Fig. 4: RPRD1B expression predicts response to radiotherapy in SBC.

A Heatmap of differentially regulated (FDR < 0.05, log2FC > 0.3) DNA repair-related proteins between radio-resistant (n = 26) and radio-sensitive groups (n = 47). B CIN scores among high-dose resistant (n = 7), low-dose resistant (n = 19), high-dose sensitive (n = 21), and low-dose sensitive (n = 26) groups. C Proteins significantly correlated with both radio-resistance degree and CIN score, n = 96. D Protein expression levels of RPRD1B among high-dose resistant (n = 7), low-dose resistant (n = 19), high-dose sensitive (n = 21), and low-dose sensitive (n = 26) groups. E, F Chordoma cell viability assays with knockdown of RPRD1B or/and exposure to 32 Gy (E) or 64 Gy (F) of irradiation. Scrambled siRNA: treated with 32 Gy or 64 Gy of irradiation. A: treated with 32 Gy or 64 Gy of irradiation and RPRD1B siRNA1-knockdown. B: treated with irradiation and RPRD1B siRNA2-knockdown. C: treated with RPRD1B siRNA1-knockdown. D: treated with RPRD1B siRNA2-knockdown (n = 6 for each group, biological replicates; mean ± SEM; Student’s t-test, two-sided). G HDR and MMR pathways significantly correlated with CIN score and RPRD1B. H Heatmap showing the copy number/mRNA/proteins/phosphoproteins levels of HDR and MMR related genes (top panel), the ssGSEA score of cell cycle pathway, and the radio-resistance degree (bottom panel), n = 96. I ssGSEA scores of HDR, MMR, G1 phase and S phase, n = 96. J Correlations of cell cycle-related proteins with HDR and MMR, n = 96. K Heatmap showing abundance/kinase activities of MCM2 phosphoprotein, MCM2_S27, CSNK2A1, CDK7, CDK2 and CDC7, n = 96. L A brief model depicting the G1 and S phase genes most affected by CIN score, HDR and MMR (n = 96). The p-values in (C) and (G–K) were calculated by Spearman’s correlation test (two sided). For boxplots in (B) and (D) the middle bar represents the median, and the box represents the interquartile range; bars extend to 1.5 × the interquartile range. Anova and Kruskal−Wallis test were used for comparisons among four groups, Wilcoxon rank-sum test were used for comparisons between two groups. n.s., not significant; *p < 0.05; **p < 0.01; ***p < 0.001.