Diverse, Potent, and Efficacious Inhibitors That Target the EED Subunit of the Polycomb Repressive Complex 2 Methyltransferase

Aberrant activity of the histone methyltransferase polycomb repressive complex 2 (PRC2) has been linked to several cancers, with small-molecule inhibitors of the catalytic subunit of the PRC2 enhancer of zeste homologue 2 (EZH2) being recently approved for the treatment of epithelioid sarcoma (ES) and follicular lymphoma (FL). Compounds binding to the EED subunit of PRC2 have recently emerged as allosteric inhibitors of PRC2 methyltransferase activity. In contrast to orthosteric inhibitors that target EZH2, small molecules that bind to EED retain their efficacy in EZH2 inhibitor-resistant cell lines. In this paper we disclose the discovery of potent and orally bioavailable EED ligands with good solubilities. The solubility of the EED ligands was optimized through a variety of design tactics, with the resulting compounds exhibiting in vivo efficacy in EZH2-driven tumors.

Abstract LB-A09: EED targeted PROTACs degrade EED, EZH2, and SUZ12 in the PRC2 complex

Deregulation of the PRC2 components EZH2, SUZ12, and EED plays critical roles in driving aberrant hypermethylation of H3K27 and tumorigenicity of many solid and hematological malignancies. Although SAM competitive small molecule inhibitors of EZH2 show promising clinical activity in PRC2-dependent cancers, preclinical data suggests that resistance can be acquired through secondary mutations in EZH2 that abrogate drug target engagement. To address these limitations, we have designed several hetero-bifunctional PROTACs (Proteolysis Targeting Chimera) to efficiently target EED for elimination. Our EED-targeting PROTACs bind to EED (pKD= 9.02-9.27) and promote stable ternary complex formation with the E3 ubiquitin ligase. The PROTACs potently inhibit PRC2 enzyme activity (pIC50= 8.11-8.17) that results in a decrease in H3K27me3 levels in cells. Interestingly, EED-targeting PROTACs induce rapid degradation of EED, as well as its associated proteins, including EZH2 and SUZ12 in the PRC2 complex. Inhibition of the ubiquitin proteasome pathway abrogates PROTAC-mediated degradation of EED and its associated proteins. Furthermore, the EED targeting PROTACs selectively inhibit proliferation and survival of PRC2-dependent cancer cells (GI50= 49-58 nM). In summary, our data demonstrate a novel therapeutic modality in treating PRC2 dependent cancer through PROTAC mediated platform.

Citation Format: Jessie Hao-Ru Hsu, Timothy Rasmusson, James Robinson, Fiona Pachl, Jon Read, Sameer Kawatkar, Daniel H O'Donovan, Sharan Bagal, Erin Code, Philip Rawlins, Argyrides Argyrou, Ronald Tomlinson, Ning Gao, Xiahui Zhu, Elisabetta Chiarparin, Kelly Jacques, Minhui Shen, Haley Woods, Emma Bednarski, David M. Wilson, Lisa Drew, M. Paola Castaldi, Stephen Fawell, Andrew Bloecher. EED targeted PROTACs degrade EED, EZH2, and SUZ12 in the PRC2 complex [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr LB-A09. doi:10.1158/1535-7163.TARG-19-LB-A09

PRMT1-Mediated Translation Regulation Is a Crucial Vulnerability of Cancer

Through an shRNA screen, we identified the protein arginine methyltransferase Prmt1 as a vulnerable intervention point in murine p53/Rb-null osteosarcomas, the human counterpart of which lacks effective therapeutic options. Depletion of Prmt1 in p53-deficient cells impaired tumor initiation and maintenance in vitro and in vivo Mechanistic studies reveal that translation-associated pathways were enriched for Prmt1 downstream targets, implicating Prmt1 in translation control. In particular, loss of Prmt1 led to a decrease in arginine methylation of the translation initiation complex, thereby disrupting its assembly and inhibiting translation. p53/Rb-null cells were sensitive to p53-induced translation stress, and analysis of human cancer cell line data from Project Achilles further revealed that Prmt1 and translation-associated pathways converged on the same functional networks. We propose that targeted therapy against Prmt1 and its associated translation-related pathways offer a mechanistic rationale for treatment of osteosarcomas and other cancers that exhibit dependencies on translation stress response. Cancer Res; 77(17); 4613-25. ©2017 AACR.

Abstract PR03: Prmt1 and Prmt1-dependent translation initiation are critical vulnerabilities of osteosarcoma

Osteosarcoma (OS) remains a challenging clinical entity for which targeted therapy is lacking. The frequent mutations of p53 and Rb in OS would be anticipated to create a genetic context in which specific vulnerabilities might exist. To discover genetic vulnerabilities in OS, we conducted high throughput shRNA-based screens in vitro and in vivo using p53/Rb-null OS cells and identified Prmt1, a protein arginine methyltransferase, among other factors as critical to growth/survival of OS cells from genetically engineered mice or human tumors. Indeed, depletion of Prmt1 in OS cells using shRNAs and a Prmt1-specific inhibitor leads to growth arrest and death in vitro. In vivo, Prmt1 inhibition impairs xenograft engraftment and proliferation. Moreover, deletion of Prmt1 in p53/Rb-null osteoblast progenitors using Cre/Lox-based technology significantly inhibits OS initiation and progression in mice, while normal bone development is largely unaffected. In rescue experiments, we find that enzymatically inactive Prmt1 cannot restore proliferation of Prmt1-depleted cells, indicating that the enzymatic activity of Prmt1 is essential for tumorigenicity. To gain mechanistic insights into the molecular functions of Prmt1, we characterized the Prmt1-associated arginine-methylome and downstream targets of Prmt1 using a SILAC-based quantitative proteomics approach. This innovative technique identified many candidate Prmt1-methylated substrates representing various molecular pathways including RNA processing, transcription and translation. In particular, we have shown that loss of Prmt1 leads to a decrease in arginine methylation of members of the eIF4F translation initiation complex, thereby disrupting their physical association and inhibiting translation. Consistent with these findings, we observed that OS cells are sensitive to inhibition of eIF4G, a major component of the eIF4F translation initiation complex, further exposing an additional OS vulnerability to translation inhibition that could be exploited therapeutically. Taken together, our findings implicate a role of Prmt1 in initiation and maintenance of OS and suggest that Prmt1-mediated effects on translation initiation are responsible for tumor proliferation and survival. Based on our findings, we propose that targeted therapy directed to inhibition of Prmt1 and its associated pathways represents a novel and promising therapeutic strategy for OS.

This abstract is also presented as Poster A17.

Citation Format: Jessie Hao-Ru Hsu, Benjamin Hubbell-Engler, Guillaume Adelmant, Jennifer Perry, Glenn Cowley, Jarrod Marto, Stuart H. Orkin. Prmt1 and Prmt1-dependent translation initiation are critical vulnerabilities of osteosarcoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr PR03.

Preclinical antitumor efficacy of selective exportin 1 inhibitors in glioblastoma

BACKGROUND

Glioblastoma (GBM) is poorly responsive to current chemotherapy. The nuclear transporter exportin 1 (XPO1, CRM1) is often highly expressed in GBM, which may portend a poor prognosis. Here, we determine the efficacy of novel selective inhibitors of nuclear export (SINE) specific to XPO1 in preclinical models of GBM.

METHODS

Seven patient-derived GBM lines were treated with 3 SINE compounds (KPT-251, KPT-276, and Selinexor) in neurosphere culture conditions. KPT-276 and Selinexor were also evaluated in a murine orthotopic patient-derived xenograft (PDX) model of GBM. Cell cycle effects were assayed by flow cytometry in vitro and immunohistochemistry in vivo. Apoptosis was determined by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) and caspase 3/7 activity assays.

RESULTS

Treatment of GBM neurosphere cultures with KPT-276, Selinexor, and KPT-251 revealed dose-responsive growth inhibition in all 7 GBM lines [range of half-maximal inhibitory concentration (IC50), 6-354 nM]. In an orthotopic PDX model, treatment with KPT-276 and Selinexor demonstrated pharmacodynamic efficacy, significantly suppressed tumor growth, and prolonged animal survival. Cellular proliferation was not altered with SINE treatment. Instead, induction of apoptosis was apparent both in vitro and in vivo with SINE treatment, without overt evidence of neurotoxicity.

CONCLUSIONS

SINE compounds show preclinical efficacy utilizing in vitro and in vivo models of GBM, with induction of apoptosis as the mechanism of action. Selinexor is now in early clinical trials in solid and hematological malignancies. Based on these preclinical data and excellent brain penetration, we have initiated clinical trials of Selinexor in patients with relapsed GBM.

Modeling initiation of Ewing sarcoma in human neural crest cells

Ewing sarcoma family tumors (ESFT) are aggressive bone and soft tissue tumors that express EWS-ETS fusion genes as driver mutations. Although the histogenesis of ESFT is controversial, mesenchymal (MSC) and/or neural crest (NCSC) stem cells have been implicated as cells of origin. For the current study we evaluated the consequences of EWS-FLI1 expression in human embryonic stem cell-derived NCSC (hNCSC). Ectopic expression of EWS-FLI1 in undifferentiated hNCSC and their neuro-mesenchymal stem cell (hNC-MSC) progeny was readily tolerated and led to altered expression of both well established as well as novel EWS-FLI1 target genes. Importantly, whole genome expression profiling studies revealed that the molecular signature of established ESFT is more similar to hNCSC than any other normal tissue, including MSC, indicating that maintenance or reactivation of the NCSC program is a feature of ESFT pathogenesis. Consistent with this hypothesis, EWS-FLI1 induced hNCSC genes as well as the polycomb proteins BMI-1 and EZH2 in hNC-MSC. In addition, up-regulation of BMI-1 was associated with avoidance of cellular senescence and reversible silencing of p16. Together these studies confirm that, unlike terminally differentiated cells but consistent with bone marrow-derived MSC, NCSC tolerate expression of EWS-FLI1 and ectopic expression of the oncogene initiates transition to an ESFT-like state. In addition, to our knowledge this is the first demonstration that EWS-FLI1-mediated induction of BMI-1 and epigenetic silencing of p16 might be critical early initiating events in ESFT tumorigenesis.

Abstract 5169: The polycomb group protein BMI-1 cooperates with Yes-Associated Protein, YAP, to suppress cell contact inhibition in Ewing sarcoma cells

The polycomb group family protein BMI-1 is frequently deregulated in cancer. BMI-1 has been shown to promote stemness and tumorigenicity largely through epigenetic repression of the CDKN2A locus, inhibiting the expression of cell-cycle inhibitors p16INK4A and p14ARF. We have previously shown that BMI-1 functions as an oncoprotein in Ewing sarcoma, promoting anchorage independent growth in vitro and tumorigenicity in vivo independently of CDKN2A repression. In the current study we have investigated the potential contribution of BMI-1 to loss of cell contact inhibition, a fundamental transforming property of cancer cells. Using cells that stably express an shRNA against BMI-1, we discovered that loss of BMI-1 expression restores contact inhibition to CDKN2A-null Ewing sarcoma cells. Significantly, although proliferation of cells in log phase growth is unaffected by loss of BMI-1, at high cell density BMI-1 knockdown cells undergo cell cycle arrest and death. In contrast, control vector-transduced cells continue to enter cell cycle and proliferate, avoiding contact inhibition. Although many signaling pathways are involved in mediating the cell contact inhibition response, inactivation of the Yes-Associated Protein (YAP), a key downstream target of the Hippo pathway, has been implicated in both Drosophila and mammalian cells. Intriguingly, our data show that, although the Hippo pathway is activated in response to increasing cell density, as evidenced by increasing YAP phosphorylation, YAP is not degraded in control cells that express high levels of BMI-1. In contrast, silencing BMI-1 expression results in loss of YAP protein at high cell density coincident with induction of contact inhibition. Together, these findings suggest that YAP is a novel downstream target of BMI-1 and that BMI-1-mediated stabilization of YAP renders cancer cells impervious to cell contact inhibition. Experiments are currently ongoing to elucidate the precise molecular mechanism linking BMI-1 to YAP; however, preliminary studies show that knockdown of BMI-1 has no effect on YAP1 transcript expression at either low or high cell density indicating that the effects of BMI-1 on YAP stabilization are most likely to be post-translational and indirect. Cancer cells escape cell contact inhibition to achieve unrestrained proliferation and enhanced invasive and metastatic properties. Our findings suggest that BMI-1 may be a key upstream mediator of this critical cancer-associated phenotype.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5169.

Abstract 4239: Ectopic expression of EWS-FLI1 in human neural crest stem cells induces polycomb genes and maintenance of stemness

Ewing sarcoma family of tumors (ESFT) are aggressive bone and soft tissue tumors of unknown cellular origin. Most ESFT express EWS-FLI1, a chimeric protein which functions as a growth-promoting oncogene in ESFT but is toxic to most normal cells. A major difficulty in understanding EWS-FLI1 function has been the lack of an adequate model in which to study EWS-FLI1-induced transformation. Although the cell of origin of ESFT remains elusive, both mesenchymal (MSC) and neural crest (NCSC) have been implicated. We recently developed the tools to generate NCSC from human embryonic stem cells (hNCSC). In the current study we have used this model to test the hypothesis that NCSC are the cells of origin of ESFT and to evaluate the consequences of EWS-FLI1 expression on human NCSC biology.

ESFT demonstrate variable degrees of neuro-mesenchymal differentiation potential. Similarly, we have found that hNCSC can be induced to differentiate into neural, glial and mesenchymal progeny. Significantly, Affymetrix whole genome expression profiling of 32 primary ESFT, 11 normal adult tissues, bone marrow-derived MSC and hNCSC revealed that ESFT are more similar to hNCSC than any other normal tissue, including MSC, thus further implicating NCSC in the origin of ESFT. To evaluate the consequences of EWS-FLI1 on these multipotent stem cells, hNCSC were stably transduced with an EWS-FLI1 lentivirus. Unlike most normal cells, hNCSC tolerated expression of the oncoprotein. Moreover, EWS-FLI1-transduced hNCSC continued to proliferate and maintain EWS-FLI1 expression in culture for several weeks after transduction. Affymetrix HuEx 1.0 expression profiling of hNCSC cells five days post-transduction with EWS-FLI1 demonstrated the expected induction and repression of well-established EWS-FLI1 targets and identified numerous other novel EWS-FLI1-regulated genes that are likely to be cell-type and situation specific. In contrast to control vector-transduced cells, EWS-FLI1 transduced hNCSC reproducibly maintained expression of the NCSC markers p75 and HNK-1, even after transfer to differentiation-inducing conditions. In addition, expression of the polycomb genes BMI1 and EZH2 was consistently and significantly upregulated in EWS-FLI1-transduced cells. In keeping with persistent expression of these stem cell-associated genes, EWS-FLI1-expressing cells retained the ability to form neurospheres upon transfer to non-adherent conditions and also the ability to differentiate into neural and mesenchymal lineages several weeks following transduction. In contrast, after six weeks in differentiation media, control cells had upregulated p16 and had undergone senescence. Together these data implicate NCSC in the origin of ESFT and suggest that EWS-FLI1 enables malignant transformation by inducing maintenance of their multipotent, stem cell state through deregulation of polycomb genes.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4239.

BMI-1 promotes ewing sarcoma tumorigenicity independent of CDKN2A repression

Deregulation of the polycomb group gene BMI-1 is implicated in the pathogenesis of many human cancers. In this study, we have investigated if the Ewing sarcoma family of tumors (ESFT) expresses BMI-1 and whether it functions as an oncogene in this highly aggressive group of bone and soft tissue tumors. Our data show that BMI-1 is highly expressed by ESFT cells and that, although it does not significantly affect proliferation or survival, BMI-1 actively promotes anchorage-independent growth in vitro and tumorigenicity in vivo. Moreover, we find that BMI-1 promotes the tumorigenicity of both p16 wild-type and p16-null cell lines, demonstrating that the mechanism of BMI-1 oncogenic function in ESFT is, at least in part, independent of CDKN2A repression. Expression profiling studies of ESFT cells following BMI-1 knockdown reveal that BMI-1 regulates the expression of hundreds of downstream target genes including, in particular, genes involved in both differentiation and development as well as cell-cell and cell-matrix adhesion. Gain and loss of function assays confirm that BMI-1 represses the expression of the adhesion-associated basement membrane protein nidogen 1. In addition, although BMI-1 promotes ESFT adhesion, nidogen 1 inhibits cellular adhesion in vitro. Together, these data support a pivotal role for BMI-1 ESFT pathogenesis and suggest that its oncogenic function in these tumors is in part mediated through modulation of adhesion pathways.