MEK is a promising target in the basal subtype of bladder cancer

Abstract

While many resources exist for the drug screening of bladder cancer cell lines in 2D culture, it is widely recognized that screening in 3D culture is more representative of in vivo response. Importantly, signaling changes between 2D and 3D culture can result in changes to drug response. To address the need for 3D drug screening of bladder cancer cell lines, we screened 17 bladder cancer cell lines using a library of 652 investigational small-molecules and 3 clinically relevant drug combinations in 3D cell culture. Our goal was to identify compounds and classes of compounds with efficacy in bladder cancer. Utilizing established genomic and transcriptomic data for these bladder cancer cell lines, we correlated the genomic molecular parameters with drug response, to identify potentially novel groups of tumors that are vulnerable to specific drugs or classes of drugs. Importantly, we demonstrate that MEK inhibitors are a promising targeted therapy for the basal subtype of bladder cancer, and our data indicate that drug screening of 3D cultures provides an important resource for hypothesis generation.

Keywords: 3D culture; MEK inhibition; basal bladder cancer; bladder cancer; drug screen.

Figure 1. Distribution of drug sensitivities across bladder cancer cell lines.

652 investigational drugs and 3 clinically relevant combinations were tested against 17 bladder cancer cell lines in 3D cell culture. Drugs are ordered along x-axis by average drug sensitivity (DSS₃), starting with the most sensitive drug. Black circles indicate average DSS₃ and brackets indicate standard deviation across the 17 cell lines.

Figure 2. Genomic landscape of bladder cell lines.

Bladder cancer subtype is indicated across the top row with each column representing an individual cell line. B-L Score was calculated from normalized RNA sequencing and is shown as a gradient from luminal (yellow) to basal (blue). Average drug sensitivity shows the average DSS₃ across all drugs for each cell line. Mutation and genotype are indicated for all prioritized mutations present in 1+ cell line. CNA are indicated for high level amplifications (≥ 2 copy gain) and deep deletions (≥ 2 copy loss) in 1+ cell line.

Figure 3. MEK inhibitors show strongest response in basal bladder cell lines.

Bladder cancer subtype is indicated across the top row with each column representing an individual cell line. B-L Score was calculated from normalized RNA sequencing and is shown as a gradient from luminal (yellow) to basal (blue). Average drug sensitivity shows the average DSS₃ for each cell line. Average DSS₃ of MEK inhibitors for each cell line shown with average DSS₃ > 0. MEK inhibitors ordered by average basal response with the best response at the top. Basal cell lines marked with bolded rectangle.

Figure 4. MEK inhibitor response correlates with basal subtype.

Average and standard deviation for DSS₃ response to (A) Trametinib, (B) TAK-733, (C) Normalized MEK inhibitors, and (D) Average drug response, grouped by cell line subtype. Each point represents an individual cell line. Center line is average and brackets are standard deviation. Significance determined using Mann-Whitney test, ^* p < 0.05, or Kruskal-Wallis with Dunn test for multiple comparisons, ^*** p < 0.001.