Dyana T. Saenz

Synergistic activity of BET protein antagonist-based combinations in mantle cell lymphoma cells sensitive or resistant to ibrutinib

Mantle cell lymphoma (MCL) cells exhibit increased B-cell receptor and nuclear factor (NF)-κB activities. The bromodomain and extra-terminal (BET) protein bromodomain 4 is essential for the transcriptional activity of NF-κB. Here, we demonstrate that treatment with the BET protein bromodomain antagonist (BA) JQ1 attenuates MYC and cyclin-dependent kinase (CDK)4/6, inhibits the nuclear RelA levels and the expression of NF-κB target genes, including Bruton tyrosine kinase (BTK) in MCL cells. Although lowering the levels of the antiapoptotic B-cell lymphoma (BCL)2 family proteins, BA treatment induces the proapoptotic protein BIM and exerts dose-dependent lethality against cultured and primary MCL cells. Cotreatment with BA and the BTK inhibitor ibrutinib synergistically induces apoptosis of MCL cells. Compared with each agent alone, cotreatment with BA and ibrutinib markedly improved the median survival of mice engrafted with the MCL cells. BA treatment also induced apoptosis of the in vitro isolated, ibrutinib-resistant MCL cells, which overexpress CDK6, BCL2, Bcl-xL, XIAP, and AKT, but lack ibrutinib resistance-conferring BTK mutation. Cotreatment with BA and panobinostat (pan-histone deacetylase inhibitor) or palbociclib (CDK4/6 inhibitor) or ABT-199 (BCL2 antagonist) synergistically induced apoptosis of the ibrutinib-resistant MCL cells. These findings highlight and support further in vivo evaluation of the efficacy of the BA-based combinations with these agents against MCL, including ibrutinib-resistant MCL.

Novel BET protein proteolysis-targeting chimera exerts superior lethal activity than bromodomain inhibitor (BETi) against post-myeloproliferative neoplasm secondary (s) AML cells

The PROTAC (proteolysis-targeting chimera) ARV-825 recruits bromodomain and extraterminal (BET) proteins to the E3 ubiquitin ligase cereblon, leading to degradation of BET proteins, including BRD4. Although the BET-protein inhibitor (BETi) OTX015 caused accumulation of BRD4, treatment with equimolar concentrations of ARV-825 caused sustained and profound depletion (>90%) of BRD4 and induced significantly more apoptosis in cultured and patient-derived (PD) CD34+ post-MPN sAML cells, while relatively sparing the CD34+ normal hematopoietic progenitor cells. RNA-Seq, Reverse Phase Protein Array and mass cytometry ‘CyTOF’ analyses demonstrated that ARV-825 caused greater perturbations in messenger RNA (mRNA) and protein expressions than OTX015 in sAML cells. Specifically, compared with OTX015, ARV-825 treatment caused more robust and sustained depletion of c-Myc, CDK4/6, JAK2, p-STAT3/5, PIM1 and Bcl-xL, while increasing the levels of p21 and p27. Compared with OTX015, PROTAC ARV-771 treatment caused greater reduction in leukemia burden and further improved survival of NSG mice engrafted with luciferase-expressing HEL92.1.7 cells. Co-treatment with ARV-825 and JAK inhibitor ruxolitinib was synergistically lethal against established and PD CD34+ sAML cells. Notably, ARV-825 induced high levels of apoptosis in the in vitro generated ruxolitinib-persister or ruxolitinib-resistant sAML cells. These findings strongly support the in vivo testing of the BRD4-PROTAC based combinations against post-MPN sAML.

BET protein bromodomain inhibitor-based combinations are highly active against post-myeloproliferative neoplasm secondary AML cells

Myeloproliferative neoplasms with myelofibrosis (MPN-MF) demonstrate constitutive activation of Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling that responds to treatment with the JAK1 and 2 kinase inhibitor (JAKi) ruxolitinib. However, MPN-MF often progresses (~20%) to secondary acute myeloid leukemia (sAML), where standard induction chemotherapy or ruxolitinib is relatively ineffective, necessitating the development of novel therapeutic approaches. In the present studies, we demonstrate that treatment with BET (bromodomain and extraterminal) protein inhibitor (BETi), for example, JQ1, inhibits growth and induces apoptosis of cultured and primary, patient-derived (PD), post-MPN sAML blast progenitor cells. Reverse-phase protein array, mass-cytometry and Western analyses revealed that BETi treatment attenuated the protein expressions of c-MYC, p-STAT5, Bcl-xL, CDK4/6, PIM1 and IL-7R, whereas it concomitantly induced the levels of HEXIM1, p21 and BIM in the sAML cells. Co-treatment with BETi and ruxolitinib synergistically induced apoptosis of cultured and PD sAML cells, as well as significantly improved survival of immune-depleted mice engrafted with human sAML cells. Although BETi or heat shock protein 90 inhibitor (HSP90i) alone exerted lethal activity, cotreatment with BETi and HSP90i was synergistically lethal against the ruxolitinib-persister or ruxolitinib-resistant sAML cells. Collectively, these findings further support in vivo testing of BETi-based combinations with JAKi and HSP90i against post-MPN sAML cells.

BET protein proteolysis targeting chimera (PROTAC) exerts potent lethal activity against mantle cell lymphoma cells

Bromodomain extraterminal protein (BETP) inhibitors transcriptionally repress oncoproteins and nuclear factor-κB (NF-κB) target genes that undermines the growth and survival of mantle cell lymphoma (MCL) cells. However, BET bromodomain inhibitor (BETi) treatment causes accumulation of BETPs, associated with reversible binding and incomplete inhibition of BRD4 that potentially compromises the activity of BETi in MCL cells. Unlike BETi, BET-PROTACs (proteolysis-targeting chimera) ARV-825 and ARV-771 (Arvinas, Inc.) recruit and utilize an E3-ubiquitin ligase to effectively degrade BETPs in MCL cells. BET-PROTACs induce more apoptosis than BETi of MCL cells, including those resistant to ibrutinib. BET-PROTAC treatment induced more perturbations in the mRNA and protein expressions than BETi, with depletion of c-Myc, CDK4, cyclin D1 and the NF-κB transcriptional targets Bcl-xL, XIAP and BTK, while inducing the levels of HEXIM1, NOXA and CDKN1A/p21. Treatment with ARV-771, which possesses superior pharmacological properties compared with ARV-825, inhibited the in vivo growth and induced greater survival improvement than the BETi OTX015 of immune-depleted mice engrafted with MCL cells. Cotreatment of ARV-771 with ibrutinib or the BCL2 antagonist venetoclax or CDK4/6 inhibitor palbociclib synergistically induced apoptosis of MCL cells. These studies highlight promising and superior preclinical activity of BET-PROTAC than BETi, requiring further in vivo evaluation of BET-PROTAC as a therapy for ibrutinib-sensitive or -resistant MCL.

SIRT2 Deacetylates and Inhibits the Peroxidase Activity of Peroxiredoxin-1 to Sensitize Breast Cancer Cells to Oxidant Stress-Inducing Agents.

SIRT2 is a protein deacetylase with tumor suppressor activity in breast and liver tumors where it is mutated; however, the critical substrates mediating its antitumor activity are not fully defined. Here we demonstrate that SIRT2 binds, deacetylates, and inhibits the peroxidase activity of the antioxidant protein peroxiredoxin (Prdx-1) in breast cancer cells. Ectopic overexpression of SIRT2, but not its catalytically dead mutant, increased intracellular levels of reactive oxygen species (ROS) induced by hydrogen peroxide, which led to increased levels of an overoxidized and multimeric form of Prdx-1 with activity as a molecular chaperone. Elevated levels of SIRT2 sensitized breast cancer cells to intracellular DNA damage and cell death induced by oxidative stress, as associated with increased levels of nuclear FOXO3A and the proapoptotic BIM protein. In addition, elevated levels of SIRT2 sensitized breast cancer cells to arsenic trioxide, an approved therapeutic agent, along with other intracellular ROS-inducing agents. Conversely, antisense RNA-mediated attenuation of SIRT2 reversed ROS-induced toxicity as demonstrated in a zebrafish embryo model system. Collectively, our findings suggest that the tumor suppressor activity of SIRT2 requires its ability to restrict the antioxidant activity of Prdx-1, thereby sensitizing breast cancer cells to ROS-induced DNA damage and cell cytotoxicity. Cancer Res; 76(18); 5467-78. ©2016 AACR.

Abstract LB-081: Novel and effective RUNX1-targeted therapy for AML expressing RUNX1 mutation

RUNX1 is a transcription factor involved in normal and malignant hematopoiesis. Somatic mutations in RUNX1 (mtRUNX1) have been documented in de novo and secondary AML (10%), MDS (~10%) and CMML (up to 37%). Germ-line, mono-allelic mutations and deletions in RUNX1 cause the highly-penetrant (~40%) autosomal dominant, Familial Platelet Disorder with a propensity to Myeloid Malignancy (FPD-MM). The majority of mtRUNX1 are missense mutations, large deletions or truncation-mutations in the DNA-binding ‘RUNT’ homology domain, or in the C-terminal transactivation domain. These mutations behave mostly as loss of function mutations, associated with relative resistance to standard chemotherapy and an unfavorable prognosis in AML. This highlights an unmet need to develop and test novel targeted therapies for AML due to germ-line or somatic mtRUNX1. In the present studies, we demonstrate that shRNA-mediated knockdown of mutant and wild-type RUNX1 repressed its target genes MYC, PU.1 and MPO (myeloperoxidase), as well as inhibited growth and induced apoptosis of AML cells expressing mtRUNX1 (OCI-AML5 and Mono-Mac-1). Ex vivo depletion of RUNX1 abrogated the leukemia initiating potential of OCI-AML5 cells. After engraftment, tetracycline-inducible shRNA-mediated in vivo knockdown of RUNX1, as compared to the non-induced controls, enhanced survival of the immune-depleted (NSG) mice engrafted with OCI-AML5 cells. RUNX1 transcription is driven by the BET protein BRD4-occupied super enhancer in the first intron of the RUNX1 gene. A heat map of Hi-C interaction scores within the RUNX1 TAD (topology-associated domain) showed triangle-shaped regions of high interaction, with CTCF binding sites defining the TAD boundaries, anchoring a loop that separates the RUNX1 TAD from other TADs. Consistent with this, our findings show that, shRNA-mediated depletion of BRD4 or treatment with BET protein (BETP) inhibitor (BETi) OTX015 reduced BRD4 occupancy at the enhancer and promoter of RUNX1. This was associated with depletion of RUNX1 and its target-gene expressions and apoptosis of cultured and patient-derived (PD), primary AML blast progenitor cells (BPCs). Additionally, treatment of NSG mice engrafted with luciferase-transduced OCI-AML5 cells with OTX015 (50 mg/kg/day X 5 days, for 3 weeks) reduced the AML burden and significantly improved their survival (p Citation Format: Christopher P. Mill, Courtney DiNardo, Warren C. Fiskus, Dyana T. Saenz, Baohua Sun, Agnieszka J. Nowak, Misun Kim, Mark Routbort, Koichi Takahashi, Kapil N. Bhalla. Novel and effective RUNX1-targeted therapy for AML expressing RUNX1 mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-081. doi:10.1158/1538-7445.AM2017-LB-081

Abstract 5067: BET protein proteolysis targeting chimera (BETP-PROTACs) exert more potent activity than BETP bromodomain inhibitor (BETi) against post-myeloproliferative neoplasm (MPN) secondary (s) AML cells

In BCR-ABL1-negative myeloproliferative neoplasms with myelofibrosis (MPN-MF) transformation to AML (sAML) occurs in up to 20% of patients. Ruxolitinib (R) is a type I, ATP-competitive, JAK1 & 2 inhibitor (JAKi), which is effective in the therapy of MPN-MF but does not significantly impact the clinical outcome in post-MPN sAML. We have previously reported that treatment with BETi, e.g. JQ1 or OTX015 inhibits growth and induces apoptosis of cultured sAML cells, including those that express JAK2 V617F and mutant TP53, e.g. HEL92.1.7 and SET2, as well as patient-derived (PD) CD34+ sAML cells. BETi treatment attenuated the protein expressions of c-MYC, p-STAT5, Bcl-xL, CDK4/6, PIM1 and IL-7R, while concomitantly inducing the levels of HEXIM1, p21, NOXA and BIM in the sAML cells. However, treatment with BETi leads to the accumulation of BETP, e.g. BRD4, which may reduce BETi-mediated repression of c-MYC, NFκB and BETP-regulated oncoproteins. In contrast, BETP-PROTACs (proteolysis targeting chimera) ARV-825 and ARV-771 (Arvinas Inc.) degrade BETPs (including BRD4) in the cultured and PD CD34+ sAML cells. At equimolar concentrations, BETP-PROTACs were significantly more potent than the BETi in inducing apoptosis of cultured and PD sAML cells (p 90%) in the sAML cells. BETP-PROTAC treatment caused more up and down regulation of mRNA and protein expressions than BETi, as determined by RNA-Seq and reversed phase protein array (RPPA) analyses, respectively. As compared to treatment with BETi, BETP-PROTAC caused greater depletion of c-MYC, JAK2, p-STAT5, STAT5, p-STAT3, STAT3, PIM1 and Bcl-xL, whereas the protein levels of p21 and p27 were upregulated. CyTOF or mass-cytometry also showed that BETP-PROTAC, more than OTX015 treatment, reduced BRD4, c-MYC and p-Rb, while inducing p21 levels in the CD34+ sAML stem/progenitor cells expressing CD90, CD244, CD123 and TIM3-Fc. Compared to treatment with each agent alone, co-treatment with BETP-PROTAC and R was synergistically lethal against the cultured and PD CD34+ sAML cells. Additionally, co-treatment with BETP-PROTAC and HSP90 inhibitor AUY922 or BCL2/BcL-xL antagonist ABT263 was synergistically lethal against R-sensitive and R-resistant sAML cells. As compared to treatment with vehicle control, R treatment alone, treatment with BETP-PROTAC ARV-771 alone or in combination with R significantly reduced the in vivo sAML burden and improved the median survival of the immune-depleted mice engrafted with luciferase-transduced HEL92.1.7 cells. These findings strongly support further in vivo development of the novel BETP-PROTACs-based combinations against post-MPN sAML. Note: This abstract was not presented at the meeting. Citation Format: Dyana T. Saenz, Warren C. Fiskus, Kanak Raina, Taghi Manshouri, Kevin G. Coleman, Yimin Qian, Andrew P. Crew, Angela Shen, Christopher P. Mill, Baohua Sun, Misun Kim, Agnieszka J. Nowak, Srdan Verstovsek, Craig M. Crews, Kapil N. Bhalla. BET protein proteolysis targeting chimera (BETP-PROTACs) exert more potent activity than BETP bromodomain inhibitor (BETi) against post-myeloproliferative neoplasm (MPN) secondary (s) AML cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5067. doi:10.1158/1538-7445.AM2017-5067

Abstract 4699: Superior lethal activity of single agent BET protein PROTAC compared to bromodomain inhibitor or in combination with JAK inhibitor against post-myelofibrosis secondary AML cells

Myeloproliferative neoplasm, myelofibrosis (MPN-MF), exhibits increased JAK-STAT signaling and often progresses (∼15-20%) to AML (sAML). JAK inhibitor (JAK-I) ruxolitinib (Rux) or standard induction chemotherapy is only modestly active against sAML, culminating in treatment-refractory relapse. Genetic alterations commonly documented in sAML include the co-occurrence of JAK2 V617F and mutant TP53. Here, we demonstrate that treatment with ARV-825 (Arvinas, Inc.), a BET (bromodomain and extraterminal) protein PROTAC (proteasome activating chimera) which degrades (through the proteasome) BET proteins by binding and recruiting E3 Ubiquitin ligase cereblon activity to them, caused efficient, and prolonged depletion of the levels of the BET protein BRD4. In contrast, treatment with the bromodomain inhibitors (BET-Is) JQ1 or OTX015 induced the levels of BRD4. ARV-825 treatment also mediated greater and more sustained attenuation than OTX-015 of the mRNA and protein expressions of BCL-xL, CDK4/6, PIM1, p-STAT5 and p-STAT3 levels, while concomitantly inducing p21 and p27 in the cultured sAML (HEL92.1.7 and SET2) cells. This correlated with high level of apoptosis in the cultured and patient-derived post-MPN-MF sAML cells, with relative sparing of the normal CD34+ progenitor cells. Compared to treatment with each agent alone, co-treatment with ARV-825 and the JAK-Is Rux (100 to 1000 nM) or pacritinib (250 to 1000 nM), was synergistically more lethal against the cultured sAML cells (CI of 10-fold resistant to ruxolitinib; HEL/JIR cells) under the in vitro selection pressure of a continuous exposure to JAK-I. Notably, compared to the parental HEL92.1.7, HEL/JIR cells were highly and collaterally sensitive to both ARV-825 and AUY922. Furthermore, co-treatment with ARV-825 and AUY922 was also synergistically lethal against HEL/JIR cells (CI Citation Format: Dyana T. Saenz, Warren C. Fiskus, Taghi Manshouri, Jing Lu, Yimin Qian, Kanak Raina, Baohua Sun, Stephanie S. Krieger, Simrit Parmar, Srdan Verstovsek, Kapil N. Bhalla. Superior lethal activity of single agent BET protein PROTAC compared to bromodomain inhibitor or in combination with JAK inhibitor against post-myelofibrosis secondary AML cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4699.