genomic dna methylation patterns  (Medicago)

Journal: Nature Medicine

Article Title: A prognostic neural epigenetic signature in high-grade glioma

doi: 10.1038/s41591-024-02969-w

Figure Lengend Snippet: a , Schematic of the study workflow. In humans ( n = 5,047) diagnosed with a CNS tumor we performed deconvolution using DNA methylation arrays (850k or 450k) for determining the neural signature. IDH-wild-type glioblastomas were stratified into subgroups with a low- or high-neural signature for further analyses. b , Epigenetic neural signature in all CNS tumor entities ( n = 5,047). c , Dichotomization of the combined dataset from Capper et al. and three institutional cohorts (Hamburg, Berlin and Frankfurt, all Germany) into low- and high-neural glioblastomas. The black line indicates a median neural score of all included patients with glioblastoma ( n = 1,058) and represents the cutoff (0.41) for stratification into low- and high-neural glioblastoma. d, External validation of the cutoff value using the TCGA-GBM dataset ( n = 187). The black line indicates the median neural score. e – i , Survival analysis of patients with low- and high-neural glioblastoma treated by radiochemotherapy after surgery. e , Overall survival (OS) of 363 patients with glioblastoma of the internal clinical cohort. log-rank test, P = 0.000005. Error bands represent 95% CI. f , PFS of 226 patients with glioblastoma of the internal clinical cohort. log-rank test, P = 0.0233. Error bands represent 95% CI. g , Overall survival of 187 patients with glioblastoma of the TCGA-GBM cohort. log-rank test, P = 0.0017. Error bands represent 95% CI. h , i , Forest plots illustrating multivariate analysis of patients with glioblastoma from the internal clinical cohort. Means are shown by closed circles and whiskers represent 95% CI. GTR, gross total resection; PR, partial resection; MGMT, O 6 -methylguanine-DNA-methyltransferase.

Article Snippet: Forty-four treatment-naive patients with glioblastoma (mean age 65 ± 9 years) underwent rs-fMRI before surgery, with tumor tissues subsequently analyzed for genome-wide DNA methylation patterns using the Illumina EPIC (850k) array.

Techniques: DNA Methylation Assay, Biomarker Discovery

Journal: Computational and Structural Biotechnology Journal

Article Title: Multi-omics in Crohn's disease: New insights from inside

doi: 10.1016/j.csbj.2023.05.010

Figure Lengend Snippet: Multi-omics researches on patients with Crohn's disease.

Article Snippet: Howell, Kate Joanne et al. 2018 , Epigenomics , 7 healthy children and 5 pediatric CD patients , Genome-wide DNA methylation patterns analysis , , • CD-associated DMPs showed a clear trend to be differentially methylated in CD-derived compared with control organoids. • CD- and UC-associated DMPs showed remarkable stability over time. • Analysis of ileal IECs revealed:(1) CD-specific changes in DNAm;(2) amongst identified rDMRs, several have previously been reported to be associated with IBD (e.g., CASP133 and APOA19). • Analysis of SC IECs revealed a major overlap between UC and CD signatures with only a single significant DEG (RARRES3). • MDS plots showed:(1) samples derived from controls clustered closely in each gut segment;(2) distinct clustering of samples by gut segment separating all TI-derived epithelium from colonic (i.e., AC and SC) samples; a subset of IBD samples distinctly separated from controls. • MDS plots showed:(1) samples derived from controls clustered closely in each gut segment;(2) distinct clustering of samples by gut segment separating all TI-derived epithelium from colonic (i.e., AC and SC) samples; a subset of IBD samples distinctly separated from controls. • Analysis of ileal IECs revealed:(1) CD-specific changes in DNAm;(2) amongst identified rDMRs, several have previously been reported to be associated with IBD (e.g., CASP133 and APOA19). • Analysis of SC IECs revealed a major overlap between UC and CD signatures with only a single significant DEG (RARRES3). • DMRs, DEGs, and rDMRs in both colonic and ileal IECs for IBD risk loci enriched. • Variation by gut segment and reduction in species diversity for CD patients were revealed. • IECs underwent changes during IBD development and could be involved in pathogenesis..

Techniques: Biomarker Discovery, Reversed-phase Chromatography, Activity Assay, Fractionation, Sequencing, RNA Sequencing, Multiplex Assay, Liquid Chromatography with Mass Spectroscopy, GWAS, Expressing, DNA Methylation Assay, Genome Wide, Functional Assay, Bacteria, Hydrophilic Interaction Liquid Chromatography, Shotgun Sequencing, Starch, Modification, Gas Chromatography-Mass Spectrometry, Clinical Proteomics, Control, Methylation, Derivative Assay, Gene Expression, Isolation

Journal: Computational and Structural Biotechnology Journal

Article Title: Multi-omics in Crohn's disease: New insights from inside

doi: 10.1016/j.csbj.2023.05.010

Figure Lengend Snippet: Brief summary of the most common pipelines in omics.

Article Snippet: Howell, Kate Joanne et al. 2018 , Epigenomics , 7 healthy children and 5 pediatric CD patients , Genome-wide DNA methylation patterns analysis , , • CD-associated DMPs showed a clear trend to be differentially methylated in CD-derived compared with control organoids. • CD- and UC-associated DMPs showed remarkable stability over time. • Analysis of ileal IECs revealed:(1) CD-specific changes in DNAm;(2) amongst identified rDMRs, several have previously been reported to be associated with IBD (e.g., CASP133 and APOA19). • Analysis of SC IECs revealed a major overlap between UC and CD signatures with only a single significant DEG (RARRES3). • MDS plots showed:(1) samples derived from controls clustered closely in each gut segment;(2) distinct clustering of samples by gut segment separating all TI-derived epithelium from colonic (i.e., AC and SC) samples; a subset of IBD samples distinctly separated from controls. • MDS plots showed:(1) samples derived from controls clustered closely in each gut segment;(2) distinct clustering of samples by gut segment separating all TI-derived epithelium from colonic (i.e., AC and SC) samples; a subset of IBD samples distinctly separated from controls. • Analysis of ileal IECs revealed:(1) CD-specific changes in DNAm;(2) amongst identified rDMRs, several have previously been reported to be associated with IBD (e.g., CASP133 and APOA19). • Analysis of SC IECs revealed a major overlap between UC and CD signatures with only a single significant DEG (RARRES3). • DMRs, DEGs, and rDMRs in both colonic and ileal IECs for IBD risk loci enriched. • Variation by gut segment and reduction in species diversity for CD patients were revealed. • IECs underwent changes during IBD development and could be involved in pathogenesis..

Techniques: Genome Wide, GWAS, Methylation, Sequencing, Selection, Polymerase Chain Reaction, Nuclear Magnetic Resonance, Gas Chromatography-Mass Spectrometry, Sample Prep, Extraction, Chromatography, Liquid Chromatography with Mass Spectroscopy, Data-independent acquisition, Mass Spectrometry, Quantitative Proteomics

Journal: Scientific Reports

Article Title: TANC1 methylation as a novel biomarker for the diagnosis of patients with anti-tuberculosis drug-induced liver injury

doi: 10.1038/s41598-021-96869-5

Figure Lengend Snippet: Statistical methylation patterns of cases and controls. ( a ) Density plot of β-values for all probes in the EPIC arrays for all 14 individuals. ( b ) PCA of whole DNA methylomes allows for the differentiation between ADLI cases (N = 7, red shapes) and matched controls (N = 7, green shapes).

Article Snippet: Genome-wide DNA methylation patterns were obtained using Infinium MethylationEPIC (EPIC) BeadChip array to analyze 14 peripheral blood samples (7 ADLI cases, 7 non-ADLI controls).

Techniques: Methylation

Journal: Scientific Reports

Article Title: TANC1 methylation as a novel biomarker for the diagnosis of patients with anti-tuberculosis drug-induced liver injury

doi: 10.1038/s41598-021-96869-5

Figure Lengend Snippet: DNA methylation values of four CpGs sites measured by the EPIC BeadChip (top) and by bisulfite pyrosequencing (bottom). DNA methylation values of cg06961147 (a) , cg24666046 (b) , cg18472223 (c) , and cg20517941 (d) were measured using EPIC BeadChip. DNA methylation values at each CpG site by percentage were measured by pyrosequencing of the ADLI patients (red) and controls (blue) in cg06961147 (e) , cg24666046) (f) , cg18472223 (g) , and cg20517941 (h).

Article Snippet: Genome-wide DNA methylation patterns were obtained using Infinium MethylationEPIC (EPIC) BeadChip array to analyze 14 peripheral blood samples (7 ADLI cases, 7 non-ADLI controls).

Techniques: DNA Methylation Assay