angenommen AFFIDAVIT I hereby declare that the dissertation titled Functional genomics identifies multiple clinical actional resistance mechanisms to CDK4/6 inhibition in bladder cancer prepared under the guidance and supervision of Univ.-Prof. Dr. Jürgen E. Gschwend at the Department of Urology and submitted to the degree-awarding institution of: The Faculty of Medicine of TUM is my own, original work undertaken in partial fulfillment of the requirements for the doctoral degree. I have made no use of sources, materials or assistance other than those specified in § 6 (6) and (7), clause 2.
AbstractThough CDK4/6 inhibition has already been proven as a promising approach for the treatment of bladder cancer in preclinical research. However, mechanisms of resistance still are unclear. Therefore, a genome-scale CRISPR-dCas9 gain of function screen for the CDK4/6 inhibitor Palbociclib was performed in the bladder cancer derived cell line T24. Enrichment of sgRNAs were detected using NGS and statistically significant sgDNAs from the screen were analyzed using MAGeCK-VISPR. 1024 sgRNAs encoding for 995 genes were significantly enriched in the screen. In order to validate these data, 8 randomly chosen sgRNAs within the first most significant 500 sgRNAs were functionally validated on a molecular and functional level for mediating resistance to Palbociclib treatment. Comparison of the screen hits to signaling pathways and clinically relevant molecular alterations was performed using DAVID, Reactome, DGIdb and and cBioPortal. We identified enriched sgRNAs in RTKs, PI3K-Akt and Ras/MAPK signaling pathways that are also frequently activated in bladder cancer. Combination of Palbociclib with compounds directed against RTKs, PI3K-Akt, Ras/MAPK and STAT pathways revealed beneficial effects in vitro and in vivo xenografts. Since activation of the signalingpathways that confer resistance are largely regulated by RTKs, we engineered cells that by sgRNA induced hyperactivation of KDR or FGFR3 mediated resistance to palbociclib. Interestingly, in these cells the combination of Palbociclib and respective inhibitors acted synergistically and overcame acquired resistance in those tumors. However, the combination of Palbociclib and mTOR inhibitors did not overcome the induced resistance of KDR or FGFR3 expression. In conclusion, identification of resistance mechanisms and rational combinational therapies could be achieved applying a genome scale CRISPR-dCas9 approach in this study.