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Fig. 1 | Clinical Epigenetics

Fig. 1

From: DNA methylation in human gastric epithelial cells defines regional identity without restricting lineage plasticity

Fig. 1

Global patterns of DNA methylation in the stomach. A Left: schematic representation of the human fundic and antral gland types and the respective location of pit cells and stem cells. Right: an experimental overview. Following sleeve resection, sample tissues (red X) from the antrum, corpus and fundus were cultivated as mucosoids using air–liquid interface cell culture inserts. The removal of WNT3A and RSPO1 (W/R) from the cell culture medium enriched for differentiated pit-like cells (− W/R) compared to stem cell-like cell populations obtained when cultivated in the presence of W/R (+ W/R). B Left: multidimensional scaling (MDS) of methylation proportions (beta) based on the 1000 most variable CpGs in the normalized data set; samples from three biological replicates under the indicated conditions. Right: hierarchical cluster analysis (dendrogram) of all CpGs (n = 738,115) in the normalized data set. C Volcano plots representing stomach inter-regional comparisons (+ W/R and − W/R combined). The dashed horizontal and vertical lines indicate cutoffs of FDR < 0.05 and delta beta between − 0.2 and 0.2, respectively. Red dots refer to hypermethylated CpGs (hyper) and blue dots to hypomethylated CpGs (hypo). D Enrichment of sets of CpGs hypermethylated (left) or hypomethylated (right) in antrum compared to corpus biopsies relative to differential methylation of CpGs between antrum and corpus mucosoids. Moderated t-scores were used for DM CpG ranking. ES—enrichment score; NES—normalized enrichment score. Hyper, Hypo indicate the direction of differential methylation in the antrum vs. corpus mucosoids comparison

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