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DNA hypermethylation and differential gene expression associated with Klinefelter syndrome

ABSTRACT: The molecular basis for the phenotypic traits and morbidity in Klinefelter syndrome (KS) are not clarified. As DNA methylation affect gene expression and thereby play a role in disease susceptibility, we performed genome-wide DNA methylation profiling of leucocytes from peripheral blood samples from 67 KS patients, 67 male controls and 33 female controls, in addition to genome-wide RNA-sequencing profiling in a subset of 9 KS patients, 9 control males and 13 female controls. Characterization of the methylome as well as the transcriptome of both coding and non-coding genes identified a unique epigenetic and genetic landscape of both autosomal chromosomes as well as the X chromosome in KS. A subset of genes show significant correlation between methylation values and expression values. Gene set enrichment analysis of differentially methylated positions yielded terms associated with well-known comorbidities seen in KS. In addition, differentially expressed genes revealed enrichment for genes involved in the immune system, wnt-signaling pathway and neuron development. Based on our data we point towards many new candidate genes (AKAP17A, AMOT, APOB, DACT1, DDX58, DOCK7, EIF2S3, FIGNL1, G3BP1, HENMT1, HERC5, IFI44, IFI44L, IFIT1, IFIT3, ISG15, KANK1, LGALS1, NSD1, PEX10, PLSCR1, RSAD2, SHROOM2, SLC25A6, SPEG, SPON2, TXLNG), which may be implicated in the phenotype and further point towards non-coding genes (RP13-216E22.4, RP13-36G14.4, G087825, G088512), which may be involved in X chromosome inactivation in KS and in the regulation of escape genes.

PROVIDER: EGAS00001002797 | EGA |

REPOSITORIES: EGA

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Project description:Background. The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African-Americans (AA) are disproportionally affected by SSc, yet dramatically underrepresented in research. The role of DNA methylation in disease risk remains unclear. This analysis was conducted to comprehensive identify differentially methylated loci associated with SSc in AA. Methods. Genomic DNA was isolated from cultured dermal fibroblasts isolated from 15 AA SSc cases and 15 AA controls. All patients met the 2013 ACR/EULAR classification criteria for SSc, most (93%) presenting with diffuse cutaneous SSc. DNA methylation patterns were profiled through reduced representation bisulfite sequencing (RRBS). Alignment and methylation calling were performed using Bismarck v0.16.3 and the GRCh37/hg19 reference genome. Data was filtered, normalized, and analyzed with RnBeads v1.6.1. Differential methylation analysis was conducted on CpG, promoter, gene and system level. Results. We generated DNA methylation data for over 5 million CpGs in each sample and between 10x to 40x coverage in CpGs sites. Using the Combined Score approach implemented in RnBeads, a total of 9 CpG islands, 17 genes and 11 promoters showed significant differential methylation levels between cases and controls at the gene-level. The top differentially methylated genes constitute mostly non-coding RNA genes (42%), followed by pseudogenes (27%), then protein coding genes (19%). Enrichment analysis revealed that both hypo- and hypermethylated genes and their promoter regions were enriched for cell differentiation and immune-related gene ontology terms (hypermethylated regions: mesenchymal cell transition and differentiation; hypomethylated regions: type I IFN signaling). Conclusion. The observed DNA methylation differences between cases and controls support a modest role for DNA methylation differences in mediating susceptibility to SSc in AA. Instead of protein-coding, most differentially methylated genes comprise non-coding RNA genes, supporting a larger contribution of dysregulated regulatory elements to disease. While previous DNA methylation profiling analyses in European-Americans reported an enrichment of extracellular matrix and focal adhesion genes, our data supports a potentially stronger immune-driven etiology in AA.

Project description:To decipher hormonal from chromosomal factors we compared DNA-methylation of 27,568 CpG-loci in genital fibroblasts from 46,XY feminized individuals (AIS) with inactivating androgen receptor mutations to those of normal males. The results of the following two subset comparisons are linked to the Series record below: CpG loci differentially methylated (q<0.04) between AIS and male controls (primary human genital fibroblasts): To decipher hormonal from chromosomal factors we compared DNA-methylation of 27,568 CpG-loci in genital fibroblasts from 46,XY feminized individuals (AIS) with inactivating androgen receptor mutations to those of normal males. Cell culture of primary fibroblasts from scrotum/ labia majora from donors with PAIS (n=13), MAIS (n=1) or CAIS (n=13) and 9 controls were analyzed using the HumanMethylation27 Bead Chip. 13 AIS samples and all controls were analyzed in duplicates. Samples with gene call rates <95% as analyzed with BeadStudio software (Illumina, Inc.) and CpGs with detection p-values >0.05 in at least one experiment were excluded from analyses. 54 hybridizations with 25,988 CpGs entered the analysis. Differential methylation analysis (DMA) was performed based on average beta-values were performed using OMICS Explorer (v.2.1(25); Qlucore, Sweden). This file contains CpG loci found differentially methylated (q<0.04) by this approach. CpG loci characterized by a high varibility in their DNA methylation value in AIS compared to male controls (primary human genital fibroblasts): To decipher hormonal from chromosomal factors we compared DNA-methylation of 27,568 CpG-loci in genital fibroblasts from 46,XY feminized individuals (AIS) with inactivating androgen receptor mutations to those of normal males. Cell culture of primary fibroblasts from scrotum/ labia majora from donors with PAIS (n=13), MAIS (n=1) or CAIS (n=13) and 9 controls were analyzed using the HumanMethylation27 Bead Chip. 13 AIS samples and all controls were analyzed in duplicates. Samples with gene call rates <95% as analyzed with BeadStudio software (Illumina, Inc.) and CpGs with detection p-values >0.05 in at least one experiment were excluded from analyses. 54 hybridizations with 25,988 CpGs entered the analysis. CpG loci with beta-values ranged in control samples up to 0.34 and a difference of the interquartiles between controls and AIS samples above 0.16 were considered as being variably methylated in AIS and are included in this file.

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DNA hypermethylation and differential gene expression associated with Klinefelter syndrome

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