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. Author manuscript; available in PMC: 2015 Oct 1.
Published in final edited form as: Mol Cancer Ther. 2014 Jul 22;13(10):2315–2327. doi: 10.1158/1535-7163.MCT-14-0258

BET protein antagonist JQ1 is synergistically lethal with FLT3 tyrosine kinase inhibitor (TKI) and overcomes resistance to FLT3-TKI in AML cells expressing FLT-ITD

Warren Fiskus 1, Sunil Sharma 2, Jun Qi 3, Bhavin Shah 4, Santhana G T Devaraj 4, Christopher Leveque 4, Bryce P Portier 4, Swaminathan Iyer 4, James E Bradner 3, Kapil N Bhalla 4
PMCID: PMC4185220  NIHMSID: NIHMS616427  PMID: 25053825

Abstract

Recently, treatment with BET (bromodomain and extraterminal) protein antagonist (BA) such as JQ1 has been shown to inhibit growth and induce apoptosis of human AML cells, including those expressing FLT3-ITD. Here, we demonstrate that co-treatment with JQ1 and the FLT3 tyrosine kinase inhibitor (TKI) ponatinib or AC220 synergistically induce apoptosis of cultured and primary CD34+ human AML blast progenitor cells (BPCs) expressing FLT3-ITD. Concomitantly, as compared to each agent alone, co-treatment with JQ1 and the FLT3-TKI caused greater attenuation of c-MYC, BCL2 and CDK4/6. Simultaneously, co-treatment with JQ1 and the FLT3-TKI increased the levels of p21, BIM and cleaved PARP, as well as mediated marked attenuation of p-STAT5, p-AKT and p-ERK1/2 levels in AML BPCs. Conversely, co-treatment with JQ1 and FLT3-TKI was significantly less active against CD34+ normal bone marrow progenitor cells. Knockdown of BRD4 by shRNA also sensitized AML cells to FLT3-TKI. JQ1 treatment induced apoptosis of mouse Ba/F3 cells ectopically expressing FLT3-ITD with or without FLT3-TKI resistant mutations F691L and D835V. Compared to the parental human AML FLT3-ITD-expressing MOLM13, MOLM13-TKIR cells resistant to AC220 were markedly more sensitive to JQ1-induced apoptosis. Further, co-treatment with JQ1 and the pan-histone deacetylase inhibitor (HDI) panobinostat synergistically induced apoptosis of FLT3-TKI resistant MOLM13-TKIR and MV4-11-TKIR cells. Collectively, these findings support the rationale for determining the in vivo activity of combined therapy with BA and FLT3-TKI against human AML cells expressing FLT3-ITD or with BA and HDI against AML cells resistant to FLT3-TKI.

INTRODUCTION

FLT3 is a member of the class III receptor tyrosine kinase (TK) family that is expressed on the cell membrane of most AML blast progenitor cells (BPCs) (1,2). Interaction with FLT3 ligand causes homo-dimerization, auto-phosphorylation and activation of FLT3 (1,2). Activated FLT3 transduces pro-growth and pro-survival signaling through STAT5, PI3K/AKT and RAS/RAF/ERK1/2 pathways (2,3). Activating, somatic, gain-of-function FLT3 internal tandem duplication (ITD) mutations and FLT3-TK domain (TKD) mutations are observed in approximately 25% and 8% of AML, respectively (2,3). In addition to FLT3-TKD-D835V/Y, other mutations within the TKD have also been reported (4). Several FLT3 kinase inhibitors (FLT3-TKI) have been clinically tested but none is yet approved for the therapy of AML (5,6). Although treatment with FLT3-TKI has been documented to induce clinical remissions, emergence of resistance that prevents durable remissions and limits leukemia-free survival remains a challenge (6). While approved for BCR-ABL TKI resistant CML, ponatinib has also been shown to potently inhibit FLT3 and its downstream signaling and exert preclinical and clinical activity against AML expressing FLT3-ITD (6,7). AC220 (quizartinib) is a highly active FLT3-TKI, which induces terminal myeloid differentiation in vivo and is currently being evaluated for efficacy in clinical trials (6,8–10). Recently, ponatinib was shown to be active against AC220-resistant kinase domain mutants of AML expressing FLT3-ITD (6,11). Several studies have documented the mechanisms of resistance to FLT-TKI in AML blasts expressing FLT3 mutation (2,4,6,12–15). These include the acquisition of secondary FLT3-TKD mutations: the gatekeeper F691I/L in the TKD1 of the ATP binding pocket, the D835V/Y/F in the activation loop of TKD2, and the compound FLT3-ITD/F691I mutation (4,6,14). FLT3-TKI resistance may also be due to amplification of the FLT3 locus on chromosome 13 with overexpression of FLT3-ITD protein (2). Recently, increased FL expression with up regulation of STAT3 activity and survivin levels has been noted in AML blasts demonstrating resistance to FLT3-TKI that otherwise did not exhibit mutations in FLT3-TKD (15–17). Levels of FL have been demonstrated to rise during treatment of AML with chemotherapy, and FLT3 ligand was shown to impede the in vitro and in vivo efficacy of FLT3-TKI (15–17). Thus, the autocrine induction of FL may mediate activation of FLT3-ITD and confer clinical resistance to FLT3-TKIs (15–17). Finally, increase in the activity of the compensatory and collateral pro-growth and pro-survival signaling pathways and up regulation of anti-apoptotic proteins may also confer resistance to FLT3-TKI treatment (2,6,13). Collectively, these observations underscore the need to develop and test novel agents and combinations that are more effective, as well as overcome resistance to FLT3-TKI in AML blast progenitor cells.

The family of BET (bromodomain and extraterminal) proteins, including BRD4, are chromatin ‘reader’ proteins that contain the N-terminal double, tandem, 110 amino acids-long bromodomains, through which they bind to the acetylated lysines on histone proteins (18,19). Through their extra-terminal (ET) protein-interacting domain in the C-terminus, BET proteins recruit co-regulatory complexes containing chromatin-modifying enzymes, chromatin remodeling factors and the mediator elements to the chromatin for regulating gene transcription (19–21). The C-terminal domain (CTD) of BRD4 interacts with pTEFb (positive transcription elongation factor b), the heterodimer composed of cyclin T and CDK9, which phosphorylates serine 2 on the CTD of RNA pol II (RNAP2) causing its pause release and mRNA transcript elongation (20–23). Recently, an RNAi screen identified BRD4 as an effective and promising target in human AML (24). Several structure/activity-based BET protein small molecule inhibitors have been developed, e.g., JQ1 and I-BET151 (25,26). Treatment with JQ1 disrupts the binding of the bromodomains of BRD4 to acetylated lysines, displacing the BET proteins, along with the associated transcript initiation and elongation factors from the enhancers and promoters of several oncogenes, including c-MYC, BCL2 and CDK6. (21,25,27). Recently, JQ1 was demonstrated to deplete the binding of BRD4, mediator and pTEFb to the clusters of enhancers called the ‘super enhancers’ of some oncogenes such as c-MYC, CDK6 and BCL2. This was associated with the depletion of their transcript levels (21,27–29). JQ1 treatment also induces hexamethylene-bis-acetamide (HMBA)-inducible protein 1 (HEXIM1), which binds to cyclin T and sequesters pTEFb in an inhibitory complex that also includes the non-coding 7SK RNA (30,31). This reduces the available kinase activity of pTEFb for phosphorylating and inducing the pause release of RNAP2, thereby contributing to the inhibition of the mRNA transcript elongation and expression of the oncogenes (21,23,28). Collectively, JQ1 mediated inhibitory effects on the oncogene transcription are associated with growth inhibition and apoptosis of AML cells (32–35). This has been especially noted for AML cells expressing the mutant NPM1 (NPM1c+) or Mixed Lineage Leukemia (MLL) containing fusion oncoproteins, with or without the expression of FLT3-ITD (33–35). We also previously reported that co-treatment with JQ1 and the pan-histone deacetylase (HDAC) inhibitor (HDI) panobinostat (PS), exerts synergistic lethality against the cultured and primary AML BPCs expressing FLT3-ITD (34). In the present studies, we demonstrate that co-treatment with JQ1 and the FLT3-TKIs ponatinib or quizartinib is synergistically lethal against human cultured or primary AML blast progenitor cells (BPCs) expressing FLT3-ITD. The combination concomitantly further attenuates the levels of pro-growth and pro-survival proteins e.g., c-MYC, BCL2 and CDK4/6, while simultaneously inducing the levels of p21, HEXIM1 and the pro-apoptotic protein BIM. Finally, JQ1 alone or in combination with PS was highly active against FLT3-TKI resistant AML cells (FLT3-TKIR) expressing FLT3-ITD.

MATERIALS AND METHODS

Reagents

(S)-JQ1 (active enantiomer, hereafter referred to as JQ1) was developed as previously described (25). I-BET151 and ABT-199 were obtained from Xcess Biologicals (San Diego, CA). Panobinostat (PS) was kindly provided by Novartis Pharmaceuticals Inc. (East Hanover, NJ). AC220 and ponatinib were obtained from Selleck Chemicals (Houston, TX). Chemical structures for the molecules are provided as Supplemental Figure 1. All compounds were prepared as 10 mM stocks in 100% DMSO and frozen at −20°C to −80°C in 10 μL aliquots to allow for single use, thus avoiding multiple freeze-thaw cycles that could result in compound decomposition and loss of activity. Anti-cleaved PARP, anti-c-MYC and anti-BIM antibodies were obtained from Cell Signaling (Danvers, MA). Anti-BCL2, anti-CDK4 and anti-CDK6 antibodies were obtained from Santa Cruz Biotechnologies (Santa Cruz, CA). Anti-p21WAF antibody was obtained from Neomarkers (Fremont, CA). Anti-HEXIM1 antibody was obtained from Bethyl Labs (Montgomery, TX). Anti-β-actin antibody and lentiviral short hairpin RNAs targeting BRD4 or non-targeted shRNA (sh-NT) were obtained from Sigma Aldrich (St. Louis, MO).

Cell Culture

MOLM13 cells were obtained from the DSMZ (Braunschweig, Germany). MV4-11 cells were obtained from ATCC (Manassas, VA). All experiments with cell lines were performed within 6 months after thawing or obtaining from ATCC or DSMZ. Cell line authentication was performed by ATCC or DSMZ. The ATCC and DSMZ utilize short tandem repeat (STR) profiling for characterization and authentication of cell lines. MOLM13-TKIR and MV4-11-TKIR cells resistant to ponatinib and quizartinib were isolated by exposing the MOLM13 and MV4-11 cells, respectively, to the continuous presence of step-wise escalating levels of ponatinib, utilizing previously described methods (36,37). Compared to the parental MOLM13 and MV4-11 cells, the TKIR cells were characterized for cell membrane expression of FLT3 and its intracellular signaling, as well for their the cell cycle and suspension culture growth.

Next Generation Sequencing of FLT3

Equal molar pools of purified PCR amplicons corresponding to FLT3 exons 1–23 were prepared separately from parental MOLM13 and MOLM13-TKIR cells, to which Ion Torrent library adapters were ligated (Ion Plus Fragment Library kit, Life Technologies, catalog no. 4471252). Libraries were amplified (Ion OneTouch 200 Solutions Kit v2, Life Technologies, catalog no. 4478319), and the template-positive Ion SphereTM Particles were sequenced on an Ion 316™ Chip (Life Technologies, catalog no. 4466616) with 500 flows (Ion PGM 200 Sequencing Kit, Life Technologies catalog no. 4474006). A total of 1.88 million (M) and 3.15 M mapped reads were obtained for the MOLM13 and MOLM13-TKIR samples, respectively. Sequences were aligned to the above-specified targeted regions of human genome (hg)19 using ion-alignment v3.6.56201 software, and variant analysis was done with VariantCaller v3.6.63335 software using the “Somatic - Low Stringency” parameter setting.

Primary normal progenitor and AML BPCs

Primary peripheral blood and/or bone marrow aspirate AML samples were obtained and prepared for the studies below, as previously described (37,38). Banked, de-linked and de-identified, normal or AML CD34+ bone marrow progenitor/stem cells were purified, as previously described (38). The clinical presentation of the patient and mutation status of the primary AML samples utilized in these studies is provided in Supplemental Table 1.

Assessment of apoptosis by annexin-V staining

Untreated or drug-treated cells were stained with Annexin-V (Pharmingen, San Diego, CA) and TO-PRO-3 iodide and the percentages of apoptotic cells were determined by flow cytometry, as previously described (36–38). For single agent treatments, the IC50 dose was determined utilizing GraphPad Prism 5 (GraphPad Software, Inc., La Jolla, CA). The combination index (CI) for each drug combination and the evaluation of the synergistic interactions were calculated by median dose effect analyses (assuming mutual exclusivity) utilizing the commercially available software Calcusyn (Biosoft, Ferguson, MO) (39). CI values of less than 1.0 represent a synergistic interaction of the two drugs in the combination.

Assessment of percentage non-viable cells

Following designated treatments, primary AML cells were washed with 1X PBS, stained with propidium iodide and analyzed by flow cytometry, as previously described (37,38).

Short hairpin RNA to BRD4

Lentiviral short hairpin (sh) RNAs targeting BRD4 or a non-target shRNA (sh-NT) were transduced into OCI-AML3 cells, as previously described (40). Forty-eight hours post transduction, the cells were washed with complete media and treated with ponatinib or AC220 for 48 hours to assess apoptosis of the AML cells.

RNA isolation and quantitative polymerase chain reaction

Following the designated treatments with JQ1, total RNA was isolated from cultured and primary AML cells with a High Pure RNA isolation kit (Roche Diagnostics, Indianapolis, IN) and reverse transcribed. Quantitative real time PCR analysis for the expression of c-MYC, BCL-2, HEXIM1 and p21 was performed on cDNA using TaqMan probes from Applied Biosystems (Foster City, CA) (34,40). Relative mRNA expression was normalized to the expression of GAPDH.

Cell lysis, protein quantitation and immunoblot analyses

Untreated or drug-treated cells were centrifuged, and the cell pellets were lysed and the protein quantitation and immunoblot analyses were performed, as previously described (34,40). Immunoblot analyses were performed at least twice. The expression levels of β-Actin served as the loading control. Representative immunoblots were subjected to densitometry analysis. Densitometry was performed using ImageQuant 5.2 (GE Healthcare, Piscataway, NJ).

Statistical Analysis

Significant differences between values obtained in a population of AML cells treated with different experimental conditions were determined using a two-tailed, paired t-test or a one way ANOVA analysis within an analysis package of Microsoft Excel 2010 software or using GraphPad Prism (GraphPad Software, Inc., CA). P values of less than 0.05 were assigned significance.

RESULTS

Synergistic lethal effects of JQ1 and FLT3 TKI against AML cells expressing FLT3-ITD

In a previous report and in present studies, we demonstrated that treatment with JQ1 or AC220 (quizartinib) (Supplemental Figure 1) dose-dependently exerts growth inhibitory and apoptotic effects against AML cells expressing MLL fusion proteins and FLT3-ITD (33,34, and Supplemental Figure 2A and 2B). In a previous study we also demonstrated that JQ1 exerted similar lethal effects against cultured and primary AML blast progenitor cells with or without expression of FLT3-ITD (34). Taken together, based on this, in the present studies we determined the lethal activity of co-treatment with JQ1 and FLT3-TKI quizartinib or ponatinib against MOLM13 and MV4-11 cells that endogenously express FLT3-ITD. Figure 1A demonstrates that co-treatment with quizartinib and JQ1 induces significantly more apoptosis in MV4-11 and MOLM13 cells, as compared to either agent alone (p < 0.01). Median dose effect and isobologram analyses demonstrated that combined therapy with JQ1 and quizartinib synergistically induced apoptosis of the two cell types, with combination indices less than 1.0 (Figure 1B and Supplemental Figure 3). Treatment with JQ1 and quizartinib, versus each drug alone, or no treatment at all, mediated greater attenuation of c-MYC, BCL2, CDK4 and CDK6 (Figure 1C). In contrast, treatment with JQ1 did not reduce the expression levels of p-FLT3 in the cultured AML cells (Supplemental Figure 2C and 2D) As shown in the representative immunoblots, combined treatment with JQ1 and quizartinib concomitantly induced more p21, BIM and cleaved PARP (Figure 1C and Supplemental Figure 2E and 2F). Similar effects of the combined treatment were observed in MOLM13 cells (Supplemental Figure 2G). Co-treatment with JQ1 and quizartinib also resulted in greater inhibition of the levels of p-STAT5, p-AKT and p-ERK1/2 without significant alterations in the un-phosphorylated versions of these proteins (Figure 1D). Treatment with JQ1, but not quzartinib, also markedly induced the levels of HEXIM1 which was slightly inhibited by co-treatment with quzartinib (Figure 1C). Figure 2A demonstrates that co-treatment with JQ1 and ponatinib also induced significantly more apoptosis of MV4-11 and MOLM13 cells, as compared to each agent alone (p < 0.01). Additionally, combined therapy with JQ1 and ponatinib was also synergistically lethal against MV4-11 and MOLM13 cells, showing combination indices of less than 1.0 (Figure 2B and Supplemental Figure 3). Synergistic apoptosis of the two cell types was also observed, following treatment with I-BET151 and ponatinib (Supplemental Figure 4A and 4B). Treatment with JQ1 and ponatinib also inhibited the expression of c-MYC, BCL2 and CDK4/6 more than the treatment with each drug alone, while simultaneously inducing more p21, BIM and cleaved PARP (Figure 2C & 2D, and Supplemental Figure 2E). Co-treatment with JQ1 and ponatinib also mediated greater attenuation of p-AKT and p-ERK1/2 but not of AKT and ERK1/2 in the cells expressing FLT3-ITD (Figure 2D). We next determined whether specific depletion of BRD4 by shRNA would phenocopy the effects of JQ1 in increasing the anti-AML activity of FLT3-TKI. Figure 2E demonstrates that, as compared to treatment with the non-targeted shRNA, treatment with BRD4 shRNA reduced the mRNA levels of BRD4, while simultaneously increasing the mRNA levels of p21. We have previously reported that shRNA-mediated knockdown of BRD4 also results in depletion of the mRNA levels of BCL2 and CDK6 (34). In the cells transduced with BRD4 shRNA, compared to cells transduced with the non-targeted shRNA, treatment with quizartinib (AC220) or ponatinib induced significantly more apoptosis of MOLM13 cells (p < 0.05) (Figure 2F).

Figure 1. Co-treatment with JQ1 and AC220 synergistically induces apoptosis of FLT3-ITD expressing AML cells.

Figure 1

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A. MOLM13 and MV4-11 cells were treated with the indicated concentrations of JQ1 and/or AC220 for 48 hours. Following this, the % annexin V-positive, apoptotic cells was determined by flow cytometry. Columns, mean of three experiments; Bars, standard error of the mean (S.E.M). * indicates apoptosis values significantly greater (p<0.05) in cells treated with the combination compared to treatment with either single agent. B. MV4-11 and MOLM13 cells were treated with JQ1 and AC220 at a constant ratio for 48 hours. The % of annexin V-positive, apoptotic cells was determined by flow cytometry. Median dose effect and isobologram analyses were conducted utilizing Calcusyn. Combination index (CI) values less than 1.0 indicate a synergistic interaction of the two agents in the combination. C–D. MV4-11 cells were treated with the indicated concentrations of AC220 and/or JQ1 for 24 hours. At the end of treatment, immunoblot analyses were conducted as indicated. The numbers beneath the blots represent densitometry analysis conducted on representative blots.

Figure 2. Co-treatment with JQ1 and ponatinib synergistically induces apoptosis of FLT-ITD expressing AML cells.

Figure 2

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A. MV4-11 and MOLM13 cells were treated with the indicated concentrations of JQ1 and ponatinib for 48 hours. Following this, the % of annexin V-positive, apoptotic cells were determined by flow cytometry. Columns, mean of three experiments; Bars, S.E.M. * indicates apoptosis values significantly greater in cells treated with JQ1 and ponatinib compared to cells treated with either single agent (p < 0.01). B. MV4-11 and MOLM13 cells were treated with JQ1 and ponatinib at a constant ratio for 48 hours. The % of annexin V-positive, apoptotic cells was determined by flow cytometry. Median dose effect and isobologram analyses were conducted utilizing Calcusyn, assuming mutual exclusivity. Combination index (CI) values less than 1.0 indicate a synergistic interaction of the two agents in the combination. C–D. MV4-11 cells were treated with the indicated concentrations of ponatinib and/or JQ1 for 24 hours. Immunoblot analyses were conducted as indicated. The numbers beneath the blots represent densitometry analysis conducted on representative blots. E. MOLM13 cells were transduced with lentiviruses expressing non-targeted (NT) shRNA or BRD4 shRNA for 48 hours. At the end of treatment, total RNA was harvested and reverse-transcribed. Quantitative PCR was performed for BRD4 and p21 expression. The relative mRNA expression was normalized to GAPDH and compared to the non-targeted shRNA transduced cells. * indicates values significantly different in BRD4 shRNA transduced cells compared to NT shRNA transduced cells (p < 0.05). F. MOLM13 cells were transduced with NT shRNA or BRD4 shRNA for 24 hours and then treated with AC220 or ponatinib for 48 hours. Following this, the % of annexin V-positive, apoptotic cells were determined by flow cytometry. Columns, mean of three experiments; Bars, S.E.M. * indicates apoptosis values significantly greater in cells with BRD4 knockdown compared to cells transduced with non-targeted shRNA (p < 0.05).

JQ1 and FLT3-TKI synergistically induce apoptosis of primary AML blast progenitor cells expressing FLT3-ITD

We next compared the lethal effects of JQ1 and ponatinib or quizartinib against samples of patient-derived, CD34+ primary AML progenitor cells expressing mutant FLT3-ITD or co-expressing NPM1c+ and FLT3-ITD. Figure 3A demonstrates that, although, the loss of viability in the primary AML progenitor cells was lower than in the cultured AML cell types, exposure to 250 nM JQ1 exerted greater lethal effects than exposure to 100 nM of ponatinib. Co-treatment with JQ1 and ponatinib was more lethal than each agent alone against the primary AML BPCs (Figure 3A). Importantly, combined treatment with JQ1 and ponatinib exerted significantly greater lethality against the primary AML versus normal progenitor cells (Figure 3A). Additionally, co-treatment with JQ1 and ponatinib or quizartinib was synergistically lethal against primary AML BPCs, showing combination indices of less than 1.0 (Figure 3B and 3C). This synergy was observed whether FLT3-ITD was expressed alone or with additional mutation such as NPM1c+ (Supplemental Figure 5A and 5B). Co-treatment with JQ1 and ponatinib or quizartinib was synergistically lethal, regardless of the co-expression of FLT3-ITD with or without NPM1c+ (Supplemental Figure 5C and data not shown). As was observed in the cultured AML cell types, treatment with JQ1 and ponatinib or quizartinib versus each drug alone, or no treatment at all, mediated greater attenuation of p-RNAP2, c-MYC, BCL2, CDK4 and CDK6 in the primary AML BPCs (Figure 3D and 3E). Here, also, co-treatment with JQ1 and ponatinib or quizartinib mediated greater attenuation of p-AKT, p-ERK1/2 and p-STAT5 but not of AKT, ERK1/2, STAT5 or pFLT3 (Figure 3D & 3E and Supplemental Figure 6). As compared to each agent alone, combined treatment with JQ1 and ponatinib or quizartinib simultaneously induced more p21, BIM and cleaved PARP in the primary AML progenitor cells (Figure 3D & 3E and Supplemental Figure 6C).

Figure 3. Co-treatment with JQ1 and FLT3-TKI exerts synergistic anti-leukemia activity against primary FLT3-ITD-expressing AML cells.

Figure 3

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A. Primary CD34+ FLT3-ITD expressing AML cells (n=5) and normal CD34+ cells were treated with JQ1 and/or ponatinib for 48 hours. At the end of treatment, the % of propidium iodide (PI)-positive, non-viable cells was determined by flow cytometry. * indicates values significantly greater (p<0.05) in the combination compared to treatment with either single agent. † indicates values significantly less (p< 0.05) in normal CD34+ cells compared to CD34+ AML cells treated with the same combination of JQ1 and ponatinib. B. Primary FLT3-ITD AML cells were treated with JQ1 and ponatinib at a constant ratio for 48 hours and the % non-viable cells was determined by flow cytometry. Median dose effect and isobologram analyses were performed utilizing Calcusyn. Combination index (CI) values less than 1.0 indicate a synergistic interaction of the two agents in the combination. C. Primary FLT3-ITD AML cells were treated with JQ1 and AC220 at a constant ratio for 48 hours and the % non-viable cells was determined by flow cytometry. Combination index (CI) values less than 1.0 indicate a synergistic interaction of the two agents in the combination. D–E. Primary FLT3-ITD-expressing AML cells were treated with AC220 or ponatinib and/or JQ1 for 24 hours. Immunoblot analyses were conducted as indicated.

JQ1 induces apoptosis of cells expressing mutations in the TKD of FLT3

Since an important secondary mechanism of resistance to therapy with FLT3-TKIs in AML is the emergence of mutations in the activation loop of FLT3-TKD2 (FLT3-D835V/Y/F) and in the FLT3-TKD1 (FLT3-F691L), we next determined the activity of JQ1 against BaF3 cells stably expressing FLT3-ITD or FLT3-ITD along with either FLT3-F691L or with FLT3D835V (4). As previously reported, unlike the parental BaF3 cells, FLT3-ITD expressing cells are able to grow in a culture medium devoid of IL3 (3,4). As shown in Figure 4A, treatment with JQ1 dose-dependently induced apoptosis of not only BaF3 cells expressing FLT3-ITD but also of those co-expressing FLT3-ITD along with either F691L or with D835V substitution. The IC50 values for JQ1 for inducing apoptosis in the three cell-types were: FLT3-ITD, 691 nM; FLT3-ITD-F691L, 1588 nM; and FLT3-ITD-D835V, 909 nM. JQ1-induced apoptosis in the BaF3 cells expressing FLT3-ITD, FLT3-ITD-F691L and FLT3-ITD-D835V was associated with JQ1-mediated attenuation of c-MYC, but induction of HEXIM1 and BIM (the extra-long, long and short isoforms) (Figure 4B). Thus JQ1 retains effectiveness against cells expressing the clinically encountered mutations in FLT3 that confer resistance to FLT3-TKI.

Figure 4. Treatment with BET protein antagonist, JQ1, depletes c-MYC and induces BIM and apoptosis of pro-B, Ba/F3 cells expressing FLT3-ITD with or without kinase inhibitor-resistant point mutations.

Figure 4

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A. Ba/F3-FLT3-ITD, Ba/F3-ITD-F691L and Ba/F3-ITD-D835V cells were treated with the indicated concentrations of JQ1 for 48 hours. Following this, cells were washed with 1X PBS and stained with annexin V-FITC and TO-PRO-3 iodide. The percentages of annexin V-positive, apoptotic cells were determined by flow cytometry. Columns, mean of three experiments; Bars, S.E.M. B. Ba/F3-FLT3-ITD, Ba/F3-ITD-F691L and Ba/F3-ITD-D835V cells were treated with the indicated concentrations of JQ1 for 24 hours. At the end of treatment, immunoblot analyses were conducted as indicated.

Superior activity of JQ1 against the FLT3-ITD expressing human AML cells highly resistant to FLT3-TKI

To determine whether JQ1 would also be active against FLT3-ITD expressing, FLT-TKI-resistant human AML cells, we generated MOLM13 cells resistant to FLT3-TKIs by culturing the cells in the continuous presence of escalating doses of ponatinib. We were able to isolate FLT3-TKI-resistant MOLM13-TKIR cells that grow in the continuous presence of 250 nM of ponatinib. Compared to the parental MOLM13 cells, MOLM13-TKIR cells express similar levels of FLT3 on the cell membrane (determined by flow cytometry) and have a similar growth rate (Figure 5A and 5B), although MOLM13-TKIR cells displayed higher % of cells in the S phase of the cell cycle (Figure 5C). Importantly, MOLM13-TKIR cells had significantly higher IC50 values for quizartinib and ponatinib, (>1000 nM and 674.6 nM respectively), as compared to the parental MOLM13 cells (13.46 nM and 13.96 nM respectively) (Supplemental Table 2). Next generation sequencing (NGS) of the 23 exons of FLT3 in the MOLM13-TKIR cells did not reveal any mutation in FLT3 that has been previously discovered and reported following in vitro or in vivo exposure to FLT3-TKIs, including quizartinib or ponatinib (2,4,6,14). However, we did detect a very low allelic frequency mutation in FLT3 represented by the A680V substitution in MOLM13-TKIR cells (Figure 5D), which has not been previously shown to confer in vivo resistance to FLT3-TKIs. Notably, compared to MOLM13, MOLM13-TKIR cells also expressed higher mRNA and protein levels of p21 and HEXIM1 (Figure 6A, 6B and 6C). Additionally, higher protein levels of BRD4, c-MYC, BCL2, Bcl-xL, CDK6, BIM, p-AKT and AKT, were observed in MOLM13-TKIR versus MOLM13 cells (Figure 6C). While markedly inducing the levels of p21, HEXIM1, BRD4, BIM and cleaved PARP, treatment with JQ1 dose-dependently attenuated the levels of c-MYC, BCL2, Bcl-xL, CDK6, p-AKT and AKT in MOLM13-TKIR and MOLM13 cells (Figure 6C). Importantly, MOLM13-TKIR cells were significantly more sensitive than the parental MOLM13 cells to JQ1-induced apoptosis, e.g., exposure to 100 nM or 1000 nM of JQ1 induced significantly more apoptosis of MOLM13-TKIR versus MOLM13 cells (p < 0.01) (Figure 6D). The IC50 values for JQ1-induced apoptosis in MOLM13-TKIR versus MOLM13 cells were 269.4 nM versus 1480 nM, respectively (Supplemental Table 2). The observed collateral sensitivity of MOLM13-TKIR cells to JQ1 was associated with greater induction of p21, HEXIM1, BIM and cleaved PARP by JQ1 treatment in MOLM13-TKIR versus MOLM13 cells. We next determined whether the combination of JQ1 with AC220 would exert greater anti-leukemia activity against the MOLM13-TKIR cells. In contrast to the synergistic anti-leukemia activity of JQ1 and AC220 in MOLM13 cells, the combination of JQ1 and AC220 was no more effective than treatment with JQ1 alone in the MOLM13-TKIR cells (Supplemental Figure 7). We also determined the effect of the knockdown of BRD4 by shRNA on the induction of apoptosis in MOLM13-TKIR versus MOLM13 cells. As shown in the Supplemental Figure 8, knockdown of BRD4 (approximately 80%) did not significantly induce apoptosis in either MOLM13-TKIR or MOLM13 cells (approximately 10% in each cell-type). However, the knock-down of BRD4 further sensitized MOLM13-TKIR more than MOLM13 cells to treatment with JQ1 (Supplemental Figure 8B). We also determined the mechanistic role of BCL2 overexpression on the sensitivity of MOLM13-TKIR versus MOLM13 cells to apoptosis. We treated MOLM13-TKIR and MOLM13 cells with the BCL2-specific antagonist ABT-199. As shown in Supplemental Figure 8C, MOLM13-TKIR cells were not more sensitive than MOLM13 cells to treatment with ABT-199.

Figure 5. Characterization of MOLM13-TKIR cells and in vitro response to anti-leukemia agents.

Figure 5

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A. FLT3 surface expression in MOLM13 and MOLM-TKIR cells measured by flow cytometry. B. MOLM13 and MOLM13-TKIR cells were plated at 50,000 cells/mL in complete media and cultured over 96 hours. Every 24 hours, 200 μL of cells were removed and counted with a coulter counter to determine the number of cells/mL. Columns, mean of three experiments; Bars, S.E.M. C. Cell cycle status of MOLM13 and MOLM-TKIR cells was determined by flow cytometry. Columns, mean of three experiments; Bars, S.E.M. D. The coding exons of FLT3 (1–23) were amplified by PCR from MOLM13 and MOLM13-TKIR cells. PCR products were annealed to adapter sequences and next generation sequencing was utilized to compare the FLT3 sequence from each with the human genome version hg19. Identified mutations were compared to those in the COSMIC mutation database. MOLM13–TKIR cells, in addition to the ITD, possess a missense mutation in exon 16 C2039T which results in an amino acid substitution of A680V in FLT3. No other mutations were identified in the FLT3 sequence.

Figure 6. JQ1 treatment depletes c-MYC and BCL2 to a greater extent with concomitant greater induction of HEXIM1 and p21 in MOLM13-TKIR cells compared to MOLM13 cells.

Figure 6

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A–B. MOLM13 and MOLM13-TKIR cells were treated with the indicated concentrations of JQ1 for 8 hours. At the end of treatment, total RNA was isolated and reverse transcribed. The resulting cDNA was utilized for quantitative PCR of c-MYC, BCL2, HEXIM1 and p21 expression. The relative mRNA expression in both cell lines was normalized against GAPDH and compared to the relative expression in parental MOLM13 cells. C. MOLM13 and MOLM-TKIR cells were treated with the indicated concentrations of JQ1 for 24 hours. Following this, cells were harvested and cell lysates were prepared. Immunoblot analyses were conducted for the expression levels of c-MYC, BRD4, BCL2, Bcl-xL, p-AKT, AKT, BIM, p21, cleaved PARP and β-actin in the cell lysates. The numbers beneath the blots represent densitometry analysis conducted on representative blots. D. MOLM13 and MOLM13-TKIR cells were treated with the indicated concentrations of JQ1 for 48 hours. The % of annexin V-positive, apoptotic cells was determined by flow cytometry. Columns, mean of three experiments; Bars, S.E.M. * indicates apoptosis values significantly greater in MOLM13-TKIR than MOLM13 treated with the same concentration of JQ1 (p < 0.01).

Co-treatment with JQ1 and panobinostat synergistically induces apoptosis of AML cells resistant to FLT3-TKI

As shown in Figure 7A, as compared to the parental MOLM13 cells, MOLM13-TKIR cells displayed higher levels of the class I and class IIB HDACs HDAC1, HDAC2, HDAC3 and HDAC6. Additionally, MOLM13-TKIR cells expressed higher levels of the polycomb repressive complex 2 (PRC2) proteins EZH2 and SUZ12 (Figure 7A). We had previously reported that PS treatment depletes EZH2 and SUZ12 in AML cells (38). As shown in Supplemental Table 2, panobinostat (PS) and vorinostat (VS) were as active in inducing apoptosis in MOLM13-TKIR as in MOLM13 cells. Additionally, Figure 7A also demonstrates that treatment with JQ1 alone dose-dependently, but modestly, attenuated the levels of HDAC1, HDAC2, HDAC3, EZH2 and SUZ12, without affecting the levels of HDAC6. We had also previously reported that combined therapy with JQ1 and PS exerts synergistic lethality against cultured and primary human AML BPCs, including those expressing FLT3-ITD such as MOLM13 cells (34). Collectively, based on this, in the present studies we determined the activity of JQ1 and PS against FLT3-TKI resistant MOLM13-TKIR cells. As compared to each agent alone, combined treatment with JQ1 and PS induced significantly more apoptosis of MOLM13-TKIR cells (Figure 7B). Furthermore, Figure 7C demonstrates that co-treatment with PS and JQ1 synergistically induced apoptosis of MOLM13-TKIR cells, with combination indices of less than 1.0 by the median dose effect and isobologram analyses. This synergistic effect of the combination was associated with greater decline in c-MYC, CDK4/6 and Bcl-xL, as well as greater induction of the levels of HEXIM1 and p21 (Figure 7D). Co-treatment with JQ1 and PS was also synergistically lethal against quizartinib-resistant MV4-11-TKIR cells that were approximately 10-fold resistant to quizartinib, and were isolated in a manner similar to MOLM13-TKIR cells (Supplemental Figure 9). We had previously confirmed the specific activity of JQ1 in this synergistic interaction by demonstrating that co-treatment with (R)-JQ1 did not enhance PS-induced apoptosis in MOLM13 cells (34).

Figure 7. Co-treatment with JQ1 and PS synergistically induces apoptosis of MOLM13 cells with and without resistance to FLT3-TKI.

Figure 7

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A. MOLM13 and MOLM-TKIR cells were treated with the indicated concentrations of JQ1 for 24 hours. Immunoblot analyses were conducted as indicated. The numbers beneath the blots represent densitometry analysis conducted on representative blots. B. MOLM-TKIR cells were treated with the indicated concentrations of JQ1 and/or PS for 48 hours. The % of annexin V-positive, apoptotic cells was determined by flow cytometry. Columns, mean of two experiments; Bars, S.D. * indicates apoptosis values significantly greater in the combination, compared to treatment with either agent alone (p < 0.05). C. MOLM-TKIR cells were treated with JQ1 and PS, as indicated for 48 hours. Following this, the % of annexin V-positive, apoptotic cells was determined by flow cytometry. Median dose effect and isobologram analysis was performed utilizing Calcusyn. CI values less than 1.0 indicate a synergistic interaction of the two agents in the combination. D. MOLM13-TKIR cells were treated with the indicated concentrations of JQ1 and PS for 24 hours. Cell lysates were prepared and immunoblot analyses were conducted as indicated. The numbers beneath the blots represent densitometry analysis conducted on representative blots.

DISCUSSION

The FLT3-TKIs quizartinib and ponatinib are potent type II FLT3 antagonists that bind and inhibit the inactive conformation of FLT3-TK where the activation loop is in the DFG ‘out’ position (4,6). Although they inhibit growth and induce differentiation and apoptosis, as well as induce complete remission in patients with AML, following treatment with the FLT3-TKI, relapse, due to residual AML in which FLT3-ITD activity is persistent, is commonly encountered (2,4,6,14). Several mechanisms of primary resistance to FLT3-TKI have been described in AML BPCs expressing FLT3-ITD. These include the protective effects of stromal niche cells (41), increased levels and activity of FLT3 ligand on FLT3 TK (15,17), trans-phosphorylation and increased activity of FLT3 by other kinases such as PIM-1 and SYK (42,43), and the collateral dependency on other important pro-growth and pro-survival signaling mechanisms (5,6,12,13). Other studies have focused on developing selective and more potent FLT3-TKI to overcome primary resistance to the first and second generation FLT3-TKI already in the clinic (44,45). Here, we document for the first time that co-treatment with the BET protein antagonist (BA) JQ1 and FLT3 inhibitor quizartinib or ponatinib synergistically induced apoptosis of not only cultured but also of the primary AML BPCs expressing FLT3-ITD. By disrupting BRD4 activity as a chromatin ‘reader’ protein and by inducing HEXIM1, JQ1 in combination with quizartinib or ponatinib depleted the levels of the pro-growth and pro-survival oncogenes in AML, including c-MYC, BCL2 and CDK4/6. The synergistic anti-AML activity of co-treatment with JQ1 and the TKIs could also be partly explained by the concomitant marked depletion of p-STAT5, p-AKT and p-ERK1//2, but significant induction of p21 and BIM, collectively known to undermine the growth and survival of AML cells expressing FLT3-ITD (2,5,6,12,13). These findings are consistent with a recent report in which JQ1 was shown to inhibit p-STAT5 and be active against myeloid malignancies (46). It is noteworthy that whereas the genetic knockdown of BRD4 enhanced the anti-AML lethality of quizartinib or ponatinib, this effect was less pronounced than the effect of BRD4 inhibition by co-treatment with JQ1, which mediates its growth inhibitory and lethal effects by inhibiting BET proteins in addition to BRD4. Collectively, these data highlight the promise of including a BET protein antagonist in combination with quizartinib or ponatinib for the treatment of high-risk AML expressing FLT3-ITD.

Findings presented here also for the first time demonstrate that JQ1 exerts significant lethal activity against the cultured mouse BaF3 cells expressing FLT3-ITD alone or with the FLT3-TKD mutations F691L or D835V. This is most likely because JQ1 is known to inhibit the ‘transcriptome’ responsible for the growth and survival that is activated downstream of the ‘gain-of-function’ mutations in FLT3 and the signaling downstream of it. Whereas the compound mutations FLT3-ITD-F691L and FLT3-ITD-D835V confer resistance to quizartinib and ponatinib, respectively, they likely continue to confer dependency on the BET protein-regulated ‘transcriptome’ for growth and survival and, hence, remain susceptible to the inhibitory effects of JQ1. A novel class I TKI inhibitor, crenolanib, which is capable of inhibiting the active ‘DFG in’ conformation of FLT3, demonstrated activity against FLT3 containing an ITD and/or D835- or F691-activating mutations (47). It would be important to determine the synergistic effects of JQ1 and crenolanib against AML expressing FLT3-ITD and/or D835-or F691-activating mutations. Due to the lack of availability of adequate samples of primary AML BPCs expressing FLT3-D835V or FLT3-F691L, or compounds mutations including FLT3-ITD with F691L or D835V, we determined the activity of JQ1 against the cultured FLT3-TKI-resistant MOLM13-TKIR cells. These cells lacked any FLT3 mutation that has been documented in the clinic to confer resistance to FLT3-TKI. Instead, they exhibited high levels of resistance to quizartinib and ponatinib associated with deregulated expressions of a number of proteins that confer growth and survival advantage in AML cells. Notably, as compared to the parental MOLM13, MOLM13-TKIR cells showed markedly elevated levels of BRD4, as well as demonstrated increased levels of c-MYC, BCL2, CDK4/6 and Bcl-xL. However, specific targeting of BCL2 by ABT-199 did not induce greater apoptosis of MOLM13-TKIR versus MOLM13 cells. Conversely, our findings show that shRNA-mediated attenuation of BRD4 levels further sensitized MOLM13-TKIR cells to JQ1-induced apoptosis. Additionally, as compared to the parental MOLM13, MOLM13-TKIR cells also exhibited markedly higher levels of PRC2 complex proteins EZH2 and SUZ12, suggesting the possibility that MOLM13-TKIR cells may be relatively more dependent on PRC2-regulated genes, hence more susceptible to inhibition of EZH2 and SUZ12. Our data demonstrate that treatment with JQ1 also attenuated the levels of EZH2 and SUZ12 (Figure 7A), which may further contribute to the greater susceptibility of MOLM13-TKIR versus MOLM13 cells to the lethal effects of JQ1. It should be noted that deregulated expressions of the epigenetic modifier proteins shown in MOLM13-TKIR cells have yet to be evaluated in patient-derived FLT3-TKIR resistant primary AML cells expressing FLT3-ITD but lacking the expression of point substitutions in FLT3 known to confer resistance to FLT3-TKIs.

In a previous report by us it was demonstrated that co-treatment with PS and JQ1 exerted synergistic lethality against AML cells co-expressing MLL fusion oncoprotein, or mutant NPM1c+, and FLT3-ITD (34). This was partially attributed to PS-induced hyperacetylation of histone proteins and recruitment of BRD4 to active gene promoters, thereby increasing the sensitivity of the AML cells to JQ1 (34). Based on this, and the demonstration here that JQ1 alone is considerably more active against the FLT3-TKI-resistant MOLM13-TKIR cells versus MOLM13 cells, we determined the lethal effects of co-treatment with PS and JQ1 against MOLM13-TKIR cells. Findings presented here confirm that co-treatment with PS and JQ1 is synergistically lethal against MOLM13-TKIR cells. Similar effect of the combination was noted against FLT3-TKIR resistant MV4-11-TKIR cells. Collectively, these findings indicate that while JQ1 alone is active against AML expressing FLT3-ITD and Ba/F3 cells with ectopic expression of FLT3-ITD with or without concurrent FLT3-TKD mutations, co-treatment with PS and JQ1 is synergistically lethal against AML expressing FLT3-ITD alone or with FLT3-TKD mutations. Recently, the AML stem/progenitor cells (LSCs) expressing DNMT3A mutation were demonstrated to exhibit repopulation potential and therapeutic resistance to chemotherapy (48). Targeting LSCs is an important goal in achieving deeper remissions and overcoming treatment refractoriness in the minimal residual AML, since LSC gene expression program confers a poor prognosis and influences the clinical outcome in AML (49,50). Previous reports have also clearly demonstrated that the synergistic combination of PS and JQ1 is lethal against AML BPCs expressing DNMT3A, such as OCI-AML3 cells, as well as against immunophenotypically defined CD34+, CD38− and lineage negative primary AML stem/progenitor cells that exhibit in vivo leukemia initiating potential (34,48). Taken together with these reported observations, our findings presented here underscore the potential of combined therapy with PS and JQ1 to eradicate AML stem cells and clonally derived AML BPCs that carry FLT3-TKD with or without FLT3-TKD mutations and documented to be responsible for therapeutic resistance in AML.

Supplementary Material

1
2

Acknowledgments

Financial Support: This work was supported by a grant from the National Institutes of Health awarded to K.N. Bhalla (R01 CA171338).

Footnotes

Conflict of Interest: All authors state that they have no financial interests to disclose.

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Supplementary Materials

1
NIHMS616427-supplement-1.docx (17.8KB, docx)
2
NIHMS616427-supplement-2.pptx (865.1KB, pptx)

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