Hansen, Nanna

Abstract Background: Treatment options for elderly acute myeloid leukemia (AML) patients, despite various novel therapies, are still limited. Relapse is common after chemotherapy, and progression on lower intensity treatment with hypomethylating agents is inevitable in all patients even after initial response. Lysine deacetylase inhibitors (KDIs or HDAC inhibitors) have shown limited single-agent clinical activity in AML. Therefore, to develop potential novel treatment options for AML, we aimed to identify synergistic KDI-based drug combinations to build upon the single-agent activity and clinical-availability of KDIs. We performed RNA-interference (RNAi) drug modifier screens of the kinome and phosphatome with the KDI vorinostat in AML cells in order to identify targets to inhibit in combination with KDIs. Based on pathway analysis of RNAi screen results that highlighted an unexpected role for p38/JNK/SAPK signaling in vorinostat activity in AML, we explored the putative p38 substrate-selective MK2 inhibitor CMPD1 combined with KDIs, and demonstrated potent synergistic activity in AML regardless of molecular, cytogenetic or lineage background. As published evidence suggests that CMPD1 can also act as a microtubule-destabilizing/targeting agent (MTA), and that MK2 can associate with microtubules and cytoskeleton-associated proteins, we examined several MTAs in combination with KDIs in AML, including vinca alkaloid microtubule-destabilizing agents vinblastine/vincristine, and taxol as a microtubule-stabilizing agent. Results: Vinblastine and vincristine dose-dependently synergized with vorinostat similarly to CMPD1 in all AML cell lines tested, with vinblastine being more potently synergistic than vincristine. Taxol only potentiated KDI activity in approximately half of AML cell lines. Importantly, preliminary data suggest preferential, dose-dependent synergy of KDIs and vinca alkaloid MTAs in the CD34+ progenitor AML cell fraction, as compared to the paired CD34-depleted fraction from the same primary AML sample in ex vivo culture. This preferential CD34+ activity was similar to that observed with CMPD1 combined with KDIs in ex vivo models. Consistent with synergistic activity of MTAs and KDIs, multiple RNAi screen hits also converged on microtubule dynamics. Subsequently, we identified the LKB1 signaling network, a critical integrator of cellular stress metabolism and hematopoietic stem cell quiescence/homeostasis, as a determinant of vorinostat activity in AML. Of 14 known kinases directly regulated by LKB1, 4 belong to microtubule-associated protein (MAP) or microtubule-affinity regulating kinases (MARK) families (e.g. screen hit MARK4). RNAi screen hits also converged on regulation of microtubule proteins, or directly on microtubule proteins themselves, (e.g. atypical MAPK4 and MAPK6 which phosphorylate microtubule-associated protein 2, or TAOK2 which has a kinase-independent role in stabilizing microtubules). Additionally, several RNAi hits such as PACSIN1 and -2, and MAST2 and -4 link the actin cytoskeleton to microtubule dynamics. Discussion: Herein we show that several types of clinically-used MTAs (i.e. vinca alkaloids or taxanes) potently synergize with KDIs in AML, and that this synergy can occur preferentially in primary CD34+ cells, as compared to the CD34-negative AML compartment. Although at high in vitro doses microtubule-destabilizing agents such as vinca alkaloids, and microtubule-stabilizing agents such as taxanes, can both induce apoptosis via mitotic perturbation, many publications show that low therapeutic MTA doses can induce apoptosis in tumor cells in vivo independent of mitosis. Therefore, we hypothesize that clinically-available KDIs (i.e. vorinostat, panobinostat) and MTAs (i.e. vinca alkaloids or taxanes) represent novel combinations with the potential to target the AML progenitor pool even in a non-proliferate state, and thus have the potential to eradicate minimal residual disease. Disclosures Mesa: Celgene: Research Funding; Incyte Corporation: Research Funding; Ariad: Consultancy; Galena: Consultancy; Novartis: Consultancy; Promedior: Research Funding; CTI: Research Funding; Gilead: Research Funding. Tibes:Italfarmaco S.p.A.: Consultancy, Honoraria.

Abstract Introduction Venetoclax (ABT-199) is an approved BCL-2 inhibitor for the treatment of patients with chronic lymphocytic leukemia (CLL). Multiple clinical trials are underway to explore its efficacy in additional indications. While venetoclax demonstrated high remission rates in combination with azacitidine in early stage clinical trials, the question of durability of responses and primary and acquired resistance remain, especially given the modest activity and rapid development of resistance as a single agent. One reported mechanism of intrinsic resistance is high expression of other BCL-2 family proteins, including MCL-1. We and others have demonstrated that the CDK9 inhibitor, alvocidib, can mediate transcriptional repression of anti-apoptotic MCL-1. It has also been shown that alvocidib can increase pro-apoptotic BIM, a dual activator and sensitizer BH3-only protein that can directly induce apoptosis and simultaneously inactivate anti-apoptotic BCL-2 family proteins such as MCL-1 and BCL-2, thus having the same effect on mitochondria-associated apoptosis as MCL-1 down-regulation, with the potential to directly induce apoptosis. An alvocidib-containing cytotoxic chemotherapy regimen demonstrated favorable remission rates in high-risk AML patients over standard therapy in a randomized Phase 2 trial indicating its potential role and safety in AML. We hypothesized that alvocidib and venetoclax would synergize against AML cells by shifting the overall balance of pro- and anti-apoptotic BCL-2 proteins in favor of apoptosis and thus represent a novel active treatment regimen in AML. Aims This study seeks to examine the efficacy of a treatment regimen containing alvocidib and venetoclax in multiple preclinical studies, including in vivo models of AML. Methods Cell viability assays interrogating alvocidib and venetoclax activity in cell lines were performed using CellTiter-Glo according to manufacturer's protocol. mRNA/miRNA expression changes were assessed using standard RT-PCR technique. Protein expression changes were assessed using standard western immunoblotting technique. To assess the efficacy of an alvocidib and venetoclax combination on tumor growth in an in vivo model, the OCI-AML3 xenograft mouse model and ex vivo studies with AML patient samples were performed. Results Herein we demonstrate that alvocidib inhibits both mRNA and protein expression of MCL-1 in a time and concentration-dependent fashion in 3 out of 4 AML cell lines analyzed, while in cells where alvocidib did not reduce MCL-1 protein levels (i.e. MOLM-13) a dose-dependent decrease in miR17-92, and concomitant increase in BIM protein was observed after 24 hours of alvocidib treatment. The alvocidib-venetoclax combination resulted in very strong synergistic reductions of cell viability (with combination indices [CI] of 0.4 to 0.7), both in venetoclax-sensitive and resistant cells. The venetoclax-sensitive lines, MV4-11 and MOLM-13, exhibited 5- to 10-fold reduction of venetoclax EC50 values in the low nM range when combined with only 80 nM alvocidib. Importantly, venetoclax-resistant lines, OCI-AML3 and THP-1, exhibited at least 20-fold reduction of venetoclax EC50 values from near 1 µM to 10-50 nM, when combined with 80 nM alvocidib.In the venetoclax-resistant OCI-AML3 xenograft model, single agent alvocidib and venetoclax achieved tumor growth inhibition (TGI) of 9.7 and 31.5%, respectively, while the combination achieved 87.9% TGI at the same dose levels of individual drugs. Conclusions Taken together, our data suggest that the combination of alvocidib with venetoclax is highly synergistic in vitro and in vivo, in both venetoclax-sensitive and -resistant AML across a heterogeneous genomic background. The particularly high level of synergy achieved in venetoclax-resistant cell lines highlights the central importance of both BCL-2 and MCL-1-mediated cell survival in AML. Importantly, the addition of alvocidib to venetoclax treatment reduced IC50s to clinically achievable concentrations. Therefore, we conclude that an alvocidib/venetoclax combination may be a novel approach for the treatment of AML and warrants further pre-clinical and clinical validation. Disclosures Whatcott: Tolero Pharmaceuticals: Employment. Kim:Tolero Pharmaceuticals: Employment. Haws:Tolero Pharmaceuticals: Employment. Mesa:Celgene: Research Funding; Galena: Consultancy; Promedior: Research Funding; Ariad: Consultancy; Novartis: Consultancy; CTI: Research Funding; Incyte: Research Funding; Gilead: Research Funding. Peterson:Tolero Pharmaceuticals: Employment. Siddiqui-Jain:Tolero Pharmaceuticals: Employment. Weitman:Tolero Pharmaceuticals: Employment. Bearss:Tolero Pharmaceuticals: Employment, Equity Ownership, Patents & Royalties. Warner:Tolero Pharmaceuticals: Employment, Equity Ownership, Patents & Royalties.

Abstract Introduction/Background Recurrent deletions of chromosome 5 and 7 are characteristic of the myeloid malignancies MDS and AML, determine prognosis and influence therapeutic decision. The pathogenetic contribution of individual genes to MDS/AML development has been shown for several of these genes. However, how and if these genetic losses may relate to therapeutic interventions or represent haploinsufficient targets has remained elusive for the most part. We hypothesized that genes found within the commonly deleted regions (CDRs) of chromosome 5/7 (chr 5/7) represent targetable vulnerabilities in malignant myeloid cells. Therefore we generated a custom RNAi library to functionally interrogate these genomic regions alone or under 5-Azacitidine (5-Aza) treatment, to identify individual genes whose silencing modulate 5-Aza responsiveness. Methods/Materials Custom siRNA plates against ~270 genes (3x sequences/gene, Qiagen) on CDRs of chr 5/7 were assembled. Genes were silenced by siRNA for 48 hours followed by 48-72 hour 5-Aza treatment after which cell viability was determined. Four cell lines (TF1, THP1, MDS-L and HEL) were investigated in parallel with combined siRNA/5-Aza incubations and appropriate 5-Aza and siRNA only control. Hits were selected as > 2 standard deviation changes in viability from the median log2 value of the ratio [(siRNA + 5-Aza)/(siRNA only)], normalized per plate and across the entire screen. Duplictae RNAis screens were performed. Synergy between 5-Aza and the SMO inhibitors LDE225 (Sonidegib) and GDC0449 (Vismodegib) was assessed with CalcuSyn in a panel of AML cell lines. Ex vivo viability and clonogenic re-population experiments in primary patient derived AML and MDS cells were performed with Sonidegib. Results Several genes within the Hedgehog (HH) pathway emerged as sensitizers to 5-Aza when silenced by siRNA in three of four cell lines examined. Specifically Shh siRNA sensitized to 5-Aza in both TF-1 and THP-1 cells, SMO in HEL and GLI3 in THP-1 cells. Shh silencing alone (siRNA only) resulted in reduction of viability only in TF-1 cells but not in THP-1 cells, while SMO and GLI3 siRNA alone did not result in significant reductions in viability but sensitized to 5-Aza, indicating true sensitization and an interactions between the HH pathway and 5-Aza treatment. The SMO inhibitor Vismodegib synergized with 5-Aza in drug dose response assays in a panel of four AML cell lines (TF-1, THP-1, ML-2, HL-60) with Combination Index (CI) values of around 0.6 or lower at low doses of both drugs. Similar results were also observed with Sonidegib in vitro in 5 molecularly heterogeneous AML cell lines. Given stem cell modulation capacity of SMO inhibition, we examined ex vivo proliferation and more importantly clonogenic growth capacity. Highly interesting, ex vivo viability was reduced and synergy observed by the Sonidegib/5-Aza combination to a much greater extend in CD34+ selected primary MDS and AML cells as compared to bulk or CD34 depleted (normal) MNCs. Clonogenic growth was reduced in the combination over single agent 5-Aza or Sonidegib in ~ 50% of samples assessed to date. No direct correlations to cytogenetics were observed. A clinical Phase 1b trial was designed based on these results and is currently accruing in the first cohorts. Conclusions RNAi screening of CDRs of chr 5/7 yielded potential targetable therapeutic vulnerabilities with several genes within the HH pathway sensitizing to 5-Aza. SMO inhibitors pharmacologically validate this concept in vitro and ex vivo with the potential to more selectively affect leukemia stem/progenitor cells. Clinical data will show if this is a specific effect involving chr 5/7 or a general concept in malignant myeloid cells. Thus, SMO inhibition in combination with 5-Aza may be a novel rational combination in AML and MDS. Disclosures Off Label Use: LDE225/Sonidegib on a clinical trial. Mesa:Incyte, CTI, NS Pharma, Inc., Gilead, Celgene: Research Funding.

Abstract Background: Histone deacetylase inhibitors (HDIs) have shown clinical activity in myeloid malignancies, albeit insufficient to justify single-agent therapy. Thus, we have sought targets/therapies that synergistically enhance the activity of HDIs for combination therapy. We conducted RNA-interference (RNAi) drug modifier screens with the HDI SAHA, and have previously reported convergence of multiple screen hits on different points of the p38-SAPK/JNK signaling pathway. However, in subsequent pharmacological studies, well-characterized p38α/β inhibitors SB2012190 and LY2228820, and JNK inhibitor SP600125 did not modulate SAHA anti-leukemic activity. Nonetheless, a putative MK2 substrate-selective p38 inhibitor known as CMPD1 (Biochemistry 2004 Sep 21; 43(37):11658-71) was found to potently synergize with SAHA in all AML cell lines tested (N=8) in a dose-dependent manner. Further, using ex vivo cultures of primary myeloid malignancies (N=14), CMPD1 showed strong, selective synergy with SAHA in malignant CD34+ isolated cells, as compared to little or no synergy in CD34-depleted cells. Furthermore, CMPD1 specifically synergized with SAHA and a similar HDI panobinostat, but was found to interact antagonistically with cytarabine, and only additively with azacitidine. Herein, we present additional data from our investigation to better understand the mechanism of CMPD1 synergy with HDIs for future clinical translation. Results: Concurrent cell cycle and apoptosis measurements by flow cytometry show that single-agent CMPD1 results in a potent G2/M arrest that is resolved over time without a significant induction of apoptosis, whereas the combination of SAHA + CMPD1 results in a similar or increased level of G2/M arrest, which conversely culminates in a significant induction of apoptosis. The synergistic dose of single-agent SAHA used in these flow cytometry studies did not cause any significant cell cycle changes, and did not induce significant apoptosis alone in the AML cell lines studied. CMPD1 is known to be a MK2 substrate-selective p38 inhibitor; however, we find that CMPD1 potently increases the phosphorylation of MK2 at doses strongly synergistic with SAHA. This is not a universal activity of p38 inhibitors in our in vitro AML models, as the p38 inhibitor SB202190 does not increase MK2 phosphorylation alone or in combination with SAHA. We further hypothesized that CMPD1 synergizes with SAHA through a transcription-based mechanism, thus we measured mRNA expression by next-generation sequencing after SAHA and CMPD1 treatment alone, and in combination, in an AML cell line TF-1. We find that SAHA + CMPD1 treatment induces a synergistic increase in transcript levels of: i) several chemokines such as IL-8, CXCL1, CXCL2, and CXCL3, ii) inhibitor of DNA binding proteins ID2 and ID3, and iii) cell cycle regulator p21. Transcript levels of the Hippo pathway transcription factor YAP1 were also found to be increased by CMPD1 treatment in TF-1. We confirm an increase of total YAP1 protein levels by western blot. We also find an increase of YAP1 phosphorylation at serine 127 in CMPD1 or CMPD1 + SAHA treated samples in several AML cell lines, yet we find that Ser-127 phosphorylated YAP1 is located in the nucleus. Consistent with YAP1 Ser-127 phosphorylation, we find that upstream signaling kinase LATS1 is activated/phosphorylated at serine 909 in AML cell lines after treatment with CMPD1 or SAHA + CMPD1. We also confirm a synergistic increase in p21 protein levels upon SAHA + CMPD1 treatment by western blot in several AML cell lines. Changes in the protein levels of ID2 and ID3 were confirmed in TF-1 by western blot; however, ID protein levels appear to be uniquely affected by CMPD1 or the combination in a cell line-dependent manner. Conclusion: CMPD1 selectively synergizes with histone deacetylases inhibitors in myeloid malignancies. The synergistic activity of this combination highlights the potential for selectively targeting malignant CD34+ cells. The phosphorylation of LATS1 observed is consistent with i) the known roles for LATS1 in cell cycle regulation, ii) the G2/M arrest observed with CMPD1, and iii) the downstream phosphorylation of YAP1 observed. These findings linking CMPD1 with LATS1/YAP1 await further study and characterization. Although CMPD1 is not a clinically-relevant compound, CMPD1 may be used as a scaffold or tool compound to enable future development and research. Disclosures Mesa: Pfizer: Research Funding; Novartis Pharmaceuticals Corporation: Consultancy; Genentech: Research Funding; NS Pharma: Research Funding; Promedior: Research Funding; Gilead: Research Funding; CTI Biopharma: Research Funding; Incyte Corporation: Research Funding.

Abstract Background: Histone deacetylase (HDAC) inhibitors (HDIs) vorinostat (SAHA) and romidepsin are approved for the treatment of cutaneous T-cell lymphoma, while belinostat has recently been approved for the treatment of peripheral T-cell lymphoma. SAHA exhibits clinical activity in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), although insufficient to justify single-agent therapy for these indications. The precise clinical mechanism of SAHA and other HDIs remains incompletely characterized, impeding the design and implementation of rational HDI-based therapeutic combinations for myeloid malignancies. To circumvent this lack of mechanistic understanding, we conducted RNA-interference (RNAi) modifier screens of the kinome and phosphatome to identify signaling pathways that modulate SAHA (HDI) anti-leukemic activity in AML cell lines TF-1, HEL and THP-1 for rapid translation of findings from ex vivo validation to clinical application. Results: Multiple screen hits (both kinases and phosphatases) converge on distinct points of the p38-SAPK/JNK signaling pathways, suggesting involvement of these stress-activated pathways in SAHA anti-leukemic activity. However, the most well characterized p38α/β inhibitors SB202190 and LY2228820 do not augment SAHA anti-leukemic activity at any dose across the broad dose ranges tested. Similarly, the JNK inhibitor SP600125 does not modulate SAHA activity at doses that inhibit JNK. However, the putative MK2a substrate-selective p38 inhibitor CMPD1 (Boehringer-Ingelheim; Davidson, W., et. al., Biochemistry 2004 Sep 21;43(37):11658-71) selectively potentiates the activity of SAHA in all AML cell lines tested (N=8), as well as in ex vivo cultures of primary myeloid malignancies (N=14), including polycythemia vera, chronic myelomonocytic leukemia, MDS/myeloproliferative neoplasm overlap syndrome, MDS transformed to AML, and de novo AML. The observed dose-dependent synergy occurs at nanomolar doses consistent with the reported apparent inhibitory constant for CMPD1 inhibition of p38-dependent phosphorylation of MK2a. Further, SAHA + CMPD1 synergy is significantly greater in CD34+-selected as compared to CD34+-depleted cell populations ex vivo. Furthermore, CMPD1 is similarly synergistic with the HDI panobinostat in vitro, but interacts antagonistically with cytarabine and additively with 5-azacitidine. This suggests that CMPD1 interacts specifically with SAHA and panobinostat in AML. The synergistic interaction between CMPD1 and SAHA is independent of ROS induction, as pretreatment with N-acetylcysteine does not abrogate synergy, despite reducing single-agent SAHA activity. While CMPD1 is reported to be an MK2a substrate-selective p38 inhibitor, CMPD1 does not affect the regulation of several canonical MK2 targets at doses that are potently synergistic in AML cell lines, including the phosphorylation of HSP27 or AATF. To begin to probe the mechanism of CMPD1 and SAHA synergy more extensively, mRNA expression was measured by next-generation sequencing after SAHA and CMPD1 treatment alone and in combination in the AML cell line TF-1. Sequencing data is currently being analyzed and findings will be presented. Conclusion: RNAi knockdown of several p38-SAPK/JNK pathway components modulates SAHA activity in malignant myeloid cells; however, common pharmacological sensitizing targets remain elusive. We hypothesize that MK2 and/or a yet unrecognized pathway modulated by CMPD1 can be targeted for HDI combination therapy in malignant myeloid cells. Current and ongoing results from this study will provide validated targets for rational HDI combination in myeloid malignancies. Disclosures Off Label Use: LDE225/Sonidegib as investigational agent. Mesa:Incyte, CTI, NS pharma, Gilead, Celgene: Research Funding.