Extended Data Fig. 10: Single-cell RNA-seq profiling of p53mCherry⁺ JPH203-resistant cells.

(a) High quality single cells from two p53mCherry⁺ JPH203-resistant samples collect at 2.5 M or 3 M of age (JR2.5 M or JR3M) were integrated with single cells shown in Fig. 4b by Harmony for cell clustering and annotation. Cells from individual samples are shown in UMAP scatter plots. Colors distinguish cell types. ISP G2M and G1/S cells were grouped together as cycling ISPs. n = 10417 and 11580 cells, respectively. (b) The cell-type composition among the two samples in (A). Cell#, the total number of high-quality cells in each sample. CD4 or CD8 single-positive T cells were grouped together as SP. Non-T, non-T cell lineage cells. (c) Violin plots of scaled Mki67 expression in cycling ISPs from different clones/subclones in WT, treatment-naïve, and treatment-resistant samples. ***, P adj. < 0.001, two-tailed Kruskal–Wallis test for between group differences with Holm’s correction for multiple comparisons. (d) Cycling ISPs from resistant samples (JR2.5 M or JR3M) were compared with those from treatment-naïve precancerous samples. Genes commonly upregulated or downregulated in ISPs from both resistant samples were subjected to GSEA analysis (P adj. < 0.01). P values and NES scores were calculated using GSEA algorithm (Methods).