Microtubule Dynamics Deregulation Induces Apoptosis in Human Urothelial Bladder Cancer Cells via a p53-Independent Pathway

Abstract

Bladder cancer (BLCA) is the sixth most common type of cancer and has a dismal prognosis if diagnosed late. To identify treatment options for BLCA, we systematically evaluated data from the Broad Institute DepMap project. We found that urothelial BLCA cell lines are among the most sensitive to microtubule assembly inhibition by paclitaxel treatment. Strikingly, we revealed that the top dependencies in BLCA cell lines include genes encoding proteins involved in microtubule assembly. This highlights the importance of microtubule network dynamics as a major vulnerability in human BLCA. In cancers such as ovarian and breast, where paclitaxel is the gold standard of care, resistance to paclitaxel treatment has been linked to p53-inactivating mutations. To study the response of BLCA to microtubule assembly inhibition and its mechanistic link with the mutational status of the p53 protein, we treated a collection of BLCA cell lines with a dose range of paclitaxel and performed a detailed characterization of the response. We discovered that BLCA cell lines are significantly sensitive to low concentrations of paclitaxel, independently of their p53 status. Paclitaxel induced a G2/M cell cycle arrest and growth inhibition, followed by robust activation of apoptosis. Most importantly, we revealed that paclitaxel triggered a robust DNA-damage response and apoptosis program without activating the p53 pathway. Integration of transcriptomics, epigenetic, and dependency data demonstrated that the response of BLCA to paclitaxel is independent of p53 mutational signatures but strongly depends on the expression of DNA repair genes. Our work highlights urothelial BLCA as an exceptional candidate for paclitaxel treatment. It paves the way for the rational use of a combination of paclitaxel and DNA repair inhibitors as an effective, novel therapeutic strategy.

A novel pipeline for prioritizing cancer type‐specific therapeutic vulnerabilities using DepMap identifies PAK2 as a target in head and neck squamous cell carcinomas

“…The largest group of enriched dependencies consisted of 8 serine/threonine kinases that have diverse signalling functions. This group notably included three Rho/Rac effector proteins: (a) the MAP3K11 gene product, mixed lineage kinase 3 (MLK3), which is an upstream regulator of MAPK signalling [34] and phosphorylates IjB kinase (IKK) a and b, thereby activating NF-jB (11), (b) PKN2, a promoter of cell cycle progression previously been explored as a target in HNSCC [35], and (c) PAK2, a multi-function kinase that integrates cellular stress responses with activation of oncogenic signalling pathways [36] and proved to be of particular interest in subsequent analyses in this study. The other two enriched functional groups were comprised of mitochondrial carrier proteins and RNA-binding proteins, which have only recently drawn interest as potential therapeutic targets in cancer.…”

“…However, the published analyses of DepMap CRISPR screen data have mostly been conducted on a pan‐cancer basis and offer limited guidance for pursuing therapeutic vulnerabilities and predictive biomarkers specific to individual cancer types. Furthermore, analyses of individual cancer types in DepMap to date have narrowly focused on features distinguishing a malignancy of interest from the pan cancer dataset [ 7 , 8 , 9 ], predetermined biological processes [ 10 , 11 , 12 , 13 ], or developing prognostic models [ 14 , 15 , 16 , 17 ].…”