Mediator Kinase Inhibition Impedes Transcriptional Plasticity and Prevents Resistance to Sustained MAPK-Targeted Therapy in KRAS-Mutant Cancers

Acquired resistance remains a major challenge for therapies targeting oncogene activated pathways. KRAS, for example, is the most frequently mutated oncogene in human cancers, yet strategies targeting its downstream signaling kinases have failed to produce durable treatment responses. Here, we developed multiple models of acquired resistance to second-generation MAPK inhibitors across KRAS-mutant pancreatic, colorectal, and lung cancers, then probed the long-term events enabling survival against this class of drugs. These studies revealed that resistance emerges secondary to large-scale transcriptional adaptations that are diverse and tumor-specific. Transcriptional reprogramming extends beyond the well-established early response, and instead represents a dynamic, evolved process that is refined to attain a stably resistant phenotype. Mechanistic and translational studies reveal that resistance to sustained MAPK inhibition is broadly susceptible to manipulation of the epigenetic machinery, and that Mediator kinase, in particular, can be co-targeted at a bottleneck point to prevent diverse, tumor-specific resistance programs. ChIP-Seq for H3K27ac (antibody from Active Motif: 39133) was performed on KRAS-mutant pancreatic cancer cells (MIA PaCa-2 cells) in biological duplicates in 3 treatment populations: 1) 0.01% DMSO 2) treated for 1 week with ERK inhibition (1 µM SCH772984) and 3) following the development of stable resistance to ERK inhibition (treated weekly with 1 µM SCH772984 and split weekly until growth rate exceeded 50% of that of %0.01 DMSO treated controls).