Cen, Ling

MYC gene amplification and somatic mutations are frequent in both adult and pediatric AML although how MYC drives and contributes to the development and maintenance of AML has not been resolved. Transcription factor EB (TFEB) is a master regulator of genes that control autophagy and lysosome biogenesis, a central catabolic recycling pathway that regulates cell survival. Given the oncogenic effects of MYC in AML and that the induction of autophagy compromises AML cell growth and survival, we tested if the oncogenic effect of MYC depends on its suppression of TFEB transcription programs in AML. In support of this hypothesis, inducible MYC expression in K562 and THP-1 leukemia cells was sufficient to suppress expression of TFEB and its target genes. Further and conversely, MYC knockdown in NB4 AML cells provoked increased expression of TFEB mRNA and protein, as well as increased expression of TFEB target genes. Notably, dose response studies demonstrated that expression of TFEBS211A, constitutively nuclear form of TFEB that is refractory to control by mTORC1 signaling, dramatically impairs proliferation of HL60, OCI-AML2 and OCI-AML3 AML cells. In addition, induction of TFEBS211A provoked rampant apoptosis. Of important, overexpression of TFEBS211A in HL-60 and OCI-AML3 cells was also sufficient to promote monocytic and granulocytic differentiation, as judged by morphological changes and the acquisition of mature monocytic and granulocytic markers including CD11b, Gr1, and CD15. To identify TFEB targets that might contribute to myeloid/granulocytic differentiation, we performed RNA-seq analysis of HL60 leukemia cells engineered to inducibly express the TFEBS211A transgene. Using a cut-off of fold change>4 with q<0.01, a total of 1152 genes were differentially regulated following the induction of TFEBS211A in HL60 cells. As expected, this included the robust induction of nearly all TFEB target genes associated with the autophagy-lysosome pathway, but also of STAT1, KLF4, KLF6, CEBPB, CSF1 and GATA2 genes that are necessary and/or sufficient to provoke terminal monocytic and granulocytic differentiation of AML cells. Surprisingly, among genes induced by TFEB in HL60 cells is IDH1, which catalyzes the production of α-ketoglutarate (α-KG), a required substrate of the TET family of dioxygenases that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). In particular, TFEBS211A expression provoked increases in levels of α-KG and significant increases in global levels of 5hmC in genomic DNA of HL60 leukemia cells both ex vivo and in vivo. Furthermore, TFEB-mediated induction of IDH1/2 mRNA and protein, and of IDH1 promoter activity, was antagonized by inducible expression of MYC. To assess the global effects of TFEB on 5mC/5hmC landscapes, we performed paired reduced representation bisulfite (BS)- and oxidation bisulfite (oxBS)-sequencing. As predicted, TFEBS211A induced both loss and gains of 5mC, but there were more losses (n = 722) than gains (n = 459) across all 22 chromosomes. Quite remarkably, and consistent with TFEB-provoked increases of 5hmC signals, TFEBS211A exclusively induced 5hmC gains (in a total of 863 genes), and 37% and 36% of these 5hmC gains occurred in promoter regions and CpG islands, and across all 22 chromosomes. Comparison of BS- and oxBS-seq versus RNA-seq analyses of HL60 cells expressing TFEB revealed significant changes in mRNA levels and concomitant differential changes in 5mC and 5hmC marks in KLF4, KLF6, STAT3, TP73, andFOXO1 that have pivotal roles in controlling myeloid cell differentiation and death. Collectively, these findings demonstrate that MYC suppresses TFEB expression and function in AML cells, and that TFEB functions as a tumor suppressor that provokes AML cell differentiation and death. Strikingly, these responses rely on epigenetic control, where TFEB directly induces the transcription of IDH1 and IDH2 to provoke global hydroxylation of 5-methylcytosine and the expression of genes that drive terminal differentiation and apoptosis. Thus, a MYC-TFEB-IDH1/2-TET2 circuit controls AML cell fate. Disclosures Murphy: Merck: Research Funding; Puma Biotech: Research Funding. Ballabio:CASMA Therapeutics: Other: Co-Founder. Kaufmann:Takeda Pharmaceuticals: Research Funding.

Abstract MYC oncoproteins regulate transcription of genes directing cell proliferation, metabolism, and tumorigenesis. A variety of alterations drive MYC expression in acute myeloid leukemia (AML), and enforced MYC expression in hematopoietic progenitors is sufficient to induce AML. Here we report that AML and myeloid progenitor cell growth and survival rely on MYC-directed suppression of Transcription Factor EB (TFEB), a master regulator of the autophagy–lysosome pathway. Notably, although originally identified as an oncogene, TFEB functions as a tumor suppressor in AML, where it provokes AML cell differentiation and death. These responses reflect TFEB control of myeloid epigenetic programs by inducing expression of isocitrate dehydrogenase-1 (IDH1) and IDH2, resulting in global hydroxylation of 5-methycytosine. Finally, activating the TFEB–IDH1/IDH2–TET2 axis is revealed as a targetable vulnerability in AML. Thus, epigenetic control by an MYC–TFEB circuit dictates myeloid cell fate and is essential for maintenance of AML. Significance: Alterations in epigenetic control are a hallmark of AML. This study establishes that a MYC–TFEB circuit controls AML differentiation and epigenetic programs by inducing IDH1/IDH2 and hydroxylation of 5-methylcytosine, that TFEB functions as a tumor suppressor in AML, and that this circuit is a targetable vulnerability in AML. See related commentary by Wu and Eisenman, p. 116.

Abstract PARP inhibition can enhance the efficacy of temozolomide and prolong survival in orthotopic glioblastoma (GBM) xenografts. The aim of this study was to evaluate the combination of the PARP inhibitor rucaparib with temozolomide and to correlate pharmacokinetic and pharmacodynamic studies with efficacy in patient-derived GBM xenograft models. The combination of rucaparib with temozolomide was highly effective in vitro in short-term explant cultures derived from GBM12, and, similarly, the combination of rucaparib and temozolomide (dosed for 5 days every 28 days for 3 cycles) significantly prolonged the time to tumor regrowth by 40% in heterotopic xenografts. In contrast, the addition of rucaparib had no impact on the efficacy of temozolomide in GBM12 or GBM39 orthotopic models. Using Madin-Darby canine kidney (MDCK) II cells stably expressing murine BCRP1 or human MDR1, cell accumulation studies demonstrated that rucaparib is transported by both transporters. Consistent with the influence of these efflux pumps on central nervous system drug distribution, Mdr1a/b−/−Bcrp1−/− knockout mice had a significantly higher brain to plasma ratio for rucaparib (1.61 ± 0.25) than wild-type mice (0.11 ± 0.08). A pharmacokinetic and pharmacodynamic evaluation after a single dose confirmed limited accumulation of rucaparib in the brain is associated with substantial residual PARP enzymatic activity. Similarly, matrix-assisted laser desorption/ionization mass spectrometric imaging demonstrated significantly enhanced accumulation of drug in flank tumor compared with normal brain or orthotopic tumors. Collectively, these results suggest that limited drug delivery into brain tumors may significantly limit the efficacy of rucaparib combined with temozolomide in GBM. Mol Cancer Ther; 14(12); 2735–43. ©2015 AACR.

Abstract Poly (ADP-ribose) polymerase (PARP) inhibition can enhance the efficacy of temozolomide (TMZ) and has been shown to significantly prolong survival in orthotopic GBM xenografts. Here the effects of PARP inhibitor AG014699 (AG699) on the efficacy of TMZ was evaluated and corresponding pharmacokinetic and pharmacodynamic studies were performed in the MGMT methylated GBM12 primary GBM xenograft line. AG699 effectively sensitized GBM12 cells to TMZ in vitro in a neurosphere formation assay: IC50 of 1.56 M for TMZ when combined with 1 μM AG699 compared to 8.16 M TMZ when used alone). Using these same cells, orthotopic xenografts were established and mice were randomized to 3–28 day cycles of placebo or TMZ (50 mg/kg days 1–5) with or without AG699 (1 mg/kg IP days 1–5). Although this model is responsive to other TMZ/PARP inhibitor combinations, the addition of AG699 was ineffective (median survival: placebo 16 days, TMZ 68 days and TMZ/AG699 81 days, p=0.883). In contrast, AG699 significantly potentiated TMZ-induced tumor regrowth delay in a flank tumor model with GBM12 (median time for tumors to reach endpoint: placebo 32 days, TMZ 86 days and TMZ/AG699 121 days, p<0.01). To more clearly understand the discrepancy between intracranial and flank studies, drug accumulation and target inhibition were assessed. Plasma and tissue distribution studies in mice bearing GBM12 orthotopic xenografts showed that 0.5 h after AG699 treatment its level in brain and tumor xenograft was much lower compared with that in liver (see table). In an assessment of catalytic activity, PARP activity in liver was inhibited more than 95% of control at least 2 h after AG699 treatment, while it was inhibited less than 50% and 30% in orthotopic xenograft tissue and normal brain, respectively (Table). Collectively, these data support the hypothesis that the efficacy of AG699 combined with TMZ is limited in the orthotopic model due to limited drug accumulation within the brain, and the mechanisms of which are under investigation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A77.

Abstract Glioblastoma multiforme (GBM) is the most common and highly malignant primary brain tumor in adults with a median survival just over 1 year, and novel therapies are urgently needed. Deregulation of the p16 (INK4A)-CDK4/6-pRb pathway are commonly found in human GBM patients and selective inhibitors of CDK4/6 may be specifically useful to suppress proliferation associated with these alterations. PD0332991 is an orally active small molecule that specifically inhibits CDK4 and CDK6. Therefore, the efficacy of PD0332991 was evaluated in the Mayo panel of primary GBM xenograft lines using short-term explant cultures. We hypothesized that expression of p15 and/or p16, endogenous inhibitors of CDK4/6 activity, would suppress the response of GBM tumors to PD0332991 treatment. To test this hypothesis, 2 GBM xenograft cell lines with wild-type p16/p15 levels (GBM5 and 28) and 2 lines without detectable p16/p15 levels (GBM22 and 43) were selected for further analysis. Tumor cells were treated with graded concentrations (10 nanoM to1 microM) of PD0332991 for 5 days and subjected to CyQUANT cell proliferation assays. Consistent with our hypothesis, treatment with 1 microM PD0332991 effectively inhibited cell proliferation to 56.6±3.5% (P<0.001) and 44.3±3.4% (P<0.001) of control in GBM22 and GBM43 cells respectively, but did not affect cell proliferation in GBM5 and GBM28 cells (98.7±15.6% and 101.8±12.0% of control, respectively). In addition, 1 microM PD0332991 induced G1-phase cell cycle arrest in GBM22 (treated 79.7±0.8% vs. control 63.4±0.5% of cells in G1 phase, P<0.001) and GBM43 (treated 70.6±1.1% vs. control 48.9±4.6% of cells in G1 phase, P<0.001) but not in GBM5 and GBM28 (treated 52.3±2.7% vs. control 54.0±5.1%, treated 52.4±4.7% vs. control 54.6±2.6%, respectively). The status of p15 and p16 was confirmed by RT-PCR, which demonstrated readily detectable expression of p15 and p16 in GBM5 and GBM28, but not in GBM22 and GBM43 cells. Additional comparative genomic hybridization (CGH) data showed that CDKN2A and 2B (genes encode for p16 and p15 respectively) are homozygously deleted in GBM22 and 43, hemizygously deleted in GBM5 and normal in GBM28. We also examined the status of CDK4, CDK6, pRb and other molecules in the p16-CDK4/6-pRb pathway by Western, RT-PCR and CGH in these GBM lines and the data will be presented. We are now testing whether shRNA knockdown and/or re-expression of p15/p16 in the relevant cell lines alters their responsiveness to PD0332991. In conclusion, CDK4/6 inhibitor PD0332991 inhibits cell proliferation and induces G1 cell cycle arrest in p15/p16- null GBM tumors, but is less effective in p15/p16 expressing tumors. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C191.

Abstract Purpose: The therapeutic benefit of temozolomide in glioblastoma multiforme (GBM) is limited by resistance. The goal of this study was to elucidate mechanisms of temozolomide resistance in GBM. Experimental Design: We developed an in vivo GBM model of temozolomide resistance and used paired parental and temozolomide-resistant tumors to define the mechanisms underlying the development of resistance and the influence of histone deacetylation (HDAC) inhibition. Results: Analysis of paired parental and resistant lines showed upregulation of O6-methylguanine-DNA methyltransferase (MGMT) expression in 3 of the 5 resistant xenografts. While no significant change was detected in MGMT promoter methylation between parental and derivative-resistant samples, chromatin immunoprecipitation showed an association between MGMT upregulation and elevated acetylation of lysine 9 of histone H3 (H3K9-ac) and decreased dimethylation (H3K9-me2) in GBM12 and GBM14. In contrast, temozolomide resistance development in GBM22 was not linked to MGMT expression, and both parental and resistant lines had low H3K9-ac and high H3K9-me2 within the MGMT promoter. In the GBM12TMZ-resistant line, MGMT reexpression was accompanied by increased recruitment of SP1, C-JUN, NF-κB, and p300 within the MGMT promoter. Interestingly, combined treatment of GBM12 flank xenografts with temozolomide and the HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) favored the evolution of temozolomide resistance by MGMT overexpression as compared with treatment with temozolomide alone. Conclusion: This study shows, for the first time, a unique mechanism of temozolomide resistance development driven by chromatin-mediated MGMT upregulation and highlights the potential for epigenetically directed therapies to influence the mechanisms of resistance development in GBM. Clin Cancer Res; 18(15); 4070–9. ©2012 AACR.