Investigating the requirement of KRAS for the maintenance of pancreatic cancer

Abstract

Pancreatic cancer, of which 85% is pancreatic ductal adenocarcinoma (PDAC), is the fourth leading cause of cancer death in the United States and a major cause of mortality and morbidity worldwide. Although recent advances in multi-agent chemotherapies have increased median survival in advanced disease, the 5-year survival rate for PDAC patients remains low at 7%, highlighting an urgent need for novel therapeutic options with improved efficacy and reduced toxicity. Genomic studies have identified mutations in the proto-oncogene KRAS as a hallmark of PDAC, making KRAS an attractive therapeutic target. While the driver role of oncogenic KRAS for PDAC initiation has been well established, the degree of KRAS oncogene addiction in established PDAC tumors remains unclear. To facilitate the development of targeted therapies for PDAC, we sought to elucidate the requirement of endogenous KRAS for PDAC maintenance and potential resistance mechanisms that may arise in response to KRAS inhibition. Since there is no effective pharmacological KRAS inhibitor to date, we interrogated the requirement of KRAS for PDAC cell survival using an inducible shRNA-based system that enables precise temporal control of endogenous KRAS expression. Surprisingly, the majority of PDAC cells analyzed tolerated acute and sustained Kras knockdown by adapting to a reversible cell state, characterized by differences in cell morphology, proliferative kinetics, and tumor-initiating capacity. While significant mutational or transcriptional changes were not observed in the KRAS-inhibited state, global phosphoproteomic profiling revealed alterations in cell signaling, including increased phosphorylation of focal adhesion pathway components. Accordingly, KRAS-inhibited cells displayed focal adhesion plaque formation, enhanced adherence properties, and increased dependency on adhesion for viability in vitro. Our analyses highlighted the possibility of adaptive non-genetic and non-transcriptional mechanisms of resistance to KRAS inhibition. As most PDAC cells tolerated partial inhibition of KRAS, we explored whether the observed adaptive resistance can be overcome by CRISPR/Cas-mediated KRAS ablation. While KRAS knockout led to decreased in vitro proliferation and impaired in vivo tumorigenic growth, KRAS was dispensable in a subset of human and mouse PDAC cells. KRAS knockout cells exhibited a unique dependency on P13K activation. Mechanistically, P13K inhibition in KRAS knockout cells led to transient MAPK blockade while impeding AKT-dependent 4EBP 1 phosphorylation and cap-dependent translation. Furthermore, comparison of gene expression profiles of cells retaining or lacking KRAS revealed a novel functional role of KRAS in the suppression of metastasis-related genes. Taken together, our data suggested that the majority of PDAC cells can tolerate sustained partial KRAS inhibition by adaptation and upregulation of focal adhesion signaling. Therefore, candidate targets from this pathway can provide a basis for rational design of combination therapeutic strategies with novel KRAS inhibitors. Importantly, KRAS is non-essential in at least a subset of human and murine PDAC cells, demonstrating the potential for resistance to even the very best of KRAS inhibitors. Finally, combination therapies with P13K inhibitors may be a viable strategy to circumvent resistance to KRAS inhibition.