Fig. 3: Label-free proteomics reveals RIPK2 as a potent activator of c-Myc.

a Venn diagrams of protein groups that are upregulated (upper) or downregulated (lower) in the three RIPK2-KO PC3 single-cell clones (#4, #12, and #16), compared with control cells. b Heatmap of the 652 overlapping differentially expressed protein groups in the control or RIPK2-KO PC3 clones (3 biological replicates × 2 LC-MS/MS runs). c Scatter plot of putative regulators upstream of the 652 differentially expressed proteins. The activation Z scores and p-values were computed by Ingenuity Pathway Analysis. d Bar plot of the relative MYC luciferase reporter activity in PC3 cells under the indicated conditions (n = 12, 4, and 6 biologically independent samples in the left three, middle three, and right two conditions, respectively). Data are shown as mean ± SEM. e Scatter plot of RIPK2-induced activity Z scores against Hallmark_MYC_Targets_V1 gene-set activity Z scores in the PCTA cohort. f Bar plot of the Spearman’s correlation coefficients (rho) of RIPK2-induced activity scores (red), RIPK2 mRNA levels (orange), and MYC mRNA levels (blue) with MYC activity scores (V1 or V2) in the PCTA or TCGA (Firehose Legacy) PC cohorts. g Venn diagram of genes contained in the RIPK2-induced protein signature (i.e., the 243 protein groups downregulated by RIPK2-KO) and those in the Hallmark_MYC_Targets_V1 (upper) or _V2 (lower) gene set. Nominal p-values were determined by two-sided Fisher’s exact test (c), unpaired two-tailed Student’s t-test (d), or using a t-distribution with n-2 degrees of freedom (e).