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: Frontiers in Endocrinology

Article Title: Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy

doi: 10.3389/fendo.2020.619989

Figure Lengend Snippet: Comparison of orbital fibroblast global DNA methylation profiles with FDR <0.05. (A) DNA methylation in active GO orbital fibroblasts (n = 4), inactive GO orbital fibroblasts (n = 4) and healthy control orbital fibroblasts (n = 4) were compared. Global DNA methylation was measured using the Illumina Infinium Human Methylation 450K beadchip on bisulphite-treated DNA and analyzed by GenomeStudio methylation analysis package. Genes with differential DNA methylation were further corrected for multiple testing using FDR < 0.05. (B) Methylation level of SLC39A8 . Methylation level ranges from 0 (unmethylated) to 1 (fully methylated). Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median. (C) SLC39A8 expression was determined by real-time quantitative (RQ)-PCR and normalized to the control gene ABL . Data from mRNA expression was analyzed using ANOVA and subsequently analyzed with the Mann Whitney U test. Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median.

Article Snippet: Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip.

Techniques: Comparison, DNA Methylation Assay, Control, Methylation, Expressing, MANN-WHITNEY

Journal: Frontiers in Endocrinology

Article Title: Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy

doi: 10.3389/fendo.2020.619989

Figure Lengend Snippet: Hypermethylated genes in orbital fibroblasts from active GO in comparison to orbital fibroblasts from inactive GO and healthy controls with a fold difference ≥ 2. DNA methylation in active GO orbital fibroblasts (n = 4) was compared with inactive GO orbital fibroblasts (n = 4). Global DNA methylation was measured using the Illumina Infinium Human Methylation 450K beadchip on bisulphite-treated DNA and analyzed by GenomeStudio methylation analysis package. Hypermethylated genes with differences in DNA methylation level of at least 2-fold in active GO orbital fibroblasts were clustered as shown in the heatmap.

Article Snippet: Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip.

Techniques: Comparison, DNA Methylation Assay, Methylation

Journal: Frontiers in Endocrinology

Article Title: Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy

doi: 10.3389/fendo.2020.619989

Figure Lengend Snippet: Hypomethylated genes in orbital fibroblasts from active GO in comparison to orbital fibroblasts from inactive GO and healthy controls with a fold difference ≥ 2. DNA methylation in active GO orbital fibroblasts (n = 4) were compared with inactive GO orbital fibroblasts (n = 4). Global DNA methylation was measured using the Illumina Infinium Human Methylation 450K beadchip on bisulphite-treated DNA and analyzed by GenomeStudio methylation analysis package. Hypomethylated genes with differences in DNA methylation level of at least 2-fold in active GO orbital fibroblasts were clustered as shown in the heatmap.

Article Snippet: Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip.

Techniques: Comparison, DNA Methylation Assay, Methylation

Journal: Frontiers in Endocrinology

Article Title: Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy

doi: 10.3389/fendo.2020.619989

Figure Lengend Snippet: Comparison of DNA methylation, mRNA expression and proteomic data. (A) Comparison of hypermethylated genes, mRNA expression and proteomic data. Gene expression was determined by real-time quantitative (RQ)-PCR and normalized to the control gene ABL . Data from mRNA expression was analyzed using ANOVA and subsequently analyzed with the Mann Whitney U test. Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median. (B) Comparison of hypomethylated genes, mRNA expression and proteomic data. Gene expression was determined by real-time quantitative (RQ)-PCR and normalized to the control gene ABL . Data from mRNA expression was analyzed using ANOVA and subsequently analyzed with the Mann Whitney U test. Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median.

Article Snippet: Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip.

Techniques: Comparison, DNA Methylation Assay, Expressing, Gene Expression, Control, MANN-WHITNEY

Journal: Frontiers in Endocrinology

Article Title: Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy

doi: 10.3389/fendo.2020.619989

Figure Lengend Snippet: Methylation based network analysis. (A) Network 1 derived from hypermethylated genes in orbital fibroblasts from active GO: linked to neurological disease, organismal injury and abnormalities, and nervous system development and function Network analysis was further performed on these differentially hypermethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information. (B) Network 2 derived from hypermethylated genes in orbital fibroblasts from active GO: linked to embryogenic development, nervous system development and function, and organ development. Network analysis was further performed on these differentially hypermethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information. (C) Network 3 derived from hypermethylated genes in orbital fibroblasts from active GO: linked to cardiovascular system development and function, organismal development, and cellular assembly and organization. Network analysis was further performed on these differentially hypermethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information. (D) Network 4 derived from hypomethylated genes in orbital fibroblasts from active GO: linked to cellular growth and proliferation, nervous system development and function, and cell-to-cell signaling and interaction. Network analysis was further performed on these differentially hypomethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information.

Article Snippet: Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip.

Techniques: Methylation, Derivative Assay