<p>This file contains 4 supplementary tables: Table S1 provides the expression values of the indicated genes (RMA) in BETi sensitive and insensitive cell lines; Table S2 shows the enrichment of subtypes of cell lines following selection with the indicated criteria; Table S3 shows SNP analysis of parental and BETi tolerant A375 cells; Table S4 shows SNP analysis of parental and BETi tolerant NOMO-1 cells.</p>
Abstract Cancer is driven in large part by dysregulated transcriptional programs that allow for the acquisition of the many ‘Hallmarks of Cancer.' Multiple regulatory factors are essential for the establishment and maintenance of these cancer-specific transcriptional programs, and this dependence creates vulnerabilities that can be therapeutically targeted. Here we describe a selective dependence on the bromodomain and extraterminal (BET) family of proteins for the reprogramming of apoptotic signaling networks and demonstrate how this dependence can be predicted prior to therapeutic intervention. We demonstrate in phenotypically sensitive cell lines that BET inhibition results in a rapid and robust transcriptional response among regulators of apoptosis, and that this transcriptional response is correlated with changes in the apoptotic threshold of target cells and subsequent apoptosis. We show that the robustness of the apoptotic response, and not that of the cytostatic response, predicts phenotypic sensitivity to BETi. Consistent with this, we observed that acquired BETi tolerance in two disparate cellular models is driven by dysregulated expression of anti-apoptotic BCL2 family proteins, and that genetic or pharmacological manipulation of apoptotic signaling can modify the phenotypic response to BETi. We further demonstrate that the basal expression levels of a set of apoptotic factors significantly predict preclinical response to BETi, and in particular note that BETi preferentially targets those cells that are dependent on BCL2 for survival. Our findings suggest that tumor cells have acquired a dependence on BET bromodomain function to evade apoptosis, and highlight opportunities to exploit this dependence in the clinic through rational patient selection and drug combination strategies. Citation Format: Andrew R. Conery, Richard C. Centore, Kerry L. Spillane, Nicole E. Follmer, Archana Bommi-Reddy, Charlie Hatton, Barbara M. Bryant, Patricia Greninger, Arnaud Amzallag, Cyril H. Benes, Jennifer A. Mertz, Robert J. Sims, III. Targeting dependencies within apoptotic pathways through inhibition of BET bromodomains. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr B19.
<p>This file contains the following: source data for the graphs shown in Figure 3A (GI50, Z sub G1, and Z G1 increase); source data for the heatmap and graph shown in Figure 3B (expression fold change, log2 fold change, and gene score); qPCR source data for the heatmap and graph in Figure 4D; measurements of Western blotting band intensity from Figure S6.</p>
<p>This file contains the source of all cell lines used for the work described in the manuscript as well as the methods by which cell lines are authenticated at the repositories.</p>
Abstract Selective inhibition of BET bromodomains by small molecule inhibitors has emerged as a promising therapeutic strategy for the treatment of cancer. Accordingly, we have recently initiated clinical trials to assess this mechanism in patients. Recent evidence demonstrates that BET bromodomain inhibition leads to anti-proliferative activity in pre-clinical models of hematological malignancies and solid tumors. This anti-proliferative activity involves down-regulation of the transcription factor MYC, among other cancer-relevant pathways. However, heterogeneity exists in the response to BET bromodomain inhibition at both the molecular and phenotypic level. Given this complexity, the molecular determinants of sensitivity and resistance to BET bromodomain inhibition remains poorly understood. Current efforts are aimed at addressing this key issue by integrating the following: (1) phenotypic endpoints observed upon BET bromodomain inhibition with transcriptional changes, including down-regulation of MYC and other transcription factors important for regulating proliferation and cell death, such as MYB and BCL-2,(2) transcriptional response with BET protein chromatin binding and eviction, and (3) phenotypic endpoints and transcriptional response with genomic context. Our data potentially stratify indications within hematologic malignancies and solid tumors, and provide insight into patient selection strategies. Citation Format: Nicole Follmer, Jennifer Mertz, Andrew Conery, Barbara Bryant, Charlie Hatton, Richard Centore, Hon-Ren Huang, Kerry Spillane, Robert Sims. Defining the determinants of sensitivity and resistance to BET bromodomain inhibition. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2327. doi:10.1158/1538-7445.AM2014-2327
<p>This file contains 4 supplementary tables: Table S1 provides the expression values of the indicated genes (RMA) in BETi sensitive and insensitive cell lines; Table S2 shows the enrichment of subtypes of cell lines following selection with the indicated criteria; Table S3 shows SNP analysis of parental and BETi tolerant A375 cells; Table S4 shows SNP analysis of parental and BETi tolerant NOMO-1 cells.</p>
The single bromodomain of the closely related transcriptional regulators CBP/EP300 is a target of much recent interest in cancer and immune system regulation. A co-crystal structure of a ligand-efficient screening hit and the CBP bromodomain guided initial design targeting the LPF shelf, ZA loop, and acetylated lysine binding regions. Structure-activity relationship studies allowed us to identify a more potent analogue. Optimization of permeability and microsomal stability and subsequent improvement of mouse hepatocyte stability afforded 59 (GNE-272, TR-FRET IC50 = 0.02 μM, BRET IC50 = 0.41 μM, BRD4(1) IC50 = 13 μM) that retained the best balance of cell potency, selectivity, and in vivo PK. Compound 59 showed a marked antiproliferative effect in hematologic cancer cell lines and modulates MYC expression in vivo that corresponds with antitumor activity in an AML tumor model.
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