Fig. 2: Single-cell profiling of the iCCA microenvironment during GOLP treatment.
A Study diagram and experimental workflow. Created with BioRender.com. B Uniform manifold approximation and projection (UMAP) plot depicting 12 cell lineages from the 18 samples (N = 131,139 cells). C Dot plot showing the average expression levels of marker genes across the 12 cell types. The dot size indicates the fraction of cells expressing the marker gene in each cluster, and the dot color represents the average expression level of the marker gene in each cluster. The dendrogram on the right represents the hierarchical clustering of different cell types based on the expression levels of the indicated marker genes. D Heatmap showing the relationship among the 12 cell types based on the correlation of gene expression between each pair of cell types as assessed by Pearson’s correlation analysis. Blue and red indicate negative and positive correlations, respectively. E Bar plots show the distribution of immune and nonimmune cells in each patient. The samples are presented in pre- and post-GOLP treatment pairs for the 8 patients (Pts. 1–8), and 2 patients underwent surgery without pre-GOLP treatment (Pts. 9 and 10). Pt., patient. For every sample, annotated cell types were divided into immune cell type (T cells, NK cells, pDCs, neutrophils, B cells, and plasma cells: Left) and non-immune cell type (fibroblasts, epithelial cells, endothelial cells, and hepatocytes: Right). For every sample, the percentage of immune cell type plus percentage of non-immune cell type is 100%. F The enrichment scores of different cell types in the pre- and post-GOLP treatment groups. The colors represent different cell types. G, H The Pi (G) and Ti (H) values of major cell types in iCCA patients treated with GOLP (N = 8 paired samples). Pi, predictive index; Ti, therapeutic index. The dot size represents the significance evaluated as -log10 (P value). *: P < 0.05, Wald test, two-sided. Source data are provided as a Source Data file.
