Fig. 3: Impacts of chromosome 1q gain in SBC.

A Volcano plot showing significant arm-level CNA events in primary SBCs (n = 106) and their associations with prognosis (Hazard ratio, 95% CI). B Survival Kaplan–Meier curves of primary SBC patients with 1q gain (n = 38) or others (n = 66) (p-value from log rank test). Upper panel, OS; lower panel, PFS. C Stacked bar plot showing the proportions of tumors with or without 1q gain in CIN+ and CIN- SBC (Fisher’s exact test, two-sided, n = 163). D Boxplot showing differential CIN score among primary/recurrent SBC tumors with/without 1q gain (Wilcoxon rank-sum test): primary with 1q gain (n = 35), primary without 1q gain (n = 71), recurrent with 1q gain (n = 25), and recurrent without 1q gain (n = 31). The middle bar represents the median, and the box represents the interquartile range; bars extend to 1.5 × the interquartile range. E Venn diagram showing the significant cis events on chromosome 1q (Spearman’s correlation, two-sided, p < 0.05, Rho > 0.2), n = 163. F Pathways enriched for significant 1q cis-effect genes (q value < 0.05), n = 163. G GSEA plot showing upregulated mitochondrial gene expression in the tumors with 1q gain versus the others. H Scatterplot showing the Spearman’s correlation coefficient and p-value (two-sided) of the CIN score versus the ssGSEA score of mitochondrion gene set (95% CI for the regression band), n = 163. I The histochemistry scores (H-scores) of ATP5A1 (n = 5) and TOMM20 (n = 3) between tumors with 1q gain and tumors with 1q WT (Student’s t-test, two-sided, mean ± SEM). J Scatterplot showing the Spearman’s correlation coefficients (two-sided) of mitochondrial gene set scores versus 1q copy number (x axis, n = 163) and the associations with prognosis (y axis, n = 119). K Heatmap of representative significant cis- and trans-event genes associated with 1q gain in SBC. L Scatterplot showing the p-values for PFS (x-axis, n = 106) and the Spearman’s correlation coefficients (two-sided) of the metabolism-related pathways(n = 187). M A model depicting the multi-level regulation of chromosome 1q copy number alteration.