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Objective Few researches have been reported on the gene methylation in children with steroid-sensitive nephrot-ic syndrome (SSNS) or steroid-dependent nephrotic syndrome (SDNS).This study aimed to investigate the possible pathogenesis and therapeutic target of SSNS and SDNS by screening differentially methylated genes ( DMGs) and bioinformatic analysis using DNA meth-ylation microarray. Methods This study included 3 hospitalized children with SSNS and another 4 with SDNS, all treated with full dose of prednisone ( 2 mg per kilogram of the body weight per day or 60 mg per m2 per day).Negative urine protein was achieved within 4 weeks in the former group , while the latter , though sensitive to hor-monal therapy , relapsed within 2 weeks after drug withdrawal or dose reduction .DNA was extracted from the peripheral blood of the patients in both groups for screening DMGs and bioinformatic analysis using DNA methylation microarray . Results Compared with the patients with SSNS, 318 DMGs were found in the SDNS group , among which 193 were hypermethylated and the other 125 hypomethylated .These abnormal genes were mainly located in the open reading frame of DNA and the CpG island region .DMGs were mainly involved in Rho guanyl-nucleotide exchange factor activity , nucleoside-triphosphatase regulator activity , GTPase activator activity , and other molecular functions .The biological processes were chiefly associ-ated with the regulation of the generation of precursor metabolites and energy , antigen processing and presentation , regulation of Rho and Ras protein signal transduction , lamellipodium assembly , regeneration , and other biological processes .The cell composition was mainly related to MHC protein complexes , perichromatin fibrils , and the MHC class I protein complex .Analysis of the KEGG signaling pathway showed that DMGs participated in 9 signaling pathways , involving type I diabetes , starch and sucrose metabolism , allograft re-jection, autoimmune thyroid disease , and others. Conclusion The heterogeneity of methylation is widespread in children with SDNS and may be one of the causes of steroid dependence , which has provided a basis for searching for potential therapeutic targets .
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Objective To investigate the regulatory networks of DNA methylation profiles in STEMI by methylation microarrays.Methods A total often male patients with STEMI and ten male healthy controls were recruited.Methyl-DNA immunoprecipitation and Nimblegen HG18 Meth 385K promoter plus CpG island microarrays were used to identify differentially methylated regions.And several bioinformatics analysis tools which included chromosomal assignment, gene ontology analysis and pathway analysis with SignalMap and The Database for Annotation, Visualization and Integrated Discovery were used to high-throughput analysis.Results Compared with healthy controls, DMRs of STEMI is 1 634, There are 1 480 (90.57％), 131 (8.02％) and23 (1.41％) methylated sites were separately located on High CpG-containing promoter, Intermediate CpG-containing promoter and Low CpG-containing promoter;Gene Ontology and Pathway analysis expressed DNA methylated genes of signaling pathway in MI identified glycerophespholipid metabolism, cysteine and methionine metabolism, Dilated cardiomyopathy, Arrhythmogenic right ventricular cardiomyopathy, regulation of actin cyteskeleton, calcium signaling pathway.However, the signal pathway about lipid metabolism is shown no significant difference.Conclusions Bioinformatics tools could provide the quick and high-throughput analysis of data from methylation microarray and enable the function classification of differentially expressed genes of STEMI.
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Objective To identify the changes of DNA methylation profile in the process of malignant transformation of BEP2D cell induced by α particles.Methods The genomic DNAs were isolated from the malignant transformation BERP35T4 cells and immortalized human bronchial epithelial cell line BEP2D.Genomic DNAs were digested by MseI and ligated of PCR linkers.Methylated DNAs were digested by BstUI and amplified by PCR.The methylated DNA probes were prepared by labeling with Cy3 and Cy5 fluorescence dyes individually and hybridized to the methylation CpG-Island microarray.The hybridization results were scanned and analyzed.Intensity values were quality controlled and normalized.The normalized data were used to identify the differentially expressed genes based on a 1.5 fold difference of the expression level.Results There were 16 genes which showed changes of methylation level in malignant transformation BERP35T4 cells, 9 of them were hypermethylation and 7 were hypomethylation.These genes were including the SKIP gene, PPP3CC gene, MAP2K6 gene, KIR2DL1 gene, KIR2DL4 gene, KIR3DP1 gene, ZNF493 gene, ZNF100 gene, NKX2-5 gene, TFAP2D gene, DR1 gene, KCNJ16 gene, CCDC18 gene, FNBP1L gene, IRX4 gene, EPB41L3 gene, TCP10 gene and so on.Conclusions The DNA methylation might have effects on ionizing radiation drived tumorigenesis.