Fig. 1
From: Prostate cancer multiparametric magnetic resonance imaging visibility is a tumor-intrinsic phenomena
Proteomics of mpMRI visibility. A Sample outline. B Summary of quantified proteins in various number of samples. Differentially abundant proteins in mpMRI-visible (n = 20) and mpMRI-invisible (n = 20) NATs (C), mpMRI-visible (n = 21) and mpMRI-invisible tumors (n = 20) (D), and tumor (n = 40) and NAT regions (n = 40) (E). Statistically significant (FDR < 0.05, Mann–Whitney U test) proteins colored in black. F Comparison of tumor/NAT in the proteome (ntumor = 40, nNAT = 40) and transcriptome (ntumor = 499, nNAT = 53). Genes that were significantly associated with tumors or NATs at both the protein and RNA levels (FDR < 0.05) are colored in black. G Associations of protein abundance changes between tumor versus NAT and mpMRI-visible tumor versus mpMRI-invisible tumor, using proteins that were significantly differentially expressed in tumor versus NAT (n = 2540). Significant (FDR < 0.05) proteins from the tumor/NAT comparison that had the same directionality in the mpMRI-visible/invisible tumor comparison are colored in black. H Distribution of Euclidean distance between each group and median protein abundance in NATs. Only proteins that were quantified in all tumor and NAT samples were used (n = 2309). IDC/CA groups were determined based on the presence of intraductal carcinoma (IDC) or cribriform architecture (CA) histology (IDC/CA+, n = 11) or not (IDC/CA−, n = 29). Hypoxia groups (n = 20 per group) were determined by median dichotomization (median Ragnum score = −1). I Gene set enrichment analysis for 3 sets of comparisons (Tumor/NAT, mpMRI-visible/invisible tumor, and mpMRI-visible/invisible NAT) using the Hallmark gene set. The union of significant terms (FDR < 0.25) are shown. The size of the dot represents the magnitude of the effect, the color denotes the direction (positive: orange; negative: blue), and background shading the FDR-adjusted p-value. Only significant associations (FDR < 0.25) have gray background. mpMRI: multiparametric magnetic resonance imaging; PI-RADSv2: Prostate Imaging Reporting and Data System version 2; pISUP: pathological International Society of Urological Pathology Grade Group; CNA: Copy number abberation; NAT: normal tissue adjacent to the tumor; FDR: Benjamini–Hochberg false discovery rate; FC: fold change; ρ: Spearman’s rho; p: p-value; NES: normalized enrichment score; and IDC/CA: Intraductal carcinoma or cribriform architecture