From resistance to sensitivity and back – the full circle of resisting the inescapable

Cancer is a genetic disease characterized by the unrestrained proliferation of malignantly transformed cells. In this thesis we study the mechanisms of resistance to targeted therapeutics, drugs that target specifically the protein products of mutated genes “driving” the progression of cancer, or signaling pathways that are hyper-activated by cancer-promoting mutations. Some of these agents have made a significant clinical success, especially in terms of prolonging progression-free survival, but with limited improvements in overall survival due to the emergence of resistance. Chapter 1 gives an overview of main strategies used to overcome the development of resistance to targeted agents, such as drug combination treatments based on genetic concepts of synthetic lethality and collateral dependency. Chapter 2 presents the discovery of a synthetic lethal drug combination of FGFR and PI3K inhibitors in FGFR-driven lung and bladder cancer. This finding was based on a functional genetic screen, an unbiased approach designed to find enhancers of sensitivity to FGFR inhibitors. We validate our findings in vitro, using both genetic and pharmacological approach, and in vivo, using xenograft mouse models. We also uncover the molecular mechanism underlying this synergy, showing that the inhibition of FGFR causes a rapid feedback activation of the receptor tyrosine kinases (RTKs) EGFR and HER3. This finding gives a solid rationale for clinical testing of FGFR inhibitors in combination with PI3K inhibitors in cancers driven by the genetic activation of the FGFR genes. Chapter 3 starts with a goal to find synthetic lethal interactions specific to mutant RAS. We describe the results of genome-wide genetic screens in yeast, and validate them in KRAS mutant colorectal cancer cells. We find that the loss of the endoplasmic reticulum (ER) stress sensor ERN1 does not affect growth, but sensitizes to MEK inhibition. Next, we uncover the mechanistic connection between ERN1 and the MAPK pathway and establish the ERN1-JNK-JUN pathway as a novel regulator of MEK inhibitor response in KRAS mutant colon cancer. This finding contributes to explaining the resistance of KRAS mutant tumor cells to MEK inhibitor treatment. Chapter 4 uncovers the unexpected connection between the osteogenic master regulator transcription factor RUNX2 and its cofactor CBFB, with the MAPK pathway. We first show that the loss of RUNX2 or CBFB can confer MEK inhibitor resistance in colorectal cancer cells. Mechanistically, we find that the inactivation of these genes results in activation of multiple RTKs which is mirrored by the high SHP2 phosphatase activity. Next, we find that high SHP2 activity has a causal role to loss of RUNX2-induced MEK inhibitor resistance. Finally, we find that SHP2 inhibitor reinstates sensitivity to MEK inhibitor in RUNX2 knockout KRAS mutant colorectal cancer cells. Chapter 5 gives an overview of the recently reported clinical studies on PI3K inhibitor buparlisib used in Chapter 2. This is relevant for understanding future perspectives of our findings. Finally, I discuss the limitations of the synthetic lethality as a concept, and give examples of RAS synthetic lethality studies, discussing how they complement the work described in Chapters 3 and 4