Extended Data Fig. 2: Characteristics of malignant cells in PT and RT samples, related to Fig. 2.
(a) Volcano plot shows differentially expressed genes (DEGs) between PT (blue) and RT (red) malignant cells, genes with top10 fold-changes are shown for each group. (b) Gene Set Enrichment Analysis (GSEA) and Gene Ontology of the DEGs between malignant cells from PT (blue) and RT (red) samples, based on the subontology of biological processes. (c) The proportion of significant interactions from fibroblasts to malignant cells compared with significant interactions from other immune cells to malignant cells inferred by LIANA. For fibroblasts, the proportion was calculated using the interaction number between fibroblasts (source) and tumor cells (target) as the numerator and the total interactions sent from fibroblasts as the denominator. For other immune cells, the proportion was calculated using the interaction number between other immune cells (source) and tumor cells (target) as the numerator and the total interactions sent from other immune cells as the denominator. Two-sided proportions z-test. (d) Schematic diagram illustrating the construction of radioresistant cell lines. (e) Representative images of the colony-forming assay of radiation-resistant (R, red) and wild type (W, blue) C666 and TW03 cell lines after being irradiated at doses of 0, 2, 4, 6, and 8 Gy. The right panel indicates the survival fractions of each cell line. Two-sided paired t-test. Scale bars, 5 mm. (f) The Spearman correlation between mutation load and the signature scores of four cancer cell-intrinsic transcriptional programs within PT and RT. Two-sided Spearman’s correlation test. (g) The Spearman correlation between mutation load and the ratios of various cell populations in TME within PT and RT. Two-sided Spearman’s correlation test. (h) Characterization of malignant cells and fibroblasts on spatial transcriptomics data using cell-type deconvolution. Scale bars, 500 µm. (i) Bar chart showing the number of significant L-R interactions from immune cells to malignant cells in PT (blue) and RT (red) samples.
