Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer.

CDK4/6 inhibitors are a promising treatment strategy in tumor therapy but are hampered by resistance mechanisms. This study was performed to reveal predictive markers, mechanisms of resistance and to develop rational combination therapies for a personalized therapy approach in bladder cancer.

A genome-scale CRISPR-dCas9 activation screen for resistance to the CDK4/6 inhibitor Palbociclib was performed in the bladder cancer derived cell line T24. sgRNA counts were analyzed using next generation sequencing and MAGeCK-VISPR. Significantly enriched sgRNAs were cloned and validated on a molecular and functional level for mediating resistance to Palbociclib treatment. Analysis was done in vitro and in vivo in the chorioallantois membrane model of the chicken embryo. Comparison of screen hits to signaling pathways and clinically relevant molecular alterations was performed using DAVID, Reactome, DGIdb and cBioPortal.

In the screen, 1024 sgRNAs encoding for 995 genes were significantly enriched indicative of mediators of resistance. 8 random sgRNAs were validated, revealing partial rescue to Palbociclib treatment. Within this gene panel, members of Receptor-Tyrosine Kinases, PI3K-Akt, Ras/MAPK, JAK/STAT or Wnt signaling pathways were identified. Combination of Palbociclib with inhibitors against these signaling pathways revealed beneficial effects in vitro and in in vivo xenografts.

Identification of potential predictive markers, resistance mechanisms and rational combination therapies could be achieved by applying a CRISPR-dCas9 screening approach in bladder cancer.

Journal of experimental & clinical cancer research : CR. 2019 Jul 22*** epublish ***

Zhichao Tong, Anuja Sathe, Benedikt Ebner, Pan Qi, Christian Veltkamp, Juergen E Gschwend, Per Sonne Holm, Roman Nawroth

Department of Urology, Klinikum rechts der Isar, Technical University of Munich, Ismaninger Strasse 22, 81675, München, Germany., Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, Technical University of Munich, Einsteinstrasse 25, 81675, Munich, Germany., Department of Urology, Klinikum rechts der Isar, Technical University of Munich, Ismaninger Strasse 22, 81675, München, Germany. .

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