Fig. 2

Trajectory of epithelial cell deterioration. A UMAP clustering of epithelial cells (n = 11,635) from scRNA-seq of patients with CRC. B Expression of marker genes in seven clusters of epithelial cells. C, D Potential trajectory of epithelial cell deterioration in adenoma and carcinoma tissues (n = 3688) inferred using Monocle2 based on gene expression. Pseudotime is shown numbered 1- 6 and the red dash indicates the direction of the pseudotime. E, F The expression levels of APCDD1 and MMP7 in different pseudotime of epithelial cell subpopulation. The average gene expression is indicated by the black dash. G The heatmap shows dynamic changes in gene expression, including benign epithelial markers, mutant genes associated with epithelial cell deterioration, epithelial apoptotic processes, and cell proliferation. H The heatmap shows expression of cell type-specific gene markers in different epithelial cell clusters. Marker genes for each cluster identified by Seurat analysis, with four genes selected for each cluster highlighted at the top