A Landscape of Therapeutic Cooperativity in KRAS Mutant Cancers Reveals Principles for Controlling Tumor Evolution

Abstract

Summary Combinatorial inhibition of effector and feedback pathways is a promising treatment strategy for KRAS mutant cancers. However, the particular pathways that should be targeted to optimize therapeutic responses are unclear. Using CRISPR/Cas9, we systematically mapped the pathways whose inhibition cooperates with drugs targeting the KRAS effectors MEK, ERK, and PI3K. By performing 70 screens in models of KRAS mutant colorectal, lung, ovarian, and pancreas cancers, we uncovered universal and tissue-specific sensitizing combinations involving inhibitors of cell cycle, metabolism, growth signaling, chromatin regulation, and transcription. Further, these screens revealed secondary genetic modifiers of sensitivity, yielding a SRC inhibitor-based combination therapy for KRAS/PIK3CA double mutant colorectal cancers with clinical potential. Surprisingly, acquired resistance to combinations of growth signaling pathway inhibitors develops rapidly following treatment, but by targeting signaling feedback or apoptotic priming, it is possible to construct three-drug combinations that greatly delay its emergence.

SHP2 Inhibition Abrogates MEK inhibitor Resistance in Multiple Cancer Models

“…Tumors evade targeted cancer therapies via an extensive repertoire of resistance mechanisms. One common theme involves activation of RTKs by upregulating their expression and/or the expression of their ligands, which leads to reactivation of the inhibited pathway (5)(6)(7)(8)(9)22,33). Consistent with these findings, multiple, distinct sets of RTKs/RTK ligands were activated in response to MEK-I treatment in the cancer cell models that we tested.…”

“…Both of these malignancies typically express WT RAS, and in some TNBC models, MEK inhibition results in RTK upregulation and adaptive resistance (8). To explore the potential generality of combination 7 MEK/SHP2 inhibition as a therapeutic strategy (and the utility of this combination in adaptive resistance to MEK-I in WT RAS-expressing cells), we tested SHP099 in combination with MEK-I in models of TNBC and HGSC.…”

SHP2 Inhibition Abrogates Adaptive Resistance to KRASG12C-Inhibition and Remodels the Tumor Microenvironment ofKRAS-Mutant Tumors

“…Here, by using two new affinity reagents that allow direct monitoring of KRAS G12C activation and inhibition, we find that G12C-Is evoke adaptive resistance in vitro and in vivo by inducing KRAS G12C re-activation. Similar to the effects of other RAS/ERK pathway inhibitors (48,49,(71)(72)(73)(74)(75), G12C-Is induce RTK/RTK ligand genes, increasing RTK signaling to RAS. SHP2 inhibition, by increasing G12C-I accessibility to mutant KRAS, abrogates adaptive resistance.…”

“…These results suggest that, similar to other "targeted therapies" (51,69,70), G12C-Is, as single agents, will have limited impact due to drug resistance. "Adaptive resistance," in which the inhibited pathway is reactivated due to induction of genes for RTKs/RTK ligands, is a common form of intrinsic resistance to targeted agents (48,49,(71)(72)(73)(74)(75). The host immune system can cure some malignancies; conceivably, all cancer cures might require generation of a durable anti-tumor response.…”

VHLSynthetic Lethality Signatures Uncovered by Genotype-specific CRISPR-Cas9 Screens

“…The site-specific DNA double-strand breaks induced by CRISPR-Cas9 are mainly repaired by non-homologous end joining, which often causes gene disruption by frameshift mutation. Given its high efficiency and scalability, CRISPR-Cas9 has been quickly adopted in genome-wide loss-of-function genetic screens to identify common and context-dependent essential genes in mammalian cells [43][44][45][46][47][48][49][50][51][52][53].…”