increased DNA methylation variability at genes associated with immune cell metabolism and the cell cycle.
doi:10.1038/ncomms13555
PMCID: PMC5141286  PMID: 27898055
3.  Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells 
Chen, Lu | Ge, Bing | Casale, Francesco Paolo | Vasquez, Louella | Kwan, Tony | Garrido-Martín, Diego | Watt, Stephen | Yan, Ying | Kundu, Kousik | Ecker, Simone | Datta, Avik | Richardson, David | Burden, Frances | Mead, Daniel | Mann, Alice L. | Fernandez, Jose Maria | Rowlston, Sophia | Wilder, Steven P. | Farrow, Samantha | Shao, Xiaojian | Lambourne, John J. | Redensek, Adriana | Albers, Cornelis A. | Amstislavskiy, Vyacheslav | Ashford, Sofie | Berentsen, Kim | Bomba, Lorenzo | Bourque, Guillaume | Bujold, David | Busche, Stephan | Caron, Maxime | Chen, Shu-Huang | Cheung, Warren | Delaneau, Oliver | Dermitzakis, Emmanouil T. | Elding, Heather | Colgiu, Irina | Bagger, Frederik O. | Flicek, Paul | Habibi, Ehsan | Iotchkova, Valentina | Janssen-Megens, Eva | Kim, Bowon | Lehrach, Hans | Lowy, Ernesto | Mandoli, Amit | Matarese, Filomena | Maurano, Matthew T. | Morris, John A. | Pancaldi, Vera | Pourfarzad, Farzin | Rehnstrom, Karola | Rendon, Augusto | Risch, Thomas | Sharifi, Nilofar | Simon, Marie-Michelle | Sultan, Marc | Valencia, Alfonso | Walter, Klaudia | Wang, Shuang-Yin | Frontini, Mattia | Antonarakis, Stylianos E. | Clarke, Laura | Yaspo, Marie-Laure | Beck, Stephan | Guigo, Roderic | Rico, Daniel | Martens, Joost H.A. | Ouwehand, Willem H. | Kuijpers, Taco W. | Paul, Dirk S. | Stunnenberg, Hendrik G. | Stegle, Oliver | Downes, Kate | Pastinen, Tomi | Soranzo, Nicole
Cell  2016;167(5):1398-1414.e24.
Summary
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14+ monocytes, CD16+ neutrophils, and naive CD4+ T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk.
Graphical Abstract
Highlights
•Genome, transcriptome, and epigenome reference panel in three human immune cell types•Identified 4,418 genes associated with epigenetic changes independent of genetics•Described genome-epigenome coordination defining cell-type-specific regulatory events•Functionally mapped disease mechanisms at 345 unique autoimmune disease loci
As part of the IHEC consortium, this study integrates genetic, epigenetic, and transcriptomic profiling in three immune cell types from nearly 200 people to characterize the distinct and cooperative contributions of diverse genomic inputs to transcriptional variation. Explore the Cell Press IHEC web portal at http://www.cell.com/consortium/IHEC.
doi:10.1016/j.cell.2016.10.026
PMCID: PMC5119954  PMID: 27863251
immune; monocyte; neutrophil; t-cell; EWAS; histone modification; DNA methylation; transription; allele specific; QTL
4.  eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data 
Cell Reports  2016;17(8):2137-2150.
Summary
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.
Graphical Abstract
Highlights
•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.
doi:10.1016/j.celrep.2016.10.059
PMCID: PMC5120369  PMID: 27851974
bioinformatics; epigenetics; epigenome-wide association study; histone marks; DNase I hypersensitive sites
5.  CORALINA: a universal method for the generation of gRNA libraries for CRISPR-based screening 
BMC Genomics  2016;17:917.
Background
The bacterial CRISPR system is fast becoming the most popular genetic and epigenetic engineering tool due to its universal applicability and adaptability. The desire to deploy CRISPR-based methods in a large variety of species and contexts has created an urgent need for the development of easy, time- and cost-effective methods enabling large-scale screening approaches.
Results
Here we describe CORALINA (comprehensive gRNA library generation through controlled nuclease activity), a method for the generation of comprehensive gRNA libraries for CRISPR-based screens. CORALINA gRNA libraries can be derived from any source of DNA without the need of complex oligonucleotide synthesis. We show the utility of CORALINA for human and mouse genomic DNA, its reproducibility in covering the most relevant genomic features including regulatory, coding and non-coding sequences and confirm the functionality of CORALINA generated gRNAs.
Conclusions
The simplicity and cost-effectiveness make CORALINA suitable for any experimental system. The unprecedented sequence complexities obtainable with CORALINA libraries are a necessary pre-requisite for less biased large scale genomic and epigenomic screens.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-016-3268-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-016-3268-z
PMCID: PMC5109649  PMID: 27842490
gRNA library; Genome-wide; Cas9; Genetic engineering; Epigenetic engineering; Elongated protospacer; Epigenome editing
6.  Correlation of an epigenetic mitotic clock with cancer risk 
Genome Biology  2016;17:205.
Background
Variation 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.
Results
Here, 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.
Conclusions
Unlike 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 material
The online version of this article (doi:10.1186/s13059-016-1064-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-016-1064-3
PMCID: PMC5046977  PMID: 27716309
DNA methylation; Epigenetic clock; Cancer; Mitotic; Stem cells; Ageing
7.  The multi-omic landscape of transcription factor inactivation in cancer 
Genome Medicine  2016;8(1):89.
Background
Hypermethylation of transcription factor promoters bivalently marked in stem cells is a cancer hallmark. However, the biological significance of this observation for carcinogenesis is unclear given that most of these transcription factors are not expressed in any given normal tissue.
Methods
We analysed the dynamics of gene expression between human embryonic stem cells, fetal and adult normal tissue, as well as six different matching cancer types. In addition, we performed an integrative multi-omic analysis of matched DNA methylation, copy number, mutational and transcriptomic data for these six cancer types.
Results
We here demonstrate that bivalently and PRC2 marked transcription factors highly expressed in a normal tissue are more likely to be silenced in the corresponding tumour type compared with non-housekeeping genes that are also highly expressed in the same normal tissue. Integrative multi-omic analysis of matched DNA methylation, copy number, mutational and transcriptomic data for six different matching cancer types reveals that in-cis promoter hypermethylation, and not in-cis genomic loss or genetic mutation, emerges as the predominant mechanism associated with silencing of these transcription factors in cancer. However, we also observe that some silenced bivalently/PRC2 marked transcription factors are more prone to copy number loss than promoter hypermethylation, pointing towards distinct, mutually exclusive inactivation patterns.
Conclusions
These data provide statistical evidence that inactivation of cell fate-specifying transcription factors in cancer is an important step in carcinogenesis and that it occurs predominantly through a mechanism associated with promoter hypermethylation.
Electronic supplementary material
The online version of this article (doi:10.1186/s13073-016-0342-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s13073-016-0342-8
PMCID: PMC4997779  PMID: 27562343
8.  Information recovery from low coverage whole-genome bisulfite sequencing 
Nature Communications  2016;7:11306.
The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important because even at the recommend 30X coverage for reference methylomes, up to 50% of high-resolution features such as differentially methylated positions (DMPs) cannot be called with current methods as determined by saturation analysis. To address this limitation, we have developed a tool that dynamically segments WGBS methylomes into blocks of comethylation (COMETs) from which lost information can be recovered in the form of differentially methylated COMETs (DMCs). Using this tool, we demonstrate recovery of ∼30% of the lost DMP information content as DMCs even at very low (5X) coverage. This constitutes twice the amount that can be recovered using an existing method based on differentially methylated regions (DMRs). In addition, we explored the relationship between COMETs and haplotypes in lymphoblastoid cell lines of African and European origin. Using best fit analysis, we show COMETs to be correlated in a population-specific manner, suggesting that this type of dynamic segmentation may be useful for integrated (epi)genome-wide association studies in the future.
Here, Libertini and colleagues devise a computation tool that can analyze whole-genome bisulfite sequencing (WGBS) data to recover of ∼30% of the lost differential methylation position information. They use COMETgazer and COMETvintage to analyze 13 diffferent methylome data to demonstrate their performance.
doi:10.1038/ncomms11306
PMCID: PMC4931220  PMID: 27346250
9.  Epigenetic reprogramming of fallopian tube fimbriae in BRCA mutation carriers defines early ovarian cancer evolution 
Nature Communications  2016;7:11620.
The exact timing and contribution of epigenetic reprogramming to carcinogenesis are unclear. Women harbouring BRCA1/2 mutations demonstrate a 30–40-fold increased risk of high-grade serous extra-uterine Müllerian cancers (HGSEMC), otherwise referred to as ‘ovarian carcinomas', which frequently develop from fimbrial cells but not from the proximal portion of the fallopian tube. Here we compare the DNA methylome of the fimbrial and proximal ends of the fallopian tube in BRCA1/2 mutation carriers and non-carriers. We show that the number of CpGs displaying significant differences in methylation levels between fimbrial and proximal fallopian tube segments are threefold higher in BRCA mutation carriers than in controls, correlating with overexpression of activation-induced deaminase in their fimbrial epithelium. The differentially methylated CpGs accurately discriminate HGSEMCs from non-serous subtypes. Epigenetic reprogramming is an early pre-malignant event integral to BRCA1/2 mutation-driven carcinogenesis. Our findings may provide a basis for cancer-preventative strategies.
Women with germline variants in BRCA genes are predisposed to ovarian cancer. In this study, the authors demonstrate that fimbrial tissue from the ovary, the site of ovarian cancer, in BRCA mutant carriers contains marked DNA methylation changes compared with the proximal region of the ovary.
doi:10.1038/ncomms11620
PMCID: PMC4890182  PMID: 27216078
10.  Genetic and environmental influences interact with age and sex in shaping the human methylome 
Nature Communications  2016;7:11115.
The methylome is subject to genetic and environmental effects. Their impact may depend on sex and age, resulting in sex- and age-related physiological variation and disease susceptibility. Here we estimate the total heritability of DNA methylation levels in whole blood and estimate the variance explained by common single nucleotide polymorphisms at 411,169 sites in 2,603 individuals from twin families, to establish a catalogue of between-individual variation in DNA methylation. Heritability estimates vary across the genome (mean=19%) and interaction analyses reveal thousands of sites with sex-specific heritability as well as sites where the environmental variance increases with age. Integration with previously published data illustrates the impact of genome and environment across the lifespan at methylation sites associated with metabolic traits, smoking and ageing. These findings demonstrate that our catalogue holds valuable information on locations in the genome where methylation variation between people may reflect disease-relevant environmental exposures or genetic variation.
Differential impact of genetic and environmental influences on DNA methylation may result in sex- and age-related physiological variation and disease susceptibility. By analysing DNA methylome of 2,603 individuals from twin families, here, the authors establish a catalogue of between-individual variation in DNA methylation.
doi:10.1038/ncomms11115
PMCID: PMC4820961  PMID: 27051996
11.  Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer 
Background
There is growing evidence that DNA methylation alterations contribute to carcinogenesis. While cancer tissue exhibits widespread DNA methylation changes, the proportion of tissue-specific versus tissue-independent DNA methylation alterations in cancer is unclear. In addition, it is unknown which factors determine the patterns of aberrant DNA methylation in cancer.
Results
Using HumanMethylation450 BeadChips (450k), we here analyze genome-wide DNA methylation patterns of ten types of fetal tissue, in addition to matched normal-cancer data for corresponding tissue types, encompassing over 3000 samples. We demonstrate that the level of aberrant cancer DNA methylation in gene promoters and gene bodies is highly correlated between cancer types. We estimate that up to 60 % of the DNA methylation variation in a cancer genome of a given tissue type is explained by the corresponding variation in a cancer genome of another type, implying that much of the cancer DNA methylation landscape is tissue independent. We further show that histone marks in normal cells are better predictors of aberrant cancer DNA methylation than the corresponding signals in human embryonic stem cells. We build predictors of cancer DNA methylation patterns and show that although inclusion of three histone marks (H3K4me3, H3K27me3 and H3K36me3) improves model accuracy, the bivalent marks are the most predictive. Finally, we show that chromatin accessibility of gene promoters in normal tissue dictates the promoter’s propensity to acquire aberrant DNA methylation in cancer in so far as it determines its level of DNA methylation in normal tissue.
Conclusions
Our data show that a considerable fraction of the aberrant cancer DNA methylation landscape results from a mechanism that is largely tissue specific. Histone marks as specified in the normal cell of origin provide highly predictive models of aberrant cancer DNA methylation and outperform those derived from the same marks in hESCs.
Electronic supplementary material
The online version of this article (doi:10.1186/s13072-016-0058-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s13072-016-0058-4
PMCID: PMC4782576  PMID: 26958079
DNA methylation; Cancer; Histone; Bivalency; Chromatin
12.  Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells 
Nature Communications  2016;7:10458.
Non-CG methylation is an unexplored epigenetic hallmark of pluripotent stem cells. Here we report that a reduction in non-CG methylation is associated with impaired differentiation capacity into endodermal lineages. Genome-wide analysis of 2,670 non-CG sites in a discovery cohort of 25 phenotyped human induced pluripotent stem cell (hiPSC) lines revealed unidirectional loss (Δβ=13%, P<7.4 × 10−4) of non-CG methylation that correctly identifies endodermal differentiation capacity in 23 out of 25 (92%) hiPSC lines. Translation into a simplified assay of only nine non-CG sites maintains predictive power in the discovery cohort (Δβ=23%, P<9.1 × 10−6) and correctly identifies endodermal differentiation capacity in nine out of ten pluripotent stem cell lines in an independent replication cohort consisting of hiPSCs reprogrammed from different cell types and different delivery systems, as well as human embryonic stem cell (hESC) lines. This finding infers non-CG methylation at these sites as a biomarker when assessing endodermal differentiation capacity as a readout.
The methylation of non-CpG residues is a poorly understood marker of pluripotent cells, gradually lost as cells differentiate. Here the authors show non-CG methylation can be used as a marker of differentiation potential.
doi:10.1038/ncomms10458
PMCID: PMC4740175  PMID: 26822956
13.  Genome-wide methylation profiling identifies novel methylated genes in neuroblastoma tumors 
Epigenetics  2016;11(1):74-84.
ABSTRACT
Neuroblastoma is a very heterogeneous tumor of childhood. The clinical spectra range from very aggressive metastatic disease to spontaneous regression, even without therapy. Aberrant DNA methylation pattern is a common feature of most cancers. For neuroblastoma, it has been demonstrated both for single genes as well as genome-wide, where a so-called methylator phenotype has been described. Here, we present a study using Illumina 450K methylation arrays on 60 neuroblastoma tumors. We show that aggressive tumors, characterized by International Neuroblastoma Risk Group (INRG) as stage M, are hypermethylated compared to low-grade tumors. On the contrary, INRG stage L tumors display more non-CpG methylation. The genes with the highest number of hypermethylated CpG sites in INRG M tumors are TERT, PCDHGA4, DLX5, and DLX6-AS1. Gene ontology analysis showed a representation of neuronal tumor relevant gene functions among the differentially methylated genes. For validation, we used a set of independent tumors previously analyzed with the Illumina 27K methylation arrays, which confirmed the differentially methylated sites. Top candidate genes with aberrant methylation were analyzed for altered gene expression through the R2 platform (http://r2.amc.nl), and for correlations between methylation and gene expression in a public dataset. Altered expression in nonsurvivors was found for the genes B3GALT4 and KIAA1949, CLIC5, DLX6-AS, TERT, and PIRT, and strongest correlations were found for TRIM36, KIAA0513, and PIRT. Our data indicate that methylation profiling can be used for patient stratification and informs on epigenetically deregulated genes with the potential of increasing our knowledge about the underlying mechanisms of tumor development.
doi:10.1080/15592294.2016.1138195
PMCID: PMC4846113  PMID: 26786290
CIMP; DLX5; DNA methylation; epigenetics; neuroblastoma; PCDHGA4; pediatric; TERT; 450K
14.  Mucosal Transcriptomics Implicates Under Expression of BRINP3 in the Pathogenesis of Ulcerative Colitis 
Inflammatory Bowel Diseases  2014;20(10):1802-1812.
Article first published online 28 August 2014.
Supplemental Digital Content is Available in the Text.
Background:
Mucosal abnormalities are potentially important in the primary pathogenesis of ulcerative colitis (UC). We investigated the mucosal transcriptomic expression profiles of biopsies from patients with UC and healthy controls, taken from macroscopically noninflamed tissue from the terminal ileum and 3 colonic locations with the objective of identifying abnormal molecules that might be involved in disease development.
Methods:
Whole-genome transcriptional analysis was performed on intestinal biopsies taken from 24 patients with UC, 26 healthy controls, and 14 patients with Crohn's disease. Differential gene expression analysis was performed at each tissue location separately, and results were then meta-analyzed. Significantly, differentially expressed genes were validated using quantitative polymerase chain reaction. The location of gene expression within the colon was determined using immunohistochemistry, subcellular fractionation, electron and confocal microscopy. DNA methylation was quantified by pyrosequencing.
Results:
Only 4 probes were abnormally expressed throughout the colon in patients with UC with Bone morphogenetic protein/Retinoic acid Inducible Neural-specific 3 (BRINP3) being the most significantly underexpressed. Attenuated expression of BRINP3 in UC was independent of current inflammation, unrelated to phenotype or treatment, and remained low at rebiopsy an average of 22 months later. BRINP3 is localized to the brush border of the colonic epithelium and expression is influenced by DNA methylation within its promoter.
Conclusions:
Genome-wide expression analysis of noninflamed mucosal biopsies from patients with UC identified BRINP3 as significantly underexpressed throughout the colon in a large subset of patients with UC. Low levels of this gene could predispose or contribute to the maintenance of the characteristic mucosal inflammation seen in this condition.
doi:10.1097/MIB.0000000000000169
PMCID: PMC4531309  PMID: 25171508
microarray; methylation; colon; inflammatory bowel disease
15.  A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation 
Genome Medicine  2015;7:128.
Background
Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for many hematological conditions. Acute graft-versus-host disease (aGVHD) is a prevalent immune-mediated complication following HSCT. Current diagnostic biomarkers that correlate with aGVHD severity, progression, and therapy response in graft recipients are insufficient. Here, we investigated whether epigenetic marks measured in peripheral blood of healthy graft donors stratify aGVHD severity in human leukocyte antigen (HLA)-matched sibling recipients prior to T cell-depleted HSCT.
Methods
We measured DNA methylation levels genome-wide at single-nucleotide resolution in peripheral blood of 85 HSCT donors, matched to recipients with various transplant outcomes, with Illumina Infinium HumanMethylation450 BeadChips.
Results
Using genome-wide DNA methylation profiling, we showed that epigenetic signatures underlying aGVHD severity in recipients correspond to immune pathways relevant to aGVHD etiology. We discovered 31 DNA methylation marks in donors that associated with aGVHD severity status in recipients, and demonstrated strong predictive performance of these markers in internal cross-validation experiments (AUC = 0.98, 95 % CI = 0.96–0.99). We replicated the top-ranked CpG classifier using an alternative, clinical DNA methylation assay (P = 0.039). In an independent cohort of 32 HSCT donors, we demonstrated the utility of the epigenetic classifier in the context of a T cell-replete conditioning regimen (P = 0.050).
Conclusions
Our findings suggest that epigenetic typing of HSCT donors in a clinical setting may be used in conjunction with HLA genotyping to inform both donor selection and transplantation strategy, with the ultimate aim of improving patient outcome.
Electronic supplementary material
The online version of this article (doi:10.1186/s13073-015-0246-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s13073-015-0246-z
PMCID: PMC4681168  PMID: 26669438
16.  A Polycomb-mir200 loop regulates clinical outcome in bladder cancer 
Oncotarget  2015;6(39):42258-42275.
Bladder cancer (BC) is a highly prevalent disease, ranking fifth in the most common cancers worldwide. Various miRNAs have recently emerged as potential prognostic biomarkers in cancer. The miR-200 family, which repressed the epithelial-to-mesenchymal transition (EMT), is repressed in multiple advanced cancers. However, its expression and function in BC is still poorly understood. Here we show that miR-200 family displays increased expression, probably due to the activation of specific oncogenic signaling pathways, and reduced promoter methylation, in BC compared to normal bladder samples. Furthermore, we show that the expression of these miRNAs is decreased in high grade and stage tumors, and the down-regulation is associated with patient's poor clinical outcome. Our data indicate that the miR-200 family plays distinct roles in Non-Muscle (NMIBC) and Muscle-Invasive BC (MIBC). In MIBC, miR-200 expression post transcriptionally regulates EMT-promoting transcription factors ZEB1 and ZEB2, whereas suppresses BMI1 expression in NMIBC. Interestingly, we show that increased EZH2 and/or BMI1 expression repress the expression of miR-200 family members. Collectively, these findings support a model of BC progression through a coordinated action between the Polycomb Repression Complex (PRC) members repressing the miR-200 expression, which ultimately favors invasive BC development. Since pharmacological inhibition of EZH2 in BC cell lines lead to increased miR-200 expression, our findings may support new therapeutic strategies for BC clinical management.
PMCID: PMC4747223  PMID: 26517683
miRNA; Polycomb; bladder cancer; recurrence; epigenetics
17.  Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome 
Frontiers in Genetics  2015;6:339.
BAH domain-containing protein 1 (BAHD1) is involved in heterochromatin formation and gene repression in human cells. BAHD1 also localizes to the inactive X chromosome (Xi), but the functional significance of this targeting is unknown. So far, research on this protein has been hampered by its low endogenous abundance and its role in epigenetic regulation remains poorly explored. In this work, we used whole-genome bisulfite sequencing (BS-seq) to compare the DNA methylation profile of HEK293 cells expressing low levels of BAHD1 (HEK-CT) to that of isogenic cells stably overexpressing BAHD1 (HEK-BAHD1). We show that increasing BAHD1 levels induces de novo DNA methylation on autosomes and a marked hypomethylation on the X chromosome (chrX). We identified 91,358 regions that have different methylation patterns in HEK-BAHD1 compared to HEK-CT cells (termed “BAHD1-DMRs”), of which 83,850 mapped on autosomes and 7508 on the X chromosome (chrX). Autosomal BAHD1-DMRs were predominantly hypermethylated and located to satellites, interspersed repeats, and intergenic regions. In contrast, BAHD1-DMRs on chrX were mainly hypomethylated and located to gene bodies and enhancers. We further found that BAHD1-DMRs display a higher-order organization by being clustered within large chromosomal domains. Half of these “BAHD1-Associated differentially methylated Domains” (BADs) overlapped with lamina-associated domains (LADs). Based on these results, we propose that BAHD1-mediated heterochromatin formation is linked to DNA methylation and may play a role in the spatial architecture of the genome.
doi:10.3389/fgene.2015.00339
PMCID: PMC4664705  PMID: 26648976
cytosine methylation; DNA methylation; whole genome bisulfite sequencing; heterochromatin; epigenetics; LAD; Xi
18.  Glioblastoma Stem Cells Respond to Differentiation Cues but Fail to Undergo Commitment and Terminal Cell-Cycle Arrest 
Stem Cell Reports  2015;5(5):829-842.
Summary
Glioblastoma (GBM) is an aggressive brain tumor whose growth is driven by stem cell-like cells. BMP signaling triggers cell-cycle exit and differentiation of GBM stem cells (GSCs) and, therefore, might have therapeutic value. However, the epigenetic mechanisms that accompany differentiation remain poorly defined. It is also unclear whether cell-cycle arrest is terminal. Here we find only a subset of GSC cultures exhibit astrocyte differentiation in response to BMP. Although overtly differentiated non-cycling astrocytes are generated, they remain vulnerable to cell-cycle re-entry and fail to appropriately reconfigure DNA methylation patterns. Chromatin accessibility mapping identified loci that failed to alter in response to BMP and these were enriched in SOX transcription factor-binding motifs. SOX transcription factors, therefore, may limit differentiation commitment. A similar propensity for cell-cycle re-entry and de-differentiation was observed in GSC-derived oligodendrocyte-like cells. These findings highlight significant obstacles to BMP-induced differentiation as therapy for GBM.
Graphical Abstract
Highlights
•Genome-wide profiling shows DNA methylation patterns during glioblastoma (GBM) differentiation•Delayed and incomplete epigenetic changes appear in GBM stem cells in response to BMP•SOX transcription factors may explain the lack of terminal differentiation•Lack of differentiation commitment limits the effectiveness of BMP-based therapies
BMP induces differentiation of glioblastoma stem cells (GSCs), but it remains unclear if differentiation commitment and permanent cell-cycle arrest occurs. Pollard, Beck, and colleagues report that differentiated progeny of GSCs fail to reconfigure DNA methylation patterns and are vulnerable to de-differentiation. Failure to suppress the activity of SOX transcription factors may explain this deficit.
doi:10.1016/j.stemcr.2015.09.014
PMCID: PMC4649264  PMID: 26607953
19.  Analysis of the Polycomb-related lncRNAs HOTAIR and ANRIL in bladder cancer 
Clinical Epigenetics  2015;7:109.
Background
Long non-coding RNAs (lncRNAs) have been claimed as key molecular players in gene expression regulation, being involved in diverse epigenetic processes. They are aberrantly expressed in various tumors, but their exact role in bladder cancer is still obscure. We have recently found a major role of the Polycomb repression complex in recurrence of non-muscle-invasive bladder cancer. Here, we report the xpression of Polycomb-related lncRNAs:antisense noncoding RNA in the INK4 locus (ANRIL) and HOX antisense intergenic RNA (HOTAIR) in these tumors.
Findings
We studied a dataset of non-invasive bladder cancer samples by quantitative reverse transcription PCR (RT-qPCR) and analyzed also invasive bladder cancer samples using TCGA data. Our results showed that, while ANRIL seemed not to have a determining role, an increased HOTAIR expression appeared in recurrent and high-graded tumors associated with poor prognosis. In addition, through genome-wide transcriptome analyses, we observed that HOTAIR-EZH2-complex-regulated genes can efficiently discriminate between non-tumoral, recurrent, and non-recurrent bladder cancer samples. We also observed a significant correlation between EZH2 and HOTAIR expression levels. Using overexpression, knockdown, and pharmacological approaches in bladder cancer cell lines, we also observed that EZH2 regulates HOTAIR expression.
Conclusions
Our findings indicate that HOTAIR expression has prognostic value for bladder cancer progression, recurrence, and survival and suggest that HOTAIR plays active roles in modulating the cancer epigenome, becoming an interesting candidate as a target for cancer diagnosis and therapy. The observed HOTAIR regulation by EZH2 and the possibility of modulating EZH2 activity with specific inhibitors open new possible paths to be explored in bladder cancer therapy.
Electronic supplementary material
The online version of this article (doi:10.1186/s13148-015-0141-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s13148-015-0141-x
PMCID: PMC4599691  PMID: 26457124
Epigenetics; Bladder cancer; LncRNA; HOTAIR; Recurrence; ANRIL
20.  Epigenetics markers of metastasis and HPV induced tumourigenesis in Penile cancer 
Purpose
Penile cancer is a rare malignancy in the developed world, with just over 1600 new cases diagnosed in the USA per year, however, the incidence is much higher in developing countries. Although HPV is known to contribute to tumourigenesis, little is known about the genetic or epigenetic alterations defining penile cancer (PeCa).
Experimental Design
Using high-density genome-wide methylation arrays we have identified epigenetic alterations associated with PeCa. Q-MSP was used to validate lymph node metastasis markers in 50 cases. 446 HNSCC and CESCC (head and neck squamous cell carcinoma and cervical squamous cell carcinoma) samples were used to validate HPV associated epigenetic alterations.
Results
We defined 6933 methylation variable positions (MVPs) between normal and tumour tissue, which include 997 hypermethylated differentially methylated regions associated with tumour supressor genes including CDO1, AR1 and WT1. Analysis of PeCa tumours identified a 4 gene epi-signature which accurately predicted lymph node metastasis in an independent cohort (AUC of 89%). Finally, we explored the epigenetic alterations associated with PeCa HPV infection and defined a 30 loci lineage independent HPV specific epi-signature which predicts HPV status and survival in independent HNSCC, CESC cohorts. Epi-signature negative patients have a significantly worse overall survival (HNSCC p=0.00073, CI 0.021-0.78, CESC p= 0.0094, HR=3.91, 95% CI =0.13-0.78), HPV epi-signature is a better predictor of survival than HPV status alone.
Conclusion
These data demonstrate for the first time genome-wide epigenetic events involved in an aggressive penile cancer phenotype and define the epigenetic alterations common across multiple HPV driven malignancies.
doi:10.1158/1078-0432.CCR-14-1656
PMCID: PMC4351916  PMID: 25538261
21.  Mucosal Transcriptomics Implicates Under Expression of BRINP3 in the Pathogenesis of Ulcerative Colitis 
Inflammatory bowel diseases  2014;20(10):1802-1812.
Background
Mucosal abnormalities are potentially important in the primary pathogenesis of ulcerative colitis (UC). We investigated the mucosal transcriptomic expression profiles of biopsies from patients with UC and healthy controls, taken from macroscopically noninflamed tissue from the terminal ileum and 3 colonic locations with the objective of identifying abnormal molecules that might be involved in disease development.
Methods
Whole-genome transcriptional analysis was performed on intestinal biopsies taken from 24 patients with UC, 26 healthy controls, and 14 patients with Crohn’s disease. Differential gene expression analysis was performed at each tissue location separately, and results were then meta-analyzed. Significantly, differentially expressed genes were validated using quantitative polymerase chain reaction. The location of gene expression within the colon was determined using immunohistochemistry, subcellular fractionation, electron and confocal microscopy. DNA methylation was quantified by pyrosequencing.
Results
Only 4 probes were abnormally expressed throughout the colon in patients with UC with Bone morphogenetic protein/Retinoic acid Inducible Neural-specific 3 (BRINP3) being the most significantly underexpressed. Attenuated expression of BRINP3 in UC was independent of current inflammation, unrelated to phenotype or treatment, and remained low at rebiopsy an average of 22 months later. BRINP3 is localized to the brush border of the colonic epithelium and expression is influenced by DNA methylation within its promoter.
Conclusions
Genome-wide expression analysis of noninflamed mucosal biopsies from patients with UC identified BRINP3 as significantly underexpressed throughout the colon in a large subset of patients with UC. Low levels of this gene could predispose or contribute to the maintenance of the characteristic mucosal inflammation seen in this condition.
doi:10.1097/MIB.0000000000000169
PMCID: PMC4531309  PMID: 25171508
microarray; methylation; colon; inflammatory bowel disease
22.  Erratum to: Brave new epigenomes: the dawn of epigenetic engineering 
Genome Medicine  2015;7(1):75.
doi:10.1186/s13073-015-0194-7
PMCID: PMC4525747  PMID: 26246858
23.  Epigenome data release: a participant-centered approach to privacy protection 
Genome Biology  2015;16(1):142.
Large-scale epigenome mapping by the NIH Roadmap Epigenomics Project, the ENCODE Consortium and the International Human Epigenome Consortium (IHEC) produces genome-wide DNA methylation data at one base-pair resolution. We examine how such data can be made open-access while balancing appropriate interpretation and genomic privacy. We propose guidelines for data release that both reduce ambiguity in the interpretation of open-access data and limit immediate access to genetic variation data that are made available through controlled access.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0723-0) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-015-0723-0
PMCID: PMC4504083  PMID: 26185018
24.  Brave new epigenomes: the dawn of epigenetic engineering 
Genome Medicine  2015;7(1):59.
Editorial summary
New methods for epigenome editing now make it possible to manipulate the epigenome in living cells with unprecedented specificity and efficiency. These ground-breaking approaches are beginning to yield novel insights into the function of individual chromatin marks in the context of cellular phenotype.
doi:10.1186/s13073-015-0185-8
PMCID: PMC4472160  PMID: 26089986

Résultats 1-25 (94)