Fig. 4: Characteristic proteins and the driver pathway of the PC-Cc.

A The volcano plot illustrates prognosis-related proteins which are also enriched in PC-Cc. The Cox proportional hazards model is used for survival analysis. B The scatter plot illustrates the correlation between APEX1 abundance and cell proliferation (n = 122 samples). The boxplot presents the correlation between APEX1 and Ki67 levels. C The plots illustrate the increased proliferation of RKN and SK-UT-1B cell lines after SHC1 overexpression (n = 3 biological repeats per group). D The volcano plot illustrates proteins significantly associated with APEX1. The Pearson’s correlation test is used for associated analysis. E Flow chart shows IP-MS steps of primary patient-derived cancer cells (PDCs) isolated from patients with different APEX1 expression. F The volcano plot shows up-regulated proteins in high-APEX1 PDCs group. The two-sided student’s t test is used for the statistical comparison. G The plots illustrate the correlation between NPM1 abundance and cell proliferation. Data is presented as Fig. 4B. H The Kaplan-Meier curve illustrate the interacted impact of APEX1 and NPM1 on patient’s overall survival times. Cox proportional hazards model is used for survival analysis. I The heatmap presents the enrichment of APEX1, NPM1 and NPM1 Ser125 in PC-Cc. Wilcoxon rank test is used for statistical analysis. J The scatter plot illustrates kinases both correlated with NPM1 Ser125 and enriched in PC-Cc. The Spearman’s correlation is used for associated analysis and the two-sided student’s t test is used for different expression analysis. K Proliferation rate of the RKN cell line is promoted by RIOK1 (n = 4 biological repeats per group). L Boxplots reveal the influence of RIOK1on APEX1, Ki67 and NPM1 Ser125 in the RKN cell line (n = 3 biological repeats per group). M Proliferation rate of the RKN cell line promoted by RIOK1 is associated with NPM1 Ser125 (n = 4 biological repeats per group). N Boxplots reveal the impact of NPM1 Ser125 mutation on APEX1, Ki67 and NPM1 Ser125 in the RKN cell line (n = 3 biological repeats per group). O The diagram illustrates the comprehensive mechanism of RIOK1, APEX1, and NPM1 in promoting cell proliferation. For scatter plots in (B, G), the Pearson’s correlation is used for associated analysis. The error band represents the 95% confidence interval of the regression line. For boxplots in (B, G, L, N), the middle bar represents the median and the box represents the interquartile range. Bars extend to 1.5× the interquartile range. Kruskal-Wallis’s test is used for statistical analysis. For (C, K, M), data is presented as the mean value +/- SE. The two-sided student’s t test is used for statistical analysis at the 5th day. Source data are provided as Source Data files.