Epigenetic modulation of<i> AREL1</i> and increased <i>HLA</i> expression in brains of multiple system atrophy patients

International audienceMultiple system atrophy (MSA) is a rare disease with a fatal outcome. To date, little is known about the molecular processes underlying disease development. Its clinical overlap with related neurodegenerative movement disorders underlines the importance for expanding the knowledge of pathological brain processes in MSA patients to improve distinction from similar diseases. In the current study, we investigated DNA methylation changes in brain samples from 41 MSA patients and 37 healthy controls. We focused on the prefrontal cortex, a moderately affected area in MSA. Using Illumina MethylationEPIC arrays, we investigated 5-methylcytosine (5mC) as well as 5-hydroxymethylcytosine (5hmC) changes throughout the genome. We identified five significantly different 5mC probes (adj. P < 0.05), of which one probe mapping to the AREL1 gene involved in antigen presentation was decreased in MSA patients. This decrease correlated with increased 5hmC levels. Further, we identified functional DNA methylation modules involved in inflammatory processes. As expected, the decreased 5mC levels on AREL1 was concordant with increased gene expression levels of both AREL1 as well as MHC Class I HLA genes in MSA brains. We also investigated whether these changes in antigen-related processes in the brain associated with changes in peripheral mononuclear cells. Using flow cytometry on an independent cohort of MSA patients, we identified a decrease in circulating non-classical CD14+CD16++ blood monocytes, whereas T and NK cell populations were unchanged. Taken together, our results support the view of an active neuroimmune response in brains of MSA patients

Identification of Type 1 Diabetes-Associated DNA Methylation Variable Positions That Precede Disease Diagnosis

Monozygotic (MZ) twin pair discordance for childhood-onset Type 1 Diabetes (T1D) is similar to 50%, implicating roles for genetic and non-genetic factors in the aetiology of this complex autoimmune disease. Although significant progress has been made in elucidating the genetics of T1D in recent years, the non-genetic component has remained poorly defined. We hypothesized that epigenetic variation could underlie some of the non-genetic component of T1D aetiology and, thus, performed an epigenome-wide association study (EWAS) for this disease. We generated genome-wide DNA methylation profiles of purified CD14(+) monocytes (an immune effector cell type relevant to T1D pathogenesis) from 15 T1D-discordant MZ twin pairs. This identified 132 different CpG sites at which the direction of the intra-MZ pair DNA methylation difference significantly correlated with the diabetic state, i.e. T1D-associated methylation variable positions (T1D-MVPs). We confirmed these T1D-MVPs display statistically significant intra-MZ pair DNA methylation differences in the expected direction in an independent set of T1D-discordant MZ pairs (P = 0.035). Then, to establish the temporal origins of the T1D-MVPs, we generated two further genome-wide datasets and established that, when compared with controls, T1D-MVPs are enriched in singletons both before (P = 0.001) and at (P = 0.015) disease diagnosis, and also in singletons positive for diabetes-associated autoantibodies but disease-free even after 12 years follow-up (P = 0.0023). Combined, these results suggest that T1D-MVPs arise very early in the etiological process that leads to overt T1D. Our EWAS of T1D represents an important contribution toward understanding the etiological role of epigenetic variation in type 1 diabetes, and it is also the first systematic analysis of the temporal origins of disease-associated epigenetic variation for any human complex disease

Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

Peer reviewe

Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing(R)

International audienceMany protocols for gene-specific DNA methylation analysis are either labor intensive, not quantitative and/or limited to the measurement of the methylation status of only one or very few CpG positions. Pyrosequencing is a real-time sequencing technology that overcomes these limitations. After bisulfite modification of genomic DNA, a region of interest is amplified by PCR with one of the two primers being biotinylated. The PCR generated template is rendered single-stranded and a pyrosequencing primer is annealed to analyze quantitatively cytosine methylation. In comparative studies, pyrosequencing has been shown to be among the most accurate and reproducible technologies for locus-specific DNA methylation analyses and has become a widely used tool for the validation of DNA methylation changes identified in genome-wide studies as well as for locus-specific analyses with clinical impact such as methylation analysis of the MGMT promoter. Advantages of the Pyrosequencing technology are the ease of its implementation, the high quality and the quantitative nature of the results, and its ability to identify differentially methylated positions in close proximity

Frequent aberrant DNA methylation of ABCB1, FOXC1, PPP2R2B and PTEN in ductal carcinoma in situ and early invasive breast cancer

Introduction Ductal carcinoma in situ (DCIS) is a non-invasive lesion of the breast that is frequently detected by mammography and subsequently removed by surgery. However, it is estimated that about half of the detected lesions would never have progressed into invasive cancer. Identifying DCIS and invasive cancer specific epigenetic lesions and understanding how these epigenetic changes are involved in triggering tumour progression is important for a better understanding of which lesions are at risk of becoming invasive. Methods Quantitative DNA methylation analysis of ABCB1, CDKN2A/p16 INK4a , ESR1, FOXC1, GSTP1, IGF2, MGMT, MLH1, PPP2R2B, PTEN and RASSF1A was performed by pyrosequencing in a series of 27 pure DCIS, 28 small invasive ductal carcinomas (IDCs), 34 IDCs with a DCIS component and 5 normal breast tissue samples. FOXC1, ABCB1, PPP2R2B and PTEN were analyzed in 23 additional normal breast tissue samples. Real-Time PCR expression analysis was performed for FOXC1. Results Aberrant DNA methylation was observed in all three diagnosis groups for the following genes: ABCB1, FOXC1, GSTP1, MGMT, MLH1, PPP2R2B, PTEN and RASSF1A. For most of these genes, methylation was already present at the DCIS level with the same frequency as within IDCs. For FOXC1 significant differences in methylation levels were observed between normal breast tissue and invasive tumours (P < 0.001). The average DNA methylation levels were significantly higher in the pure IDCs and IDCs with DCIS compared to pure DCIS (P = 0.007 and P = 0.001, respectively). Real-time PCR analysis of FOXC1 expression from 25 DCIS, 23 IDCs and 28 normal tissue samples showed lower gene expression levels of FOXC1 in both methylated and unmethylated tumours compared to normal tissue (P < 0.001). DNA methylation levels of FOXC1, GSTP1, ABCB1 and RASSF1A were higher in oestrogen receptor (ER) positive vs. ER negative tumours; whereas methylation levels of FOXC1, ABCB1, PPP2R2B and PTEN were lower in tumours with a TP53 mutation. Conclusions Quantitative methylation analysis identified ABCB1, FOXC1, PPP2R2B and PTEN as novel genes to be methylated in DCIS. In particular, FOXC1 showed a significant increase in the methylation frequency in invasive tumours. Low FOXC1 gene expression in both methylated and unmethylated DCIS and IDCs indicates that the loss of its expression is an early event during breast cancer progression

Identification of Susceptibility Genes for Peritoneal, Ovarian, and Deep Infiltrating Endometriosis Using a Pooled Sample-Based Genome-Wide Association Study

Characterizing genetic contributions to endometriosis might help to shorten the time to diagnosis, especially in the most severe forms, but represents a challenge. Previous genome-wide association studies (GWAS) made no distinction between peritoneal endometriosis (SUP), endometrioma (OMA), and deep infiltrating endometriosis (DIE). We therefore conducted a pooled sample-based GWAS and distinguished histologically confirmed endometriosis subtypes. We performed an initial discovery step on 10-individual pools (two pools per condition). After quality control filtering, a Monte-Carlo simulation was used to rank the significant SNPs according to the ratio of allele frequencies and the coefficient of variation. Then, a replication step of individual genotyping was conducted in an independent cohort of 259 cases and 288 controls. Our approach was very stringent but probably missed a lot of information due to the Monte-Carlo simulation, which likely explained why we did not replicate results from “classic” GWAS. Four variants (rs227849, rs4703908, rs2479037, and rs966674) were significantly associated with an increased risk of OMA. Rs4703908, located close to ZNF366, provided a higher risk of OMA (OR = 2.22; 95% CI: 1.26–3.92) and DIE, especially with bowel involvement (OR = 2.09; 95% CI: 1.12–3.91). ZNF366, involved in estrogen metabolism and progression of breast cancer, is a new biologically plausible candidate for endometriosis

DNA methylation dynamics during pregnancy

International audiencePregnancy is a state of multiple physiological adaptations. Since methylation of DNA is an epigenetic mechanism that regulates gene expression and contributes to adaptive phenotypic variations, we investigated methylation changes in maternal blood of a longitudinal cohort of pregnant women from the first trimester of gestation to the third. Interestingly, during pregnancy, we found a gain of methylation in genes involved in morphogenesis, such as ezrin, while we identified a loss of methylation in genes promoting maternal-infant bonding (AVP and PPP1R1B). Together, our results provide insights into the biological mechanisms underlying physiological adaptations during pregnancy

Unique epigenetic signature in T cell compartment after epicutaneous immunotherapy in peanut sensitized mice

International audienceRationale Epicutaneous immunotherapy (EPIT) induces naïve Tregs, which play a crucial role in the bystander effect identified in a model of food allergic mice. Previously, EPIT was shown to alter epigenetic modifications and expression of Th2 and Tregs without influencing the expression of Th1 in peanut-sensitized mice. This study investigates methylation modifications occurring in specific T cell compartments. Methods Mice were orally sensitized to peanut and then treated with EPIT or non-treated. Mice were sacrificed at the end of treatment or 8 weeks after the end of immunotherapy. Regulatory T cells (CD62L+Foxp3+ and CD62L-Foxp3+) were sorted directly from the spleen and Th2 and Th1 cells were purified after a short in vitro reactivation of splenocytes. DNA methylation at Gata3 promoter and Foxp3 CNS2 was analysed in all sorted cells by pyrosequencing. Results Epicutaneous immunotherapy did not modify proportions of Th1 and Th2 cells in the spleen. The hypermethylation of CpG islands of Gata3 only occurred in Th2 cells for EPIT-treated mice at the end of immunotherapy and was sustained 8 weeks later (p<0.05 vs Sham). In parallel, significant hypomethylation was observed in the Foxp3 CpG islands of naïve Tregs only (p<0.05), not effector Tregs, at the end of EPIT, and persisted for 8 weeks following the end of treatment (p<0.001). Conclusions The unique epigenetic signature of EPIT is confirmed at cellular level for Gata3 (Th2) and Foxp3 (naïve Tregs), suggesting the induction of tolerance and prevention of further sensitization. Foxp3 hypomethylation occurring only on naïve Tregs underlines the crucial role of EPIT-induced naïve Tregs

TNFR2(+) Regulatory T CELLS (Tregs) Subpopulations Are Highly Suppressive And Are Increased On Anti-Tnf Treatment In Rheaumtoid Arthrtis (RA) Patients

International audienceIntroduction: In RA, Tregs fail to control chronic inflammation. TNF-α is involved in inhibition of Tregs differentiation and activation but the respective roles of its two receptors is unclear. We aimed to establish the role of TNFR2 on Tregs in control of inflammation by studying: 1) the action of TNF on Treg function in the presence and absence of TNFR2 in vitro and 2) in a model of skin inflammation in TNFR2KO mice, 3) the evolution of TNFR2-expressing Tregs from RA patients during anti-TNF-treatment. Methods: Mice deficient in the TNFR2 gene (TNFR2KO) and CREFoxP3-TNFR2 lox/lox mice were used. Cell phenotype was evaluated by FACS. Tregs stability was evaluated by analyzing methylation status of 9 CpG motifs of the Foxp3-locus (bisulfite sequencing of CD4+CD25+ purified cells). Skin inflammation was induced by an imiquimodcontaining ointment. Peripheral blood Tregs were characterized before and after 3 months of anti–TNF treatment in 12 RA-patients and in 19 patients with axial spondylaorthritis (AxSpA). Results: In vitro, TNF-α enhanced Foxp3 maintenance through TNFR2 signaling in cultured Tregs. In vivo, TNFR2-negative-Treg cells from both TNFR2KO and CRE-FoxP3-TNFR2 lox/lox mice, had lower spontaneous suppressive capacities (lower inhibition of effector T cell proliferation and IFN-g production). FoxP3 methylation was higher in Tregs from TNFR2KO mice than wt mice. This suggested that TNFR2 expression confers higher stability to Tregs. TNFR2KO mice had enhanced skin-inflammation and decreased Tregs and CD39+ Tregs frequencies in lymph nodes. In RA patients responding to anti-TNF treatment, an increase in TNFR2-expressingTregs frequencies was evident at 3 months of treatment vs. the baseline. Conversely, no variation was observed in AxSpA patients Conclusion: TNFR2 signaling on Tregs may play a major role in controlling inflammation and can be activated both by TNF-α and antiTNF treatment. Further studies to dissect TNFR2 dependent pathways on Tregs are warranted