Journal: Scientific Reports

Article Title: Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression

doi: 10.1038/s41598-019-44765-4

Figure Lengend Snippet: Neither SOD1 nor C9orf72 CpG islands are differentially methylated between mutation-positive ALS-discordant twins/triplets. The relative location of targeted CpG islands (CGI) and exon 1 are indicated for SOD1 ( A , top) and C9orf72 ( B , top). ( A ) Methylation of the CpG island spanning the promoter region and exon 1 of SOD1 does not show differential methylation between an ALS-affected triplet and unaffected co-triplets, concordant for SOD1 p.I114T. Methylation status was determined using both EpiTYPER (bottom) and 450K (middle) assays. ( B ) Transcript variants (T1, T2, and T3) and the position of the repeat expansion (black diamond) relative to exon 1 are shown for C9orf72 (top). Methylation of the C9orf72 promoter region/expansion flanking CpG islands are not differentially methylated between ALS-discordant co-twins that carry the C9orf72 hexanucleotide repeat expansion in either EpiTYPER (bottom) or 450K data sets (middle).

Article Snippet: To perform a high-density, targeted analysis, we used EpiTYPER, with additional support from a number of Infinium HumanMethylation450K CpG sites present in the same region.

Techniques: Methylation, Mutagenesis

Journal: Scientific Reports

Article Title: Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression

doi: 10.1038/s41598-019-44765-4

Figure Lengend Snippet: Twin cohort details.

Article Snippet: To perform a high-density, targeted analysis, we used EpiTYPER, with additional support from a number of Infinium HumanMethylation450K CpG sites present in the same region.

Techniques: Mutagenesis, Sampling, Control

Journal: Nature immunology

Article Title: A comprehensive analysis of AID's effects on the transcriptome and methylome of activated B cells

doi: 10.1038/ni.2616

Figure Lengend Snippet: ( a,b ) Pairwise comparisons of methylation frequency in AID-overexpressing and Aicda −/− B cells for ( a ) 1 kb windows and ( b ) all CpGs, as determined by RRBS. ( c,d ) Comparison of DNA methylation frequencies as determined by RRBS and Epityper for a random subset of CpGs with ( c ) > 20% greater methylation in Aicda −/− than in WT and ( b ) CpGs with < 10% difference between Aicda −/− and WT. Lines are linear fit for Aicda −/− or pooled WT and AID–miR-155T data. ( e ) Comparison of differences in gene expression and methylation in the associated promoters for AID–miR-155T and Aicda −/− B cells. (n = 1 mouse per genotype; r = Pearson's correlation coefficient)

Article Snippet: Epityper assays were performed by the Weill Cornell Medical College Epigenomics Core.

Techniques: Methylation, Comparison, DNA Methylation Assay, Gene Expression

Journal: Nature Communications

Article Title: The DNA methylation landscape of primary triple-negative breast cancer

doi: 10.1038/s41467-025-58158-x

Figure Lengend Snippet: a NMF clustering of 175 TNBCs from the main Basal epitype defined three subgroups: Basal1, Basal2, and Basal3. Heatmap shows beta values for 2845 differentially methylated CpGs between the three Basal subgroups. Sample annotation tracks show PAM50 subtypes, TNBCtype, and homologous recombination deficiency (HRD) status. CpGs (rows) were clustered using Euclidean distance and ward.D linkage. CpG annotation tracks also show if CpGs are located within transcription factor (TF) binding sites (color = yes, white = no), different CpG contexts, and beta values seen in normal breast samples. b Boxplots of tumor purity (as estimated from whole genome sequencing data), tumor infiltrating lymphocyte counts, and gene expression rank scores for the immune response metagene for Basal1-3 tumors. Two-sided p -values calculated using the Kruskal-Wallis test. c Kaplan-Meier plot using DRFI as endpoint for patients treated with adjuvant chemotherapy stratified by Basal1-3 subgroups. P -value calculated using the log-rank test. d Number of differentially expressed genes per Basal subgroup divided into whether the gene is up or down in expression compared to the other two groups. e Comparison of correlation between CpG-gene expression pairs in Basal epitype tumors (y axis) and in TNBC cell lines, demonstrating that most significant correlations with same direction in both data sets (red) are negative (e.g., hypermethylation and reduced gene expression). f Mean ATAC-signal in eight TNBC cell lines aggregated for 142 CpGs with correlated gene expression and methylation in cell line and tumor data. The x axis is centered at the CpG position showing e.g., that nonBasal cell lines (e.g., SUM185PE) do not have a signal for these positions (i.e., closed chromatin). g Similar plot as in ( f ), but for mean H3K27Ac signal across different cell types, showing e.g., that the signal is present in luminal progenitor cell lines but not immune cells. Boxplot elements correspond to: (i) center line = median, (ii) box limits = upper and lower quartiles, (iii) whiskers = 1.5x interquartile range. Top-axis in boxplots reports group sizes. Source data are provided as a Source Data file.

Article Snippet: Similarly, while 93% of all HRD-positive tumors (primarily driven by BRCA1 / BRCA2 -deficiency) were found in the Basal epitype, these did not match a distinct Basal subgroup (two-sided Chi-squared test, p = 0.94) suggesting that the latter would not be informative for PARP-inhibitor usage.

Techniques: Methylation, Homologous Recombination, Binding Assay, Sequencing, Gene Expression, Adjuvant, Expressing, Comparison