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  • 1
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2013
    In:  Molecular Cancer Therapeutics Vol. 12, No. 11_Supplement ( 2013-11-01), p. C223-C223
    In: Molecular Cancer Therapeutics, American Association for Cancer Research (AACR), Vol. 12, No. 11_Supplement ( 2013-11-01), p. C223-C223
    Abstract: Systematic discovery of actionable cancer targets could fill an unmet need for improved approaches to manage Glioblastoma Multiforme (GBM). Critical barriers to the discovery of druggable targets in cancer include: 1) molecular heterogeneity of the disease across patients, 2) implementation of a systematic approach to utilize existing knowledge and molecular data for target discovery, and 3) the lack of a relevant, rapid and systematic pipeline to enable empirical testing of hypotheses. We describe a network-based method to stratify GBM clinical samples into molecularly homogeneous subsets based on gene expression, gene copy number, and miRNAs, which we term “molecular contexts," or mCs. Within these mCs, a knowledge-based topological analysis of pathway elements was used to uncover discrete mC-specific targets. An empiric chemical screen probed the target space across different mCs, mC-4 and mC-14, which were molecularly orthogonal to each other. Specimens in mC-4 were enriched with samples previously classified as Mesenchymal-type GBM, while mC-14 was enriched with Proneural-subtype GBM. The chemical screen was carried out using short-term in vitro cultures derived from patient-derived GBM xenografts, which mapped to mC4 and mC14 based on gene expression. We employed a network-based topological approach to discern targets and pathways as candidate druggable vulnerabilities. The chemical validation screen was carried out with an assembled chemical biology fingerprint (CBF) library comprised of 650 small molecules targeting multiple cancer-associated pathways and processes. Matching specific chemical hits to their respective targets allowed for validation of specific gene hits from the topological analysis. Of particular interest were two molecular context specific lethal compounds in the screen, tamoxifen citrate and arsenic trioxide, specific to the mC4 and mC14, respectively. PKC, among the targets of Tamoxifen citrate, was a predicted node of vulnerability for mC-4 GBM, while PML gene, a target of Arsenic Trioxide, was a predicted target for mC-14. In summary, our results suggest that context analysis coupled with knowledge-based enrichment and topological analysis identifies specific GBM contexts with novel unique drugable targets. Supported by NIH U01 CA168397. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C223. Citation Format: Harshil D. Dhruv, Seungchan Kim, Jeff Kiefer, Dorothea Emig-Agius, Darren Finlay, Sungwon Jung, Kristiina Vuori, Michael Berens. Network-based approach aids in the discovery of context-specific druggable targets for treatment of glioblastoma. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C223.
    Type of Medium: Online Resource
    ISSN: 1535-7163 , 1538-8514
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
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  • 2
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    Online Resource
    American Association for Cancer Research (AACR) ; 2015
    In:  Cancer Research Vol. 75, No. 15_Supplement ( 2015-08-01), p. 4671-4671
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 15_Supplement ( 2015-08-01), p. 4671-4671
    Abstract: Glioblastoma Multiforme (GBM) is an aggressive brain tumor with very poor prognosis and extremely limited therapeutic options. GBM is the most common malignant brain tumor and the search for novel targets and/ or the repurposing of already extant drugs to treat the disease is therefore of utmost importance. We describe here a comprehensive multidisciplinary approach to identifying said targets and ergo potential therapies. We have applied a novel analytical strategy to The Cancer Genome Atlas (TCGA) GBM expression data to stratify GBM into novel subtypes we call molecular contexts, or mCs. Subsequently, a panel of patient-derived GBM xenografts was ascribed to our novel mCs. Utilizing a technique we term Chemical Biology Fingerprinting, or CBF, short-term cultures derived from these clinically-relevant preclinical models were screened for chemosensitivity with a deeply annotated, yet clinically relevant, chemical library. Agents that were statistically more toxic to one context than another were then re-tested in true drug dose response experiments to confirm sensitivity. Preliminary data demonstrated that mC14, characterized by mutant p53 and transcriptionally similar to the GBM proneural subtype, showed distinct vulnerability to Arsenic Trioxide (ATO) as compared to mC4, enriched for NF1 mutations and with transcriptional patterns similar to the GBM mesenchymal subtype. To validate the ATO vulnerability signature in GBM, we acquired 20 treatment naïve archival patient samples, that were part of a Phase I/II clinical trial to study the efficacy of ATO and Temozolomide in combination with ionizing radiation (NCT00275067). Participants in the trial exhibited varied survival with ATO treatment (91 days to & gt;1000 days) and the clinical samples were subtyped into our molecular contexts using RNAseq data. In summary, we demonstrate a subclassification of GBM into novel molecular contexts (mCs) and show that these contexts are differentially sensitive to clinically relevant drugs. Citation Format: Darren Finlay, Harshil Dhruv, Lisa Evers, Sen Peng, Jeff Kiefer, Seungchan Kim, Jeffrey Raizer, Michael Berens, Kristiina Vuori. Identification of novel drugs for glioblastoma using chemical biology fingerprinting. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4671. doi:10.1158/1538-7445.AM2015-4671
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
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  • 3
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 16_Supplement ( 2020-08-15), p. 1434-1434
    Abstract: As a disease that has not seen lasting advances in its standard of care for decades, glioblastoma (GBM) calls for novel therapeutic approaches, and given GBM's heterogeneous and aggressive nature, precision medicine stands out as an appealing treatment modality for this tragic disease. Neddylation is a post-translational modification process that regulates protein function and turnover. MLN4924, or Pevonedistat, inhibits the E1 ligase Nedd8 activating enzyme (NAE) and, in doing so, the E1, E2, and E3 neddylation cascade. In its most researched role, NEDD-8 is conjugated to the cullin subunit of cullin-RING ligases (CRLs), a family of E3 ligases that facilitate the ubiquitination of different substrates. Thus, inhibition of neddylation decreases ubiquitination and degradation of particular substrates: e.g., p21, p27, wee-1, and other cell cycle regulatory and pro-apoptotic proteins. We and others have shown that neddylation stands out a promising therapeutic approach to cancer and GBM, given the vulnerability to MLN4924 in subset of different in vitro and in vivo models. In this work, we establish the selective vulnerability to MLN4924 in GBM and explore the biological mechanisms that underlie this differential response. Using the Cancer Cell Line Encyclopedia (CCLE) and the Genomics of Drug Sensitivity in Cancer (GDSC) databases, we found that mutations and deletions in phosphatase and tensin homolog (PTEN) are associated with resistance to MLN4924 in both low-grade gliomas and GBM. Our established models validated these findings, as our sensitive models – GB1 (IC50= 0.28 μM) and LN18 (IC50 = 0.19 μM), – expressed PTEN, while our resistant models – M059K (IC50 = 5.5 μM) and SNU1105 (IC50 = 20.9 μM) – did not. Knocking down PTEN with siRNA in our sensitive models increased their IC50 values three- to four-fold. This relationship was further validated in multiple isogenic systems. We sought to uncover whether this PTEN-status dependent resistance was contingent on its well-studied lipid phosphatase activity and PI3K/AKT signaling. While the resistant models had higher baseline levels of phosphorylated AKT (p-AKT), we found that MLN4924 treatment did not consistently alter p-AKT levels in our sensitive and/or resistant models. We also used a PTEN null isogenic glioma stem cell system (GSC23), in which wild-type PTEN and lipid phosphatase dead (G129A) PTEN was re-expressed, and found that both PTEN models sensitized GSC23 to MLN4924 treatment equally. While independent of the PI3K/AKT axis, we did find that there were significant increases in topoisomerase II alpha (TOP2A) levels in the post-treatment lysate of our resistant (PTEN-null) models. Targeting this increase in TOP2A expression, we found strong synergy with two different TOP2 poisons – etoposide and doxorubicin – and MLN4924 in a combination DDR. For the first time, we show that PTEN status not only serves as a novel biomarker for MLN4924 response but also reveals a vulnerability to TOP2A inhibitors when used in combination with MLN4924. Citation Format: Brett Taylor, Shayesteh Ferdosi, Nanyun Tang, Rita Bybee, George Reid, Lauren Hartman, Darren Finlay, Kristiina Vuori, Matthew Lee, Sen Peng, Frank Furnari, Harshil Dhruv, Michael Berens. Loss of PTEN confers resistance to neddylation inhibition through TOP2A in glioblastoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1434.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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  • 4
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2016
    In:  Neuro-Oncology Vol. 18, No. suppl_6 ( 2016-11-01), p. vi71-vi71
    In: Neuro-Oncology, Oxford University Press (OUP), Vol. 18, No. suppl_6 ( 2016-11-01), p. vi71-vi71
    Type of Medium: Online Resource
    ISSN: 1522-8517 , 1523-5866
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2016
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  • 5
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2018
    In:  Neuro-Oncology Vol. 20, No. suppl_6 ( 2018-11-05), p. vi70-vi70
    In: Neuro-Oncology, Oxford University Press (OUP), Vol. 20, No. suppl_6 ( 2018-11-05), p. vi70-vi70
    Type of Medium: Online Resource
    ISSN: 1522-8517 , 1523-5866
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
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  • 6
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2017
    In:  Cancer Research Vol. 77, No. 13_Supplement ( 2017-07-01), p. 1177-1177
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. 1177-1177
    Abstract: Neddylation is a post-translational mechanism that marks proteins for degradation through activity of NEDD8 Activating Enzyme (NAE). NAE blocks cullin-RING ligases from initiating proteosomal degradation of select substrates including cell cycle regulators and apoptosis modulators. MLN4924, or Pevonedistat, targets NAE and inhibits Neddylation and induces apoptosis in sensitive cells. We have discovered, in a cohort of glioblastoma PDX models, an exceptional responder to MLN4924 (GBM102). Most pertinently the effects we observe are in a PDX cultured as 3D neurospheres that more closely resemble the true tumor architecture, heterogeneity, and “stem-like” phenotype characteristic of tumor growth. We have leveraged RNAseq expression data from Cancer Cell Line Encyclopedia (CCLE) and Pevonedistat response data from The Cancer Therapeutics Response Portal (CTRP) to apply a network-based analysis to identify pathways enriched with differential dependencies between cell lines sensitive and non-sensitive to MLN4924. The analysis also identifies potential mediating genes that appear to play critical roles in such differential dependency networks. Identified differential networks and mediators provide insight for cellular mechanisms underlying drug response. Additionally, we also investigated the efficacy of MLN4924 against orthotopic glioma PDX models (GBM102 and GBM116) in vivo to validate our findings in vitro. Thus genomic characterization of patient samples may lead to the identification of a molecular signature which is associated with a subset of GBMs vulnerable to MLN4924. As the treatment options for GBM are extremely limited, this may highlight a novel alternative opportunity to treat a select fraction of patients with this aggressive disease. Citation Format: Lauren K. Hartman, Darren Finlay, Peiwen Pan, Seungchan Kim, Gil Speyer, Jeff Kiefer, Harshil Dhruv, Kristiina Vuori, Michael Berens. Targeting NEDD8 to uncover an exceptional responder molecular subtype in glioblastoma [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 1177. doi:10.1158/1538-7445.AM2017-1177
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 7
    In: Molecular Cancer Research, American Association for Cancer Research (AACR), Vol. 16, No. 1 ( 2018-01-01), p. 32-46
    Abstract: Mesenchymal (MES) and proneural (PN) are two distinct glioma stem cell (GSC) populations that drive therapeutic resistance in glioblastoma (GBM). We screened a panel of 650 small molecules against patient-derived GBM cells to discover compounds targeting specific GBM subtypes. Arsenic trioxide (ATO), an FDA-approved drug that crosses the blood–brain barrier, was identified as a potent PN-specific compound in the initial screen and follow-up validation studies. Furthermore, MES and PN GSCs exhibited differential sensitivity to ATO. As ATO has been shown to activate the MAPK-interacting kinase 1 (MNK1)-eukaryotic translation initiation factor 4E (eIF4E) pathway and subsequent mRNA translation in a negative regulatory feedback manner, the mechanistic role of ATO resistance in MES GBM was explored. In GBM cells, ATO-activated translation initiation cellular events via the MNK1–eIF4E signaling axis. Furthermore, resistance to ATO in intracranial PDX tumors correlated with high eIF4E phosphorylation. Polysomal fractionation and microarray analysis of GBM cells were performed to identify ATO's effect on mRNA translation and enrichment of anti-apoptotic mRNAs in the ATO-induced translatome was found. Additionally, it was determined that MNK inhibition sensitized MES GSCs to ATO in neurosphere and apoptosis assays. Finally, examination of the effect of ATO on patients from a phase I/II clinical trial of ATO revealed that PN GBM patients responded better to ATO than other subtypes as demonstrated by longer overall and progression-free survival. Implications: These findings raise the possibility of a unique therapeutic approach for GBM, involving MNK1 targeting to sensitize MES GSCs to drugs like arsenic trioxide. Mol Cancer Res; 16(1); 32–46. ©2017 AACR.
    Type of Medium: Online Resource
    ISSN: 1541-7786 , 1557-3125
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 8
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. 1142-1142
    Abstract: The most common adult brain tumor is Glioblastoma Multiforme (GBM), an extremely aggressive cancer with only scant treatment options. Even with standard of care most patients present with a recurrence and the median survival is only circa 15 months. The need, therefore, for new therapeutic targets and treatment options is pressing. Here we describe here a multipronged approach to identifying said targets. We present an established methodology for the isolation and culture of patient derived GBM samples that retain the “stem-like” fraction thought to underlie resistance and recurrence. Furthermore we show genomically that these samples represent specific subtypes of the disease yet still form distinct groups in unbiased clustering analysis. Thus we have multiple representative patient derived cultures that are suitable for our drug discovery and chemical biology analyses. Using a process we term Chemical Biology Fingerprinting (CBF) we utilize small focused, and clinically relevant, chemical collections in order to identify patterns of chemovulnerabilities across multiple samples. This allows an unbiased yet cancer relevant sub-stratification and the identification of agents, and therefore targets, which may be relevant for GBM patient subtypes. Indeed our use of the highly annotated NCI CTD2 Informer Set of chemicals allows ready drug-to-target mapping and facilitates data sharing across the CTD2 network. Moreover, already defined subgroups can be clustered to find agents, or groups of agents, that show selective activity against traditional classifications (e.g. proneural, mesenchymal etc.). Finally our strategy is permissive for the identification of “exceptional responders”. That is, individual patient samples that respond to a specific drug whilst most samples are refractory. In sum we demonstrate generation of patient derived models and identify specific, and novel, drugs that may be relevant for specific GBM subtypes. Supported by NIH U01CA168397 Citation Format: Darren Finlay, Pedro Aza-Blanc, Harshil Dhruv, Alexey Eroshkin, Craig Hauser, Jeff Kiefer, Seungchan Kim, Tao Long, Robert G. Oshima, Sen Peng, Gil Speyer, Michael Berens, Kristiina Vuori. Novel target discovery for glioblastoma using chemical biology fingerprinting [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 1142. doi:10.1158/1538-7445.AM2017-1142
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 9
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2018
    In:  Cancer Research Vol. 78, No. 13_Supplement ( 2018-07-01), p. 881-881
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 881-881
    Abstract: Neddylation is a post-translational mechanism that marks proteins for degradation through activity of NEDD8 Activating Enzyme (NAE). NAE activates cullin-RING ligases (CRL), which ubiquitylate selected substrates and mark them for proteosomal degradation. MLN4924, or Pevonedistat, targets NAE and inhibits Neddylation and induces apoptosis in sensitive cells. To assess the preferential sensitivity of cell lines to MLN4924, we performed a 10-point drug dose response (DDR) assay on long-term established GBM cell lines. Efficacy of MLN4924 in glioma cell lines was evaluated by measuring cell viability (CellTiterGlo®) and cell cycle progression (flow cytometry with propidium iodide staining). To identify mechanism of differential response to MLN4924 treatment, cell cycle regulatory pathway and DNA damage were also examined by Western blotting. GB1 (IC50 = 0.28 μM) & LN18 (IC50 = 0.19 μM) were established as sensitive and M059K (IC50 = 5.5 μM) & SNU1105 (IC50 = 20.9 μM) as non-sensitive cell lines based on the IC50 values. Flow cytometry analysis of DNA content revealed significant arrest of cells in G2/M even at low doses of 100 nM of MLN4924 preferentially in GB1 and LN18. This was consistent with an increase in CRL substrates p21, p27 and WEE1 in GB1 and LN18 possibly contributing to the G2/M arrest. While CDT1 accumulation was observed starting at 2h post MLN4924 treatment in sensitive cell lines, it took upto 8h for CDT1 accumulation in the non-sensitive cell lines. Increases in CDT1 induced re-replication causing massive arrest in G2/M phase lead to increased DNA damage, validated by higher expression of γH2AX in the sensitive cell lines. Additionally, we also investigated the efficacy of MLN4924 against orthotopic glioma PDX models in vitro and in vivo to validate our findings. In a cohort of glioblastoma PDX models we discovered that GBM PDX models with lower Neddylation gene set enrichment score (GBM116, GBM59, SF7300) were markedly more vulnerable to MLN4924 than GBM PDX models with higher Neddylation gene set enrichment score (GBM91 and GBM102) in vitro and in vivo. Orthotopic PDX models of selected GBM revealed survival prolongation of GBM116, but minimal survival benefit to GBM102 tumors. Validation of the predictive markers of vulnerability to MLN4924 in additional PDX models will set the stage for prospective clinical trials of MLN4924 in glioblastoma patients. Citation Format: Leena Chaudhuri, Rita L. Bybee, Lauren K. Hartman, Sen Peng, Darren Finlay, Kristiina Vuori, Michael E. Berens, Harshil D. Dhruv. Identifying the context of vulnerability to MLN4924 in glioblastoma (GBM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 881.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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