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Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex.

ABSTRACT: Targeting the dysregulated BRAF-MEK-ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRAF and MEK, resistance develops often involving nongenomic adaptive bypass mechanisms. Inhibition of MEK1/2 by trametinib in patients with triple-negative breast cancer (TNBC) induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTK) comparing tumor samples before and after one week of treatment. In preclinical models, MEK inhibition induced genome-wide enhancer formation involving the seeding of BRD4, MED1, H3K27 acetylation, and p300 that drives transcriptional adaptation. Inhibition of the P-TEFb-associated proteins BRD4 and CBP/p300 arrested enhancer seeding and RTK upregulation. BRD4 bromodomain inhibitors overcame trametinib resistance, producing sustained growth inhibition in cells, xenografts, and syngeneic mouse TNBC models. Pharmacologic targeting of P-TEFb members in conjunction with MEK inhibition by trametinib is an effective strategy to durably inhibit epigenomic remodeling required for adaptive resistance.Significance: Widespread transcriptional adaptation to pharmacologic MEK inhibition was observed in TNBC patient tumors. In preclinical models, MEK inhibition induces dramatic genome-wide modulation of chromatin, in the form of de novo enhancer formation and enhancer remodeling. Pharmacologic targeting of P-TEFb complex members at enhancers is an effective strategy to durably inhibit such adaptation. Cancer Discov; 7(3); 302-21. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 235.

SUBMITTER: Zawistowski JS

PROVIDER: S-EPMC5340640 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex.

Zawistowski Jon S JS Bevill Samantha M SM Goulet Daniel R DR Stuhlmiller Timothy J TJ Beltran Adriana S AS Olivares-Quintero Jose F JF Singh Darshan D Sciaky Noah N Parker Joel S JS Rashid Naim U NU Chen Xin X Duncan James S JS Whittle Martin C MC Angus Steven P SP Velarde Sara Hanna SH Golitz Brian T BT He Xiaping X Santos Charlene C Darr David B DB Gallagher Kristalyn K Graves Lee M LM Perou Charles M CM Carey Lisa A LA Earp H Shelton HS Johnson Gary L GL

Cancer discovery 20170120 3

Targeting the dysregulated BRAF-MEK-ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRAF and MEK, resistance develops often involving nongenomic adaptive bypass mechanisms. Inhibition of MEK1/2 by trametinib in patients with triple-negative breast cancer (TNBC) induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTK) comparing tumor samples before and af ...[more]

PMID: 28108460

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Project description:Triple negative breast cancer (TNBC) is heterogeneous with patients exhibiting at least two molecular subtypes, basal-like (BL) and claudin-low (CL). MEK inhibitor (MEKi) treatment of BL and CL cell lines and mouse model tumors induced subtype-specific alterations in overall kinome activity referred to as protein kinase reprogramming. BL- and CL-specific reprogramming involving increases in receptor tyrosine kinases was also seen in TNBC patients comparing tumor samples before and after a one week treatment with the MEKi, trametinib. Combination of kinase inhibitors targeted to the BL and CL reprogrammed signatures would need to be individually selected due to the heterogeneous resiliency of BL and CL kinomes. To overcome this “reprogramming dilemma” we targeted the transcriptional co-activator BRD4 with BET bromodomain inhibitors, JQI and IBET151; both strongly inhibited kinome reprogramming and onset of MEKi resistance in BL and CL cells. Targeting chromatin modifiers may therapeutically block resistance due to kinome reprogramming.BL and CL TNBC are commonly treated as a single disease despite genomic studies showing they represent distinct molecular subtypes1. Recent Cancer Genome Atlas data demonstrated that the 518 protein kinases in the human genome (the kinome) were infrequently mutated in BL breast cancer; however, EGFR, KRAS and BRAF were amplified in 22, 32 and 31% of BL tumors, respectively. These findings are consistent with frequent activation of the BRAF-MEK-ERK pathway in TNBC2,3 and inhibitors targeting kinases in this pathway are currently in clinical trials for TNBC. As single agents, targeted kinase inhibitors generally fail to sustain durable responses when used to treat a range of human cancers including TNBC4-6. Onset of kinase inhibitor resistance can be due to selection of mutations in the targeted kinase7,8, activating mutations or amplification of RAS or downstream kinases9,10 or kinome reprogramming, a process in which there are system-wide changes in kinase networks11-13. Each of these resistance mechanisms allows the cancer cell to circumvent the targeted inhibition of specific kinases14. We previously developed chemical, proteomic methods that assay the activation state of protein kinases en masse15,16. Our methods utilize ¬Multiplexed Inhibitor Beads (MIBs), mixtures of covalently immobilized, linker adapted, kinase inhibitors. The immobilized inhibitors are primarily type I kinase inhibitors that preferentially bind activated (versus inactive) kinase17. Kinase capture is highly reproducible and is a function of kinase affinity for different immobilized inhibitors as well as the kinase activation state. Activated kinases preferentially bind, inactive kinases do not. By coupling MIB capture with mass spectrometry (MIB/MS), the technique allows quantitative interrogation of hundreds of kinases in a single mass spectrometry run. This also interrogates kinases known by sequence but which have been understudied due to lack of reagents such as specific phospho-antibodies. We report here both in preclinical models and patients that BL and CL TNBC have different baseline kinome activation states and both respond differently to MEKi with subtype-specific tyrosine kinase reprogramming. To avoid treatment strategy that uses multiple kinase inhibitors in individual patients, we discovered a novel pharmacologic strategy to block the initial reprogramming response to MEKi involving inhibition of epigenetic processes.

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Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex.

Publications

Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex.

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