Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization

DNA methylation (DNAme) is a key epigenetic mark that regulates critical biological processes maintaining overall genome stability. Given its pleiotropic function, studies of DNAme dynamics are crucial, but currently available tools to interfere with DNAme have limitations and major cytotoxic side effects. Here, we present cell models that allow inducible and reversible DNAme modulation through DNMT1 depletion. By dynamically assessing whole genome and locus-specific effects of induced passive demethylation through cell divisions, we reveal a cooperative activity between DNMT1 and DNMT3B, but not of DNMT3A, to maintain and control DNAme. We show that gradual loss of DNAme is accompanied by progressive and reversible changes in heterochromatin, compartmentalization, and peripheral localization. DNA methylation loss coincides with a gradual reduction of cell fitness due to G1 arrest, with minor levels of mitotic failure. Altogether, this system allows DNMTs and DNA methylation studies with fine temporal resolution, which may help to reveal the etiologic link between DNAme dysfunction and human disease.

OP0235 GENOME-WIDE DNA METHYLATION ANALYSIS IN MULTIPLE IMMUNE CELL POPULATIONS REVEALS WIDESPREAD PROMOTER AND INTERGENIC B CELL HYPERMETHYLATION IN SYSTEMIC LUPUS ERYTHEMATOSUS

Background

Patients with systemic lupus erythematosus (SLE) display an aberrant DNA methylation (DNAm) pattern with a predominant interferon signature. However, the DNAm patterns in purified immune cell populations are not well described.

Objectives

To examine genome-wide DNAm changes in sorted CD4+ T cells, monocytes, granulocytes and B cells in SLE patients compared to healthy controls (HC).

Methods

Genome-wide analysis was performed in 20 SLE patients with active lupus nephritis (LN) and 20 age-, sex- and ethnicity-matched HCs. Peripheral blood was processed using gradient density centrifugation for the granulocyte fraction, and CD4+ T-cells, monocytes and B cells were isolated from the mononuclear cell fraction using a RoboSep device (Stemcell Technologies). DNA was extracted using the DNA/RNA/miRNA Universal kit (Qiagen). Genome-wide DNAm was evaluated using Infinium MethylationEPIC BeadChips (Illumina Inc.). Top differentially methylated CpG sites (DMC) were validated using pyrosequencing, and further analysed in follow-up samples, as well as extended to another 36 SLE patients with inactive LN, 36 SLE with never-LN and 20 HCs. Patients and HCs were compared using a paired t-test stratified by cell type. A false discovery rate (FDR) <0.05 was considered statistically significant. Clustering of non-gene annotated CpGs was defined as distance <5000 bp with proximity to neighbouring genes <1x105 bp, identified through mapping of Entrez Gene Identifiers.

Results

Overall, SLE patients with active LN compared to HCs exhibited DMCs in 22, 46, 312 and 78,068 probes in CD4+ T cells, monocytes, granulocytes and B cells, respectively. In CD4+ T cells, monocytes and granulocytes, the majority of DMCs were hypomethylated and related to interferon-regulated genes. In B cells, the majority of DMCs were hypermethylated with 1360 genes in the promoter region restricted to differential methylation >10% and ≥2 DMCs, of which 1087 were hypermethylated. Of these, the most significantly hypermethylated CpGs in the promoter region included CABYR, TMPRSS7, SLC6A2, KLK10/KLK11, WIZ, LPAR1, ZNF385B and IL1R1 (Figure 1). Top hypomethylated genes included IFI44L and MX1. Ingenuity Pathway Analysis (IPA) predicted top upstream regulators in B cells to be IL4, TNF and IFNG. In addition, we identified 1437 DMCs associated with ncRNA and 4626 DMCs with no genic association. The non-gene associated DMCs were related to 275 non-coding clusters. Top non-coding clusters were in proximity to BMP7, ARHGEF10, PRDM1, RIN2 and CCR6, which themselves were differentially methylated. IPA predicted IL2, CD40LG and NFKB1 as the most important upstream regulators for neighbouring genes of non-coding clusters.

Pyrosequencing confirmed B cell hypermethylation in CXCR5, DDR1, MTA3, RAB30 and TRAF5, and in non-coding clusters located on chromosome 3 upstream of FGF12 and chromosome 22 downstream of XPNPEP3 and RBX1. Hypermethylation in CXCR5, DDR1, MTA3, RAB30 and hypomethylation in IFI44L, LGALS3BP and PARP9 was stable at follow-up as well as in patients with inactive and never-LN. Patients in the active LN group exhibited significantly more pronounced hypomethylation in PLSCR1 in CD4+ T-cells, granulocytes and B-cells compared to the other patient groups. Greater β2 microglobulin, anti-DNA antibodies and disease activity were significantly associated with greater B cell CXCR5 hypermethylation (p<0.001), IFI44L hypomethylation in all but CD4+ T cells, LGALS3BP hypomethylation in granulocytes (p<0.0001), PARP9 hypomethylation in all but B cells and PLSCR1 hypomethylation in all but monocytes. Proteinuria was related to PLSCR1 hypomethylation in all but monocytes, as well as hypermethylation at the non-coding cluster in chromosome 3 (p=0.05) and MTA3 (p=0.03) in B cells.

Conclusion

B cell hypermethylation in SLE patients is widespread, and may indicate a novel mechanism for SLE pathogenesis. Differential methylation of several interferon-regulated genes may be associated with disease activity.

Disclosure of Interests

None declared

O-074 No methylome differences observed in IVF children born after embryo culture in different culture media

Study question

Does human embryo culture in different IVF culture media lead to DNA methylation alterations in IVF offspring?

Summary answer

Genome-wide analyses identified no significant DNA methylation differences between culture medium groups in IVF children (neonates or 9-year olds) from two culture media studies.

What is known already

During in vitro fertilisation (IVF) treatments, embryos undergo preimplantation development in an artificial environment, while concurrently undergoing epigenetic reprogramming. Adversity during this period, such as peri-conception calorie restriction, has been linked to persistent DNA methylation aberrations and increased risk of cardiometabolic disease. Early environmental adversity is suspected in IVF offspring as they are born with lower birthweights and show increased risk of cardiometabolic dysfunction in adulthood as compared to their naturally-conceived counterparts. This is further supported by the observation from two culture media trials (MEDIUM0 and MEDIUM1) that embryo culture in different culture media leads to differences in birthweight.

Study design, size, duration

We recruited singleton offspring from two IVF culture media trials. The MEDIUM0 study, a pseudo-randomized trial comparing G3 (Vitrolife) and K-SICM (Cook), was conducted from 2003-2006. At the 9-year follow-up, saliva was collected (cohort-A). The MEDIUM1 study, a multi-center randomized controlled trial comparing G5 (Vitrolife) and HTF (Lonza), was conducted from 2010-2012. Umbilical cord blood (UCB) was collected at birth (cohort-B).

Participants/materials, setting, methods

DNA methylation was analysed in 120 saliva samples (65 G3, 55 Cook) and 106 UCB samples (47 HTF, 59 G5) using the Infinium MethylationEPIC array (Illumina). Mixed effects linear models, correcting for (gestational) age, sex, sample composition and batch effects alongside maternal age, pregnancy complications and IVF centre for cohort-B, were implemented at single or aggregated sites. Methylation outliers were defined as values over three interquartile ranges below or above 25th and 75th percentiles respectively.

Main results and the role of chance

111 of the 120 saliva samples (60 G3, 51 Cook) and 105 of the 106 UCB samples (47 HTF, 58 G5) passed our quality control criteria. We filtered sites on sex chromosomes, and based on quality, proximity to single-nucleotide polymorphisms, and proportion of missing values, leaving 650,000-700,000 of the 850,000 sites included on the EPIC array for our analyses. To account for heterogeneity in the cellular composition of our samples we estimated their cell compositions using a reference-based approach. First, we investigated individual CpG sites, finding no differentially methylated sites in either cohort after correction for multiple testing (false discovery rate adjusted p. value threshold &lt; 0.1). Sites were then aggregated into regions based on their allocations to genes, promoters and CpG islands. No differentially methylated regions were identified in either cohort. A targeted analysis of DNA methylation of imprinting genes showed no differentially methylated sites or regions. To examine the contribution of stochastic epigenetic alterations we quantified the number of methylation outliers per sample. Although this revealed a predominance of hypomethylation outliers, there was no difference in the total number or distribution of DNA methylation outliers between the two culture media groups of cohort-A and cohort-B.

Limitations, reasons for caution

This analysis is currently limited by the lack of comparison to a naturally-conceived control group. As such, we cannot yet conclude whether IVF embryo culture, in any medium, is associated with DNA methylation aberrations. Additionally, given the large number of comparisons, we may lack power to detect small differences.

Wider implications of the findings

Although there are disparities in birth weight and childhood growth after embryo culture in different media, we observed no DNA methylation alterations preserved postnatally. Whether DNA methylation of these individuals deviates from that of naturally-conceived individuals will be determined in the near future.

Trial registration number

MEDIUM1: NTR 1979 /NL1866 (Netherlands Trial Registry)

Gata3 hypermethylation and Foxp3 hypomethylation are associated with sustained protection and bystander effect following epicutaneous immunotherapy in peanut-sensitized mice

Background

Epicutaneous immunotherapy (EPIT) is a promising method for treating food allergies. In animal models, EPIT induces sustained unresponsiveness and prevents further sensitization mediated by Tregs. Here, we elucidate the mechanisms underlying the therapeutic effect of EPIT, by characterizing the kinetics of DNA methylation changes in sorted cells from spleen and blood and by evaluating its persistence and bystander effect compared to oral immunotherapy (OIT).

Methods

BALB/c mice orally sensitized to peanut proteins (PPE) were treated by EPIT using a PPE‐patch or by PPE‐OIT. Another set of peanut‐sensitized mice treated by EPIT or OIT were sacrificed following a protocol of sensitization to OVA. DNA methylation was analyzed during immunotherapy and 8 weeks after the end of treatment in sorted cells from spleen and blood by pyrosequencing. Humoral and cellular responses were measured during and after immunotherapy.

Results

Analyses showed a significant hypermethylation of the Gata3 promoter detectable only in Th2 cells for EPIT from the 4th week and a significant hypomethylation of the Foxp3 promoter in CD62L⁺ Tregs, which was sustained only for EPIT. In addition, mice treated with EPIT were protected from subsequent sensitization and maintained the epigenetic signature characteristic for EPIT.

Conclusions

Our study demonstrates that EPIT leads to a unique and stable epigenetic signature in specific T‐cell compartments with downregulation of Th2 key regulators and upregulation of Treg transcription factors, likely explaining the sustainability of protection and the observed bystander effect.

A polymorphism in the TH 2 locus control region is associated with changes in DNA methylation and gene expression

BACKGROUND

Genomewide association and epigenetic studies found a region within the RAD50 gene on chromosome 5q31 to be associated with total serum IgE levels and asthma. In mice, this region harbors a locus control region for nearby TH 2 cytokines, which is characterized by four Rad50 DNase I hypersensitive sites (RHS4-7). Among these, RHS7 seems to have the strongest impact on TH 2 differentiation. We investigated whether within the human homolog of RHS7, functional polymorphisms exist, which could affect DNA methylation or gene expression in the 5q31 locus and might have an influence on asthma status or IgE regulation.

METHODS

The human RHS7 region was fine mapped using 1000 genomes database information. In silico analysis and electrophoretic mobility shift assays were used to assess SNP function. Allele-specific effects on DNA methylation were evaluated in cord blood (n = 73) and at age of 4.5 years (n = 61) by pyrosequencing. Allele-specific effects on RAD50, IL4, and IL13 expression were analyzed in 100 subjects. Associations with asthma and IgE levels were investigated in the MAGICS/ISAAC II population (n = 1145).

RESULTS

Polymorphism rs2240032 in the RHS7 region is suggestive of allele-specific transcription factor binding, affects methylation of the IL13 promoter region and influences RAD50 and IL4 expression (lowest P = 0.0027). It is also associated with total serum IgE levels (P = 0.0227).

CONCLUSION

A functional relevant polymorphism in the TH 2 locus control region, equivalent to RHS7 in mice, affects DNA methylation and gene expression within 5q31 and influences total serum IgE on the population level.

Upregulation of membrane-bound CD40L on CD4+ T cells in women with primary Sjögren's syndrome

Epigenetic deregulation of genes encoded on the X chromosome as reported for CD40L in lupus could explain the female predominance of autoimmune diseases. We compared CD40L expression on CD4(+) T cells from primary Sjögren's syndrome (pSS) women and healthy controls and investigated DNA methylation patterns of the promoter and enhancer regions of CD40L. The expression of CD40L on activated CD4(+) T cells was higher in patients with pSS than controls after phorbolmyristate acetate and ionomycin activation (P = 0.02). CD40L mRNA level in CD4(+) T cells did not differ between patients with pSS and controls and was similar in both groups in cultures treated with the demethylating agent 5-azacytidine C. Pyrosequencing analysis revealed no significant differences in methylation profiles between patients and controls. Inducible membrane-bound CD40L on CD4(+) T cells is increased in patients with pSS but was not related to epigenetic deregulation by demethylation patterns of the regulatory regions of CD40L.

Farm exposure and time trends in early childhood may influence DNA methylation in genes related to asthma and allergy

BACKGROUND

Genetic susceptibility and environmental influences are important contributors to the development of asthma and atopic diseases. Epigenetic mechanisms may facilitate gene by environment interactions in these diseases.

METHODS

We studied the rural birth cohort PASTURE (Protection against allergy: study in rural environments) to investigate (a) whether epigenetic patterns in asthma candidate genes are influenced by farm exposure in general, (b) change over the first years of life, and (c) whether these changes may contribute to the development of asthma. DNA was extracted from cord blood and whole blood collected at the age of 4.5 years in 46 samples per time point. DNA methylation in 23 regions in ten candidate genes (ORMDL1, ORMDL2, ORMDL3, CHI3L1, RAD50, IL13, IL4, STAT6, FOXP3, and RUNX3) was assessed by pyrosequencing, and differences between strata were analyzed by nonparametric Wilcoxon-Mann-Whitney tests.

RESULTS

In cord blood, regions in ORMDL1 and STAT6 were hypomethylated in DNA from farmers' as compared to nonfarmers' children, while regions in RAD50 and IL13 were hypermethylated (lowest P-value (STAT6) = 0.001). Changes in methylation over time occurred in 15 gene regions (lowest P-value (IL13) = 1.57*10(-8)). Interestingly, these differences clustered in the genes highly associated with asthma (ORMDL family) and IgE regulation (RAD50, IL13, and IL4), but not in the T-regulatory genes (FOXP3, RUNX3).

CONCLUSIONS

In this first pilot study, DNA methylation patterns change significantly in early childhood in specific asthma- and allergy-related genes in peripheral blood cells, and early exposure to farm environment seems to influence methylation patterns in distinct genes.

Abstract P5-05-03: The 5p12 breast cancer susceptibility locus is associated with MRPS30 expression in estrogen receptor - positive tumors

Genome-wide association studies (GWAS) have identified numerous loci linked to breast cancer susceptibility, but few of these loci have been convincingly linked to causal variants. We identified genes whose mRNA expression is linked to germline variation in normal mammary tissue and breast tumors by performing a genome-wide expression Quantitative Trait Locus (eQTL) analysis in 97 samples of normal mammary tissue and 286 breast adenocarcinomas. In the tumors we found 164 cis-acting loci, which affect expression of nearby genes. Twenty nine of these loci are previously unreported in other eQTL studies, including a cis-acting locus at 5p12 affecting expression of the mitochondrial ribosomal 28S subunit protein MRPS30 in estrogen receptor-positive but not estrogen receptor-negative tumors. This locus has been associated with susceptibility to estrogen receptor-positive breast cancer in several GWAS, with MRPS30 being the suggested candidate gene. One of these studies found that the rs771660 variant was most significantly associated with breast cancer in the 5p12 region, and we found that rs771660 was most strongly associated with MRPS30 gene expression. We provide the first evidence that this breast cancer susceptibility locus affects MRPS30 expression specifically in estrogen receptor-positive tumors and suggest a mechanism for estrogen activation of MRPS30 via proteins in the AP-1 complex.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-05-03.

MeQA: a pipeline for MeDIP-seq data quality assessment and analysis

MOTIVATION

We present a pipeline for the pre-processing, quality assessment, read distribution and methylation estimation for methylated DNA immunoprecipitation (MeDIP)-sequence datasets. This is the first MeDIP-seq-specific analytic pipeline that starts at the output of the sequencers. This pipeline will reduce the data analysis load on staff and allows the easy and straightforward analysis of sequencing data for DNA methylation. The pipeline integrates customized scripting and several existing tools, which can deal with both paired and single end data.

AVAILABILITY

The package and extensive documentation, and comparison to public data is available at http://life.tongji.edu.cn/meqa/.

Epigenetic mechanisms and the relationship to childhood asthma

Epigenetic mechanisms mediate genomic adaption to the environment and epigenetic alterations can contribute to the development of disease phenotypes, as can genetic variants. A variety of molecular mechanisms are involved in epigenetic regulation, including post-transcriptional histone modifications, histone variants, ATP-dependent chromatin remodelling complexes, polycomb/trithorax protein complexes, small and other noncoding RNAs (small interfering RNA and micro RNAs) and DNA methylation. Epigenetic mechanisms have been identified in cancer but very little is known about these effects in complex diseases such as asthma. Epigenetic mechanisms have been found to play a primordial role in T-cell differentiation and novel aspects of asthma and allergy development are now investigated by systematic epigenetic studies. Here we give an introduction to epigenetics, review the existing literature in relation to asthma and asthma-related mechanisms and hypothesise on feasible approaches for the study of epigenetics in asthma in the future.

Gene expression profiling in insulinomas of Men1 beta-cell mutant mice reveals early genetic and epigenetic events involved in pancreatic beta-cell tumorigenesis

Mutations of the MEN1 gene lead to the occurrence of multiple endocrine neoplasia type 1 (MEN1). To gain insights into the mechanisms of the tumorigenesis related to MEN1 inactivation, we have used mice in which the Men1 gene was specifically disrupted in pancreatic beta-cells. In these mice, we observed full penetrance of insulinoma with defined histological characteristics of tumorigenesis. To identify the genetic factors taking part in the tumour development, we performed gene expression profiling analysis of these insulinomas at different stages. Here, we show that in late stage insulinomas, 56 genes are up-regulated and 194 are down-regulated more than fourfold compared with normal pancreatic islets. Clustering analysis reveals the deregulation of Hox gene family and the genes involved in cell proliferation and cell cycle control. The altered expression of Igf2, Igfbp3 and Igfbp6 as well as cyclin A2, B2 and D2 are confirmed by quantitative RT-PCR, with the overexpression of all the three cyclins found in early stage insulinomas. Moreover, an increased proportion of cyclin A2- and D2-expressing cells and the overexpression of insulin-like growth factor 2 (IGF2) protein are detected in mouse Men1 insulinomas by immunostaining. Interestingly, the analysis of DNA methylation patterns by quantitative serial pyrosequencing reveals that four specific CpGs in the intragenic differentially methylated region 2 (DMR2) region of the Igf2 gene known to augment transcription through methylation are significantly hypermethylated in insulinomas of Men1 beta-cell mutant mice at 6 and 10 months of age, even before IGF2 overexpression can be detected. Thus, our data indicate the involvement of both genetic and epigenetic mechanisms in early tumorigenesis of beta-cells related to MEN1 inactivation.