Epigenetic Perturbations by Arg882-Mutated DNMT3A Potentiate Aberrant Stem Cell Gene-Expression Program and Acute Leukemia Development

DNA methyltransferase 3A (DNMT3A) is frequently mutated in hematological cancers; however, the underlying oncogenic mechanism remains elusive. Here, we report that the DNMT3A mutational hotspot at Arg882 (DNMT3A(R882H)) cooperates with NRAS mutation to transform hematopoietic stem/progenitor cells and induce acute leukemia development. Mechanistically, DNMT3A(R882H) directly binds to and potentiates transactivation of stemness genes critical for leukemogenicity including Meis1, Mn1, and Hoxa gene cluster. DNMT3A(R882H) induces focal epigenetic alterations, including CpG hypomethylation and concurrent gain of active histone modifications, at cis-regulatory elements such as enhancers to facilitate gene transcription. CRISPR/Cas9-mediated ablation of a putative Meis1 enhancer carrying DNMT3A(R882H)-induced DNA hypomethylation impairs Meis1 expression. Importantly, DNMT3A(R882H)-induced gene-expression programs can be repressed through Dot1l inhibition, providing an attractive therapeutic strategy for DNMT3A-mutated leukemias.

Abstract B39: Multitarget approach against PI3K, Aurora kinase, and BRD4 leads to improved antitumor activity in Myc-overexpressing lymphoma cells

Background: Myc has proven extremely difficult to target therapeutically. Therefore, we hypothesized that optimal inhibition of several key targetable pathways involved in Myc signaling could overcome this long-standing problem. We identified phosphoinositide 3-kinase (PI3K), aurora kinase (Aurk), and bromodomain protein (BRD)4 as the primary therapeutic targets to counteract Myc deregulation based on strong evidence that these pathways are essential for tumor maintenance in Myc-driven malignancies.

Methods: Cytotoxicity assays using MTS and trypan blue were used to compare levels of drug sensitivity in lymphoma cell lines with high and low Myc mRNA expression. Apoptosis and cell cycle assays were performed using Annexin V and Propidium Iodide staining. Murine xenograft models were used to assess the efficacy and tolerability of single vs. combined inhibition.

Results: Myc-overexpressing Burkitt lymphoma (Raji) cells were treated with various concentrations of small molecule inhibitors against PI3K (BEZ-235), Aurk (MLN-8237), or BRD4 (I-BET-151) for 48 to 72 hours and cell viability was evaluated. BEZ-235, MLN-8237, and I-BET-151 inhibited cell growth individually with IC-50 of 30 nM, 10 nM, and 650 nM, respectively. Dual treatment with BEZ-235/MLN-8237, BEZ-235/I-BET-151, or MLN-8237/I-BET-151 induced more significant cell growth inhibition as compared to treatment with the single agent alone. The combination index (CI) values were less than 1 at various drug concentrations, indicating that different combinations of BEZ-235, MLN-8237, and I-BET-151 were synergistic in terms of inhibitory effect on tumor cell viability. Superior activity of the dual inhibition was also noted in other Myc-overexpressing lymphoma cells, including Ramos and SUDHL4. Combination treatments also increased apoptosis and induced more pronounced cell cycle arrest compared to the single agent treatment alone. We then analyzed protein expression by Western blot in Myc-overexpressing cells treated with various combinations of BEZ-235, MLN-8237, and I-BET-151. Treatment with BEZ-235 in Myc-overexpressing lymphoma cells resulted in reduced phosphorylated levels of the downstream effector RPS6K, which promotes protein translation and proliferation. MLN-8237 reduced the expression of p-HisH3 and p-Aurk while increasing the expression of p-S6K. Treatment with I-BET-151 resulted in significant reduction of Myc expression. Combined treatments had minimal impact on protein expression patterns compared to individual treatments, and the synergistic effect was independent of depletion of cytoplasmic levels of Myc. Lastly, athymic nude mice bearing Ramos lymphoma xenografts were treated with BEZ-235, MLN-8237, I-BET-151, and various dual-combinations of each agent. The mean tumor volumes in mice treated with negative control, BEZ-235, I-BET-151, and MLN-8237 as single agents were 3480, 2364, 2320, and 671 mm3, respectively, at Day 28. Mice treated with BEZ-235/I-BET-151, MLN-8237/I-BET-151, and BEZ-235/MLN-8237 combinations had mean tumor volumes of 1709, 461, and 166 mm3, respectively, at Day 28. The survival rates for mice treated with negative control, BEZ-235, I-BET-151, and MLN-8237 as single agents were 0%, 10%, 10%, and 70%, respectively, at Day 35. The combination of BEZ-235 and MLN-8237 was associated with significant toxicity with 60% of mice dying from weight loss and failure to thrive despite tumor regression. Mice treated with the MLN-8237 and I-BET-151 combination demonstrated the best survival rate of 100% at Day 35.

Conclusion: Our data demonstrated that Myc-overexpressing tumors can be successfully targeted by inhibiting kinases associated with Myc-signaling. Specifically, MLN-8237, a small molecule inhibitor against AURK, induced apoptosis of Myc-overexpressing tumor cells in vitro and showed the most promising anti-tumor activity in mice bearing Myc-overexpressing lymphoma, especially when combined with I-BET-151, a BRD4 inhibitor.

Citation Format: Steven I. Park, Carolina P. Lin, Michael Foote, Trevor Parton, David B. Darr, Daniel Roth, Aadra P. Bhatt, Dirk P. Dittmer, Norman E. Sharpless, Blossom Damania. Multitarget approach against PI3K, Aurora kinase, and BRD4 leads to improved antitumor activity in Myc-overexpressing lymphoma cells. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr B39.

An orally bioavailable chemical probe of the Lysine Methyltransferases EZH2 and EZH1

EZH2 or EZH1 is the catalytic subunit of the polycomb repressive complex 2 that catalyzes methylation of histone H3 lysine 27 (H3K27). The trimethylation of H3K27 (H3K27me3) is a transcriptionally repressive post-translational modification. Overexpression of EZH2 and hypertrimethylation of H3K27 have been implicated in a number of cancers. Several selective inhibitors of EZH2 have been reported recently. Herein we disclose UNC1999, the first orally bioavailable inhibitor that has high in vitro potency for wild-type and mutant EZH2 as well as EZH1, a closely related H3K27 methyltransferase that shares 96% sequence identity with EZH2 in their respective catalytic domains. UNC1999 was highly selective for EZH2 and EZH1 over a broad range of epigenetic and non-epigenetic targets, competitive with the cofactor SAM and non-competitive with the peptide substrate. This inhibitor potently reduced H3K27me3 levels in cells and selectively killed diffused large B cell lymphoma cell lines harboring the EZH2(Y641N) mutant. Importantly, UNC1999 was orally bioavailable in mice, making this inhibitor a valuable tool for investigating the role of EZH2 and EZH1 in chronic animal studies. We also designed and synthesized UNC2400, a close analogue of UNC1999 with potency >1,000-fold lower than that of UNC1999 as a negative control for cell-based studies. Finally, we created a biotin-tagged UNC1999 (UNC2399), which enriched EZH2 in pull-down studies, and a UNC1999-dye conjugate (UNC2239) for co-localization studies with EZH2 in live cells. Taken together, these compounds represent a set of useful tools for the biomedical community to investigate the role of EZH2 and EZH1 in health and disease.

Investigation of the in vitro metabolism profile of a phosphodiesterase-IV inhibitor, CDP-840: leading to structural optimization

CDP-840 is a selective and potent phosphodiesterase type IV inhibitor, whose in vitro metabolism profile was first investigated using liver microsomes from different species. At least 10 phase I oxidative metabolites (M1-M10) were detected in the microsomal incubations and characterized by capillary high-performance liquid chromatography continuous-flow liquid secondary ion mass spectrometry (CF-LSIMS). Significant differences in the microsomal metabolism of CDP-840 were found between rat and other species. The major route of metabolism in rat involved para-hydroxylation on the R4 phenyl. This pathway was not observed in human and several other species. The in vitro metabolism profile of CDP-840 was further examined using freshly isolated hepatocytes from rat, rabbit, and human. The hepatocyte incubations indicated more extensive metabolism relative to that in microsomes. In addition to the phase I oxidative metabolites observed in microsomal incubations, several phase II conjugates were identified and characterized by CF-LSIMS. Interspecies differences in phase II metabolism were also found in these hepatocyte incubations. The major metabolite in human hepatocytes was identified as the pyridinium glucuronide, which was not detected in rat hepatocytes. Simple structural modification on R4, such as p-Cl substitution, greatly reduced the species differences in microsomal metabolism. Furthermore, modifications on R3, such as the N-oxide, eliminated the N-glucuronide formation in human. These results not only helped in determining the suitability of animal species used in the preclinical safety studies but also provided valuable directions for the synthetic efforts in finding backup compounds that are more metabolically stable.