Targeting MYCN in Neuroblastoma by BET Bromodomain Inhibition
TL;DR: A cell-based screen of genetically defined cancer cell lines using a prototypical inhibitor of BET bromodomains revealed a robust correlation between MYCN amplification and sensitivity to bromidomain inhibition, and characterized the mechanistic and translational significance of this finding in neuroblastoma.
Abstract: Bromodomain inhibition comprises a promising therapeutic strategy in cancer, particularly for hematologic malignancies. To date, however, genomic biomarkers to direct clinical translation have been lacking. We conducted a cell-based screen of genetically defined cancer cell lines using a prototypical inhibitor of BET bromodomains. Integration of genetic features with chemosensitivity data revealed a robust correlation between MYCN amplification and sensitivity to bromodomain inhibition. We characterized the mechanistic and translational significance of this finding in neuroblastoma, a childhood cancer with frequent amplification of MYCN. Genome-wide expression analysis showed downregulation of the MYCN transcriptional program accompanied by suppression of MYCN transcription. Functionally, bromodomain-mediated inhibition of MYCN impaired growth and induced apoptosis in neuroblastoma. BRD4 knockdown phenocopied these effects, establishing BET bromodomains as transcriptional regulators of MYCN. BET inhibition conferred a significant survival advantage in 3 in vivo neuroblastoma models, providing a compelling rationale for developing BET bromodomain inhibitors in patients with neuroblastoma.
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TL;DR: Recent progress in the development of bromodomain inhibitors is highlighted, and their potential applications in drug discovery are highlighted.
Abstract: Lysine acetylation is a key mechanism that regulates chromatin structure; aberrant acetylation levels have been linked to the development of several diseases. Acetyl-lysine modifications create docking sites for bromodomains, which are small interaction modules found on diverse proteins, some of which have a key role in the acetylation-dependent assembly of transcriptional regulator complexes. These complexes can then initiate transcriptional programmes that result in phenotypic changes. The recent discovery of potent and highly specific inhibitors for the BET (bromodomain and extra-terminal) family of bromodomains has stimulated intensive research activity in diverse therapeutic areas, particularly in oncology, where BET proteins regulate the expression of key oncogenes and anti-apoptotic proteins. In addition, targeting BET bromodomains could hold potential for the treatment of inflammation and viral infection. Here, we highlight recent progress in the development of bromodomain inhibitors, and their potential applications in drug discovery.
1,090 citations
TL;DR: ARV-825 is designed, a hetero-bifunctional PROTAC (Proteolysis Targeting Chimera) that recruits BRD4 to the E3 ubiquitin ligase cereblon, leading to fast, efficient, and prolonged degradation ofBRD4 in all BL cell lines tested.
791 citations
Cites background from "Targeting MYCN in Neuroblastoma by ..."
...Also, not surprisingly, high sensitivity to BRD4 inhibitors, such as JQ1, has been associated with high level of either c-MYC or n-MYC in different tumor types, including c-MYC-driven BL (Baratta et al., 2015; Loosveld et al., 2014; Mertz et al., 2011; Puissant et al., 2013)....
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...Indeed, the development of small-molecule BRD4 inhibitors, such as JQ1, iBET, and OTX015, has quickly demonstrated their promising therapeutic potential in preclinical models of various cancers, including BL (Asangani et al., 2014; Baratta et al., 2015; Boi et al., 2015; Chapuy et al., 2013; Delmore et al., 2011; Loven et al., 2013; Mertz et al., 2011; Puissant et al., 2013)....
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...…OTX015, has quickly demonstrated their promising therapeutic potential in preclinical models of various cancers, including BL (Asangani et al., 2014; Baratta et al., 2015; Boi et al., 2015; Chapuy et al., 2013; Delmore et al., 2011; Loven et al., 2013; Mertz et al., 2011; Puissant et al., 2013)....
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TL;DR: It is shown that AR-signalling-competent human CRPC cell lines are preferentially sensitive to bromodomain and extraterminal (BET) inhibition, which provides a novel epigenetic approach for the concerted blockade of oncogenic drivers in advanced prostate cancer.
Abstract: Men who develop metastatic castration-resistant prostate cancer (CRPC) invariably succumb to the disease. Progression to CRPC after androgen ablation therapy is predominantly driven by deregulated androgen receptor (AR) signalling. Despite the success of recently approved therapies targeting AR signalling, such as abiraterone and second-generation anti-androgens including MDV3100 (also known as enzalutamide), durable responses are limited, presumably owing to acquired resistance. Recently, JQ1 and I-BET762 two selective small-molecule inhibitors that target the amino-terminal bromodomains of BRD4, have been shown to exhibit anti-proliferative effects in a range of malignancies. Here we show that AR-signalling-competent human CRPC cell lines are preferentially sensitive to bromodomain and extraterminal (BET) inhibition. BRD4 physically interacts with the N-terminal domain of AR and can be disrupted by JQ1 (refs 11, 13). Like the direct AR antagonist MDV3100, JQ1 disrupted AR recruitment to target gene loci. By contrast with MDV3100, JQ1 functions downstream of AR, and more potently abrogated BRD4 localization to AR target loci and AR-mediated gene transcription, including induction of the TMPRSS2-ERG gene fusion and its oncogenic activity. In vivo, BET bromodomain inhibition was more efficacious than direct AR antagonism in CRPC xenograft mouse models. Taken together, these studies provide a novel epigenetic approach for the concerted blockade of oncogenic drivers in advanced prostate cancer.
784 citations
TL;DR: How transcriptional control is disrupted by genetic alterations in cancer cells, why transcriptional dependencies can develop as a consequence of dysregulated programs, and how these dependencies provide opportunities for novel therapeutic interventions in cancer are discussed.
767 citations
Cites background from "Targeting MYCN in Neuroblastoma by ..."
...Moreover, BRD4 function has emerged as a transcriptional addiction in MYCN-amplified neuroblastomas (Puissant et al., 2013), as a positive regulator of anti-apoptotic gene expression in AMLs (Dawson et al., 2011), and as a mediator of resistance to Notch pathway inhibition in T-ALLs (Yashiro-Ohtani…...
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...Moreover, BRD4 function has emerged as a transcriptional addiction in MYCN-amplified neuroblastomas (Puissant et al., 2013), as a positive regulator of anti-apoptotic gene expression in AMLs (Dawson et al....
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TL;DR: The current understanding of molecular mechanisms that underlie the promising therapeutic effects of BET bromodomain inhibition are reviewed.
698 citations
Cites background from "Targeting MYCN in Neuroblastoma by ..."
...Neuroblastomas that harbor NMYC amplifications are also sensitive to JQ1, correlating with suppression of NMYC transcription (Puissant et al., 2013)....
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References
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TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Abstract: Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.
34,830 citations
TL;DR: The results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents and the generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of ‘personalized’ therapeutic regimens.
Abstract: The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens.
6,417 citations
"Targeting MYCN in Neuroblastoma by ..." refers background in this paper
...In an independent study of 24 anti-cancer drugs in 479 human cancer cell lines, new connections were also observed between smallmolecule sensitivities and cell lineage, gene expression, and genotype (17)....
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TL;DR: STI571 is well tolerated and has significant antileukemic activity in patients with CML in whom treatment with interferon alfa had failed and demonstrates the potential for the development of anticancer drugs based on the specific molecular abnormality present in a human cancer.
Abstract: Background BCR-ABL is a constitutively activated tyrosine kinase that causes chronic myeloid leukemia (CML). Since tyrosine kinase activity is essential to the transforming function of BCR-ABL, an inhibitor of the kinase could be an effective treatment for CML. Methods We conducted a phase 1, dose-escalating trial of STI571 (formerly known as CGP 57148B), a specific inhibitor of the BCR-ABL tyrosine kinase. STI571 was administered orally to 83 patients with CML in the chronic phase in whom treatment with interferon alfa had failed. Patients were successively assigned to 1 of 14 doses ranging from 25 to 1000 mg per day. Results Adverse effects of STI571 were minimal; the most common were nausea, myalgias, edema, and diarrhea. A maximal tolerated dose was not identified. Complete hematologic responses were observed in 53 of 54 patients treated with daily doses of 300 mg or more and typically occurred in the first four weeks of therapy. Of the 54 patients treated with doses of 300 mg or more, cytogenetic res...
5,037 citations
TL;DR: A new version of the database, MSigDB 3.0, is reported, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site.
Abstract: Motivation: Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets.
Results: We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site.
Availability and Implementation: MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.
Contact: gsea@broadinstitute.org
4,128 citations
"Targeting MYCN in Neuroblastoma by ..." refers methods in this paper
...N IH -PA Author M anuscript N IH -PA Author M anuscript N IH -PA Author M anuscript Fisher tests for the MSigDB signatures enriched with genes selectively downregulated by JQ1 in neuroblastoma cells....
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...Depicted is the plot of the running sum for the molecular signature data base (MSigDB) gene set within the JQ1 neuroblastoma dataset including the maximum enrichment score and the leading edge subset of enriched genes....
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...(E) Quantitative comparison of all transcription factor target gene sets available from the MSigDB by GSEA for downregulation in JQ1-treated neuroblastoma cells....
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...Because the MYCN signature in the Molecular Signature Database (MSigDB) was derived in small cell lung cancer cells (19), we sought to develop a custom MYCN upregulated signature in neuroblastoma cells utilizing a publicly available data set of primary neuroblastoma tumors characterized for MYCN amplification status (20)....
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...GENE-E version 1, GenePattern version 3.5.0, GSEA version 13, Cytoscape version 2.8.3 and MSigDB version 3.1....
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TL;DR: The inhibition of ALK in lung tumors with the ALK rearrangement resulted in tumor shrinkage or stable disease in most patients, and the drug resulted in grade 1 or 2 gastrointestinal side effects.
Abstract: Background Oncogenic fusion genes consisting of EML4 and anaplastic lymphoma kinase (ALK) are present in a subgroup of non–small-cell lung cancers, representing 2 to 7% of such tumors. We explored the therapeutic efficacy of inhibiting ALK in such tumors in an early-phase clinical trial of crizotinib (PF-02341066), an orally available small-molecule inhibitor of the ALK tyrosine kinase. Methods After screening tumor samples from approximately 1500 patients with non–small-cell lung cancer for the presence of ALK rearrangements, we identified 82 patients with advanced ALK-positive disease who were eligible for the clinical trial. Most of the patients had received previous treatment. These patients were enrolled in an expanded cohort study instituted after phase 1 dose escalation had established a recommended crizotinib dose of 250 mg twice daily in 28-day cycles. Patients were assessed for adverse events and response to therapy. Results Patients with ALK rearrangements tended to be younger than those without the rearrangements, and most of the patients had little or no exposure to tobacco and had adenocarcinomas. At a mean treatment duration of 6.4 months, the overall response rate was 57% (47 of 82 patients, with 46 confirmed partial responses and 1 confirmed complete response); 27 patients (33%) had stable disease. A total of 63 of 82 patients (77%) were continuing to receive crizotinib at the time of data cutoff, and the estimated probability of 6-month progression-free survival was 72%, with no median for the study reached. The drug resulted in grade 1 or 2 (mild) gastrointestinal side effects. Conclusions The inhibition of ALK in lung tumors with the ALK rearrangement resulted in tumor shrinkage or stable disease in most patients. (Funded by Pfizer and others; ClinicalTrials.gov number, NCT00585195.)
4,091 citations