To approximate intra-tumor heterogeneity, we used the bulk transcriptomic profiles and the consensus clustering results for the UROMOL cohort and applied the Weighted in silico pathology (WISP, R package v. 2.3) method with default settings. Only samples with a positive silhouette score were used for the WISP analysis (n = 505). WISP consists of two main steps: (1) Calculation of pure population centroid profiles and (2) Estimation of pure population weights for each sample. First, WISP selects features for each class by iteratively considering ANOVA p-values (FDR adjusted p-values < 0.05), AUC scores (AUC > 0.8) and expression log-fold changes between classes, fitting a non-negative least squares model and removing samples considered mixed. A model is then built from the core of pure samples for each class (154 samples were kept as “pure” and 199 top marker genes were included in the centroid profiles). Next, WISP class weights were estimated for all the samples in the cohort (n = 505) using the centroid profiles (hence, each sample is weighted between all four transcriptomic classes). We recovered the estimated WISP class weights and used Pearson and Spearman correlations to investigate their association to silhouette scores and MCPcounter immune scores86, respectively. Finally, we used Wilcoxon rank-sum tests to associate WISP class weights to genetic mutations and clinical variables.

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