Disrupting Adaptive Bypass Pathways Activated By Targeted Kinase Inhibitors

Small molecule kinase inhibitors that target oncogene‐driven cancers often elicit dramatic initial clinical outcomes, but adaptive responses from the kinome and transcriptome limit their efficacy and generate resistance. Such adaptive bypass responses activate signaling networks driving proliferation and survival. To understand the adaptive response in triple negative breast cancer (TNBC), we used a chemical proteomics method [multiplexed inhibitor beads coupled to mass spectrometry (MIB/MS)] to quantify global changes in kinase activity coupled with RNAseq for transcriptional changes to the MEK1/2 inhibitor trametinib. A primary component of the adaptive response to MEK1/2 inhibition is the transcriptional upregulation and activation of receptor tyrosine kinases (RTKs), which contributes to drug resistance by reactivating ERK, as well as by initiating growth signaling through additional kinases. RTKs activated differ between TNBC basal‐like and claudin‐low subtypes, and adaptive upregulation of RTKs is heterogeneous even among the same TNBC subtype. This makes designing effective targeted kinase inhibitor combinations for durable responses challenging. Targeting the chromatin reader protein BRD4 via BET bromodomain inhibition attenuates the transcriptional adaptive response to MEK inhibition, yielding a durable growth suppression. We have discovered using ChIP‐seq the dynamic formation of BRD4‐dense enhancers that are formed in response to 24 h MEK1/2 inhibition in TNBC cells. In SUM159PT claudin‐low breast cancer cells, de novo enhancers validated by ChIP‐seq of histone H3K27ac, MED1 and p300, demonstrating their co‐occupancy with BRD4. Enhancers were found proximal to genomic loci of DDR1, KDR, ROS1 and MYLK, kinases previously defined to be upregulated in the adaptive MEK1/2 inhibitor response. We identified 110 putative MEK inhibitor‐induced SUM159PT “super‐enhancers”, 40% of which reside within 100 kilobases 5′ or 3′ of a gene whose transcript is upregulated 2‐fold or greater by MEK1/2, suggesting that de novo super‐enhancer formation is a general mechanism of transcriptional regulation of the adaptive response. The MEK1/2 inhibitor‐induced super‐enhancers are disrupted by the BET bromodomain inhibitors JQ1 or I‐BET151, providing a mechanism for the growth suppression synergism obtained by combining MEK1/2 + BET bromodomain inhibition. Mouse xenograft and orthotopic serial transplant TNBC tumor studies show significantly enhanced growth suppression in vivo using combination trametinib/I‐BET151 treatment relative to trametinib or I‐BET151 treatment alone. These data demonstrate novel insight into mechanisms underlying the transcriptional control of the adaptive resistance response to MEK1/2 inhibition. Similar findings have been discovered for lapatinib inhibition of HER2‐driven breast cancers. Cumulatively, the findings indicate that targeting drug‐induced enhancer elements is a potential therapeutic treatment for TNBC. Support or Funding Information Supported by NIH grants GM101141, Susan G. Komen foundation IIR12‐225201, NCIBreast SPORE CA58223 and the University Cancer Research Fund.