Figure 3.

UM PDOs have differential gene expression based on BAP1 status. (A) Heatmap of z-scores for differential gene expression between BAP1-retained and BAP1-loss PDOs using DeSeq2. Differential expression determined using ±1 log fold change and P ≤ 0.1. (B) Heatmap of z-scores for gene expression of a subset of genes used on a well-validated clinical prognostic gene expression profiling test and further analyzed in TCGA samples shows that uveal melanoma PDOs simulated expression patterns seen in the clinical samples. BAP1 loss is a known poor prognostic indicator. Genes with low expression in high-risk primary UM by gene expression profiling and TCGA are denoted by the yellow panel, and those with high expression in high-risk tumors are denoted by the green panel. High-risk PDOs, defined by those with BAP1 loss, followed the expected pattern of prognostic gene expression.