Project description:Background: Epigenetic marks, like asthma, are heritable. They are influenced by the environment, direct the maturation of T cellslymphocytes, and have been shown to enhance the development of allergic airways disease in mice. Thus, we hypothesized that epigenetic marks are associated with allergic asthma in inner-city children. Methods: We compared methylation patterns and gene expression in inner-city children with persistent atopic asthma versus healthy controls, using DNA and RNA from peripheral blood mononuclear cells (PBMCs) from inner city children aged 6-12 years with persistent atopic asthma children and healthy controls. Results were externally validated with the GABRIELA study population. Results: Comparing asthmatics (N=97) to controls (N=97), we identified 81 regions that were differentially methylated. Several immune genes were hypomethylated in asthmatics, including IL-13, RUNX3, and a number of specific genes relevant to natural killer cells (KIR2DL4, KIR2DL3, KIR3DL1, and KLRD1) and T cells lymphocytes (TIGIT). 14 differentially methylated regions (DMRs) were associated with the serum IgE concentration of IgE, including RUNX3. These results were internally and externally validated with a global methylation assessment using a different methodology in our inner-city cohort and an independent European cohort (GABRIELA). Hypo- and hypermethylated genes tended to be associated with increased and decreased gene expression, respectively (P<0.6x10-11 for asthma and ; P<0.01 for IgE). To further explore the relationship between methylation and gene expression, we created a matrix of genomic changes in methylation versus transcriptional changes (methyl eQTL) for asthma, and identified cis- and trans-regulated genes whose expression was related to asthma asthma-associated methylation marks. peripheral blood mononuclear cells (PBMCs) from 97 atopic asthmatic and 97 nonatopic nonasthmatic children
Project description:We investigated the effects of experimental EBV infection of B cells on DNA methylation profiles by using high-throughput analysis. Remarkably, we observed hypomethylation of around 250 genes, but no hypermethylation. Hypomethylation did not occur at repetitive sequences, consistent with the absence of genomic instability in lymphoproliferative cells. Changes in methylation only occurred after cell divisions started, without the participation of the active demethylation machinery, and were concomitant with acquisition of B cells of the ability to proliferate. Gene ontology analysis, expression profiling, high-throughput analysis of the presence of transcription factor-binding motifs and occupancy revealed that most genes undergoing hypomethylation are active and display the presence of NFkB p65 and other B cell-specific transcription factors. Promoter hypomethylation associated with upregulation of genes relevant for the phenotype of proliferating lymphoblasts. Interestingly, pharmacologically-induced demethylation increased the efficiency of transformation of resting B cells to lymphoblastoid cells, suggesting the establishment of a productive cooperation between hypomethylation and lymphocyte proliferation. Bisulfite-converted DNA from 12 samples (6 Bcell, 6 Bcell immortalized) were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.
Project description:In this study, in 3 Han Chinese NTD pedigrees (2 with multiple affected children), with no information on folic acid deficiency or supplement, we examined genome-wide methylation profiles of each individual in these families.
Project description:Breast cancer metastasis may occur rapidly after tumor development and is responsible for the high mortality rate of this disease. ITIH5 has been shown being lost in tumor progression of various cancer types including breast cancer. Its dysfunction was associated with poor prognosis, while mechanisms of ITIH5 biology are still unrevealed. ITIH5 promoter methylation and expression was analyzed using an Infinium HumanMethylation450 BeadChip Array and Affymetrix 1.0 ST gene array, respectively, to identify ITIH5-associated gene signatures and signaling pathways. MDA-MB-231 cells were transfected with ITIH5-pBK-CMV expression vector, containing the full-length human ITIH5 cDNA derived from normal breast tissue, or the empty vector. Single-cell clones were selected by limited dilution under geneticine (G418) pressure. We compared the transcriptomic and epigenomic profile of wildtype MDA-MB-231 cells, mock clones without ITIH5 expression (clone 1 and 2) and ÎpBK-ITIH5 clones (clone 4, 7 and 12). Related transcription profiling data are found under accession <a href=\../E-MTAB-1813/\>E-MTAB-1813</a>.
Project description:The DNA methylation patterns associated with the development and progression of cancer. The aim of the present study was to identify novel methylation markers that can discriminate between normal and Non-muscle-invasive bladder cancer (NMIBC), and between good and poor prognosis using microarray analysis of DNA methylation and RNA expression patterns in NMIBC patients. From the 24 matched microarray-based DNA methylation and gene expression profiling data set, tumor specific hypermethylated genes were selected and clinical relevance of these genes were verified by quantitative PQS analyses. Methylation statues of several genes were significantly associated with decreased gene expression levels and aggressive clinicopathological characteristics. In multivariate regression analyses, hypermethylation of these genes were the independent predictors of recurrence and progression. Genomic DNA was extracted by standard methods using the Wizard Genomic DNA Purification System (Promega, Madison, WI). Total RNA was extracted with TRIzol reagent (Life Technologies, NY) according to the manufacturer’s protocol. Methylation patterns were assayed using the genome-wide Illumina Infinium HumanMethylation27 BeadChip array (Illumina Inc., San Diego, CA). Methylation assays were carried out according to the manufacturer’s protocol. Bisulfite conversion of genomic DNA was performed using the EZ DNA Methylation Kit (Zymo Research, Orange, CA). Fluorescence signals corresponding to C or T nucleotides were measured and the data were used to assign a quantitative measure of methylation level (β value). The β value is a quantitative measure of DNA methylation levels of specific CpGs and ranges from 0 for completely unmethylated to 1 for completely methylated.
Project description:The objective of this study was to analyze genome-wide differential methylation patterns in maternal leukocyte DNA in early pregnant and non-pregnant states. This is an age- and body mass index-matched case-control study comparing the methylation patterns of 27,578 cytosine-guanine (CpG) sites in 14,495 genes in maternal leukocyte DNA in early pregnancy (n=14), in the same women postpartum (n=14), and in nulligravid women (n=14) on a BeadChip platform. Transient widespread hypomethylation was found in early pregnancy as compared with the non-pregnant states. Methylation of nine genes was significantly different in early pregnancy compared to both postpartum and nulligravid states (< 10% False Discovery Rate). Early pregnancy may be characterized by widespread hypomethylation compared to non-pregnant states; there is no apparent permanent methylation imprint after a normal-term gestation. Nine potential candidate genes were identified as differentially methylated in early pregnancy and may play a role in the maternal adaptation to pregnancy. This is an age- and body mass index-matched case-control study comparing the methylation patterns of 27,578 cytosine-guanine (CpG) sites in 14,495 genes in maternal leukocyte DNA in early pregnancy (n=14), in the same women postpartum (n=14), and in nulligravid women (n=14) on a BeadChip platform.
Project description:We identified genome-wide DNA methylation patterns within neutrophils and low-density granulocytes of Lupus patients and demographically matched controls Comparison of 15 Lupus patients vs 15 age-, sex-, and ethnicity-matched controls using the Illumina HumanMethylation 450 beadchip array
Project description:The series was designed to identify the different methylated single CpGs involved in the pathophysiology of ulcerative colitis. A cohort of n=20 monozygotic twins, discordant for ulcerative colitis was selected. Illumina and Nimblegen platforms were used.
Project description:Methylation analysis of 12 corresponding pairs of tumor endothelial cells (TECs) and normal endothelial cells (NECs) isolated from human colorectal carcinoma (CRC) patients with different prognostic tumor microenvironments (TMEs: Th1-TME vs Control-TME): High and low GBP-1 expression in the tumors detected by IHC was used to categorize the patient-derived cells into Th1-TME and Control-TME (compare Naschberger et al, J Clin Invest 2016 and Naschberger et al, Int J Cancer 2008). Isolation of the samples was done according to Naschberger et al, JoVE 2018. The analysis is paralleled by omics-analysis of the same cell cultures at the transcriptome (E-MTAB-10465) and genome level (E-MEXP-3993).
Project description:The aim of the study is to identify differentially methylated positions (DMPs) and regions (DMRs) that predict response to Methotrexate (MTX) in early rheumatoid arthritis (RA) patients. DNA from baseline peripheral blood mononuclear cells was extracted from treatment naive RA patients. DNA methylation, quantified using the Infinium MethylationEPIC, was assessed in relation to response to MTX (combination) therapy (deltaDAS28) over the first 3 months in 69 RA patients.