Figure 4 from Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia
Year: 2023
Type: other
Abstract: E-GM and atrophic gastritis share early features of developing IM. A, UMAP of columnar cells of gastric cell types (NGC and NGB, top left), E-GM (top right), and atrophic gastritis (NAG and CAG, bottom left) with cell-type annotation highlighted. Bottom right, UMAP with clusters 6 and 16 (identified during reclustering of columnar cells and overlapping gastric neck cells) highlighted. EE, enteroendocrine. B, Stacked bar chart of tissue contribution to the cells assigned to clusters 6 and 16. C, Gene set enrichment analysis (GSEA) using the C3 gene set database of differentially expressed genes between neck-like cells from E-GM and NGC samples. HNF4A- and MYC-related pathways are highlighted. The differential analysis was done between E-GM cells and NGC + NSCJ neck-like cells with each patient treated as an individual replicate. NES, normalized enrichment score. D, GSEA using the C3 gene set database of differentially expressed genes between NAG/CAG and NGC/NGB/NSCJ sample neck-like cells. AP-1–related pathways are highlighted. The differential analysis was done between cluster 16 cells (including NAG, CAG, and E-GM cells) and cluster 6 (including NGC + NGB + NSCJ neck-like cells) with each patient treated as an individual replicate. E, Venn diagram demonstrating the overlap between genes enriched in the comparison of atrophic gastritis (NAG and CAG) and normal gastric samples or E-GM and normal gastric samples. Bottom left: bubble plot of top 25 expressed genes shared between the comparison. Bottom right, violin plots of selected genes. F, WGS-based analysis of E-GM and BE-IM. Top, mutational burden [single-nucleotide variants/megabase (SNV/Mb)] of NGC, E-GM, and BE-IM samples. Bottom, distribution of COSMIC SNV signatures in the E-GM and BE-IM samples.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W4379137486