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Cerda-Smith CG, Hutchinson HM, Liu A, Goel VY, Sept C, Kim H, Casaní-Galdón S, Burkman KG, Bassil CF, Hansen AS, Aryee MJ, Johnstone SE, Eyler CE, Wood KC. Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer Organization. bioRxiv 2023:2023.09.20.558459. [PMID: 37786671 PMCID: PMC10541578 DOI: 10.1101/2023.09.20.558459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Enhancers possess both structural elements mediating promoter looping and functional elements mediating gene expression. Traditional models of enhancer-mediated gene regulation imply genomic overlap or immediate adjacency of these elements. We test this model by combining densely-tiled CRISPRa screening with nucleosome-resolution Region Capture Micro-C topology analysis. Using this integrated approach, we comprehensively define the cis-regulatory landscape for the tumor suppressor PTEN, identifying and validating 10 distinct enhancers and defining their 3D spatial organization. Unexpectedly, we identify several long-range functional enhancers whose promoter proximity is facilitated by chromatin loop anchors several kilobases away, and demonstrate that accounting for this spatial separation improves the computational prediction of validated enhancers. Thus, we propose a new model of enhancer organization incorporating spatial separation of essential functional and structural components.
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Affiliation(s)
- Christian G. Cerda-Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Haley M. Hutchinson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Annie Liu
- Department of Surgery, Duke University School of Medicine; Durham, NC 27710, USA
| | - Viraat Y. Goel
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, 02139, USA
- Broad Institute; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Corriene Sept
- Broad Institute; Cambridge, MA 02139, USA
- Department of Biostatistics, Harvard School of Public Health; Boston, MA 02215, USA
| | - Holly Kim
- Department of Radiation Oncology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Salvador Casaní-Galdón
- Broad Institute; Cambridge, MA 02139, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute; Boston, MA 02215, USA
- Departments of Cell Biology and Pathology, Harvard Medical School; Boston, MA 02114, USA
| | - Katherine G. Burkman
- Department of Radiation Oncology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Christopher F. Bassil
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Anders S. Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, 02139, USA
- Broad Institute; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Martin J. Aryee
- Broad Institute; Cambridge, MA 02139, USA
- Department of Pathology, Harvard Medical School; Boston, MA 02114, USA
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA 02215, USA
| | - Sarah E. Johnstone
- Broad Institute; Cambridge, MA 02139, USA
- Department of Pathology, Dana-Farber Cancer Institute; Boston, MA 02215, USA
| | - Christine E. Eyler
- Department of Radiation Oncology, Duke University School of Medicine; Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine; Durham, NC 27710, USA
| | - Kris C. Wood
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine; Durham, NC 27710, USA
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2
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Bassil CF, Anderson GR, Mayro B, Askin KN, Winter PS, Gruber S, Hall TM, Hoj JP, Cerda-Smith C, Hutchinson HM, Killarney ST, Singleton KR, Qin L, Jubien-Girard K, Favreau C, Martin AR, Robert G, Benhida R, Auberger P, Pendergast AM, Lonard DM, Puissant A, Wood KC. MCB-613 exploits a collateral sensitivity in drug resistant EGFR-mutant non-small cell lung cancer through covalent inhibition of KEAP1. bioRxiv 2023:2023.01.17.524094. [PMID: 36711936 PMCID: PMC9882253 DOI: 10.1101/2023.01.17.524094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Targeted therapies have revolutionized cancer chemotherapy. Unfortunately, most patients develop multifocal resistance to these drugs within a matter of months. Here, we used a high-throughput phenotypic small molecule screen to identify MCB-613 as a compound that selectively targets EGFR-mutant, EGFR inhibitor-resistant non-small cell lung cancer (NSCLC) cells harboring diverse resistance mechanisms. Subsequent proteomic and functional genomic screens involving MCB-613 identified its target in this context to be KEAP1, revealing that this gene is selectively essential in the setting of EGFR inhibitor resistance. In-depth molecular characterization demonstrated that (1) MCB-613 binds KEAP1 covalently; (2) a single molecule of MCB-613 is capable of bridging two KEAP1 monomers together; and, (3) this modification interferes with the degradation of canonical KEAP1 substrates such as NRF2. Surprisingly, NRF2 knockout sensitizes cells to MCB-613, suggesting that the drug functions through modulation of an alternative KEAP1 substrate. Together, these findings advance MCB-613 as a new tool for exploiting the selective essentiality of KEAP1 in drug-resistant, EGFR-mutant NSCLC cells.
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Affiliation(s)
| | - Gray R Anderson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Benjamin Mayro
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Kayleigh N Askin
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Peter S Winter
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Samuel Gruber
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Tierney M Hall
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Jacob P Hoj
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | - Haley M Hutchinson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Shane T Killarney
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | - Li Qin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Kévin Jubien-Girard
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272 - 06108 Nice, France
| | | | - Anthony R Martin
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272 - 06108 Nice, France
- IBMM, Université de Montpellier, ENSCM, CNRS, Montpellier, France
| | | | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272 - 06108 Nice, France
- Chemical & Biochemical Sciences Green-Process Engineering (CBS) Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Benguerir, Morocco
| | | | | | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Alexandre Puissant
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
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3
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Lin KH, Rutter JC, Xie A, Killarney ST, Vaganay C, Benaksas C, Ling F, Sodaro G, Meslin PA, Bassil CF, Fenouille N, Hoj J, Washart R, Ang HX, Cerda-Smith C, Chaintreuil P, Jacquel A, Auberger P, Forget A, Itzykson R, Lu M, Lin J, Pierobon M, Sheng Z, Li X, Chilkoti A, Owzar K, Rizzieri DA, Pardee TS, Benajiba L, Petricoin E, Puissant A, Wood KC. P2RY2-AKT activation is a therapeutically actionable consequence of XPO1 inhibition in acute myeloid leukemia. Nat Cancer 2022; 3:837-851. [PMID: 35668193 PMCID: PMC9949365 DOI: 10.1038/s43018-022-00394-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 05/04/2022] [Indexed: 12/12/2022]
Abstract
Selinexor is a first-in-class inhibitor of the nuclear exportin XPO1 that was recently approved by the US Food and Drug Administration for the treatment of multiple myeloma and diffuse large B-cell lymphoma. In relapsed/refractory acute myeloid leukemia (AML), selinexor has shown promising activity, suggesting that selinexor-based combination therapies may have clinical potential. Here, motivated by the hypothesis that selinexor's nuclear sequestration of diverse substrates imposes pleiotropic fitness effects on AML cells, we systematically catalog the pro- and anti-fitness consequences of selinexor treatment. We discover that selinexor activates PI3Kγ-dependent AKT signaling in AML by upregulating the purinergic receptor P2RY2. Inhibiting this axis potentiates the anti-leukemic effects of selinexor in AML cell lines, patient-derived primary cultures and multiple mouse models of AML. In a syngeneic, MLL-AF9-driven mouse model of AML, treatment with selinexor and ipatasertib outperforms both standard-of-care chemotherapy and chemotherapy with selinexor. Together, these findings establish drug-induced P2RY2-AKT signaling as an actionable consequence of XPO1 inhibition in AML.
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Affiliation(s)
- Kevin H Lin
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Justine C Rutter
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Abigail Xie
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Shane T Killarney
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Camille Vaganay
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Chaima Benaksas
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Frank Ling
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Gaetano Sodaro
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Paul-Arthur Meslin
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | | | - Nina Fenouille
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Jacob Hoj
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Rachel Washart
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Hazel X Ang
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | | | | | | | - Antoine Forget
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Raphael Itzykson
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Min Lu
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Jiaxing Lin
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Zhecheng Sheng
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Xinghai Li
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - David A Rizzieri
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Timothy S Pardee
- Department of Internal Medicine, Section on Hematology and Oncology, Wake Forest Baptist Health, Winston-Salem, NC, USA
| | - Lina Benajiba
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Emanuel Petricoin
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Alexandre Puissant
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France.
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
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4
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Ali M, Lu M, Ang HX, Soderquist RS, Eyler CE, Hutchinson HM, Glass C, Bassil CF, Lopez OM, Kerr DL, Falcon CJ, Yu HA, Hata AN, Blakely CM, McCoach CE, Bivona TG, Wood KC. Small-molecule targeted therapies induce dependence on DNA double-strand break repair in residual tumor cells. Sci Transl Med 2022; 14:eabc7480. [PMID: 35353542 PMCID: PMC9516479 DOI: 10.1126/scitranslmed.abc7480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Residual cancer cells that survive drug treatments with targeted therapies act as a reservoir from which eventual resistant disease emerges. Although there is great interest in therapeutically targeting residual cells, efforts are hampered by our limited knowledge of the vulnerabilities existing in this cell state. Here, we report that diverse oncogene-targeted therapies, including inhibitors of epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), KRAS, and BRAF, induce DNA double-strand breaks and, consequently, ataxia-telangiectasia mutated (ATM)-dependent DNA repair in oncogene-matched residual tumor cells. This DNA damage response, observed in cell lines, mouse xenograft models, and human patients, is driven by a pathway involving the activation of caspases 3 and 7 and the downstream caspase-activated deoxyribonuclease (CAD). CAD is, in turn, activated through caspase-mediated degradation of its endogenous inhibitor, ICAD. In models of EGFR mutant non-small cell lung cancer (NSCLC), tumor cells that survive treatment with small-molecule EGFR-targeted therapies are thus synthetically dependent on ATM, and combined treatment with an ATM kinase inhibitor eradicates these cells in vivo. This led to more penetrant and durable responses in EGFR mutant NSCLC mouse xenograft models, including those derived from both established cell lines and patient tumors. Last, we found that rare patients with EGFR mutant NSCLC harboring co-occurring, loss-of-function mutations in ATM exhibit extended progression-free survival on first generation EGFR inhibitor therapy relative to patients with EGFR mutant NSCLC lacking deleterious ATM mutations. Together, these findings establish a rationale for the mechanism-based integration of ATM inhibitors alongside existing targeted therapies.
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Affiliation(s)
- Moiez Ali
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Min Lu
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Hazel Xiaohui Ang
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Ryan S. Soderquist
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Christine E. Eyler
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Haley M. Hutchinson
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Carolyn Glass
- Department of Pathology, Duke University, Durham, NC 27710, USA
| | - Christopher F. Bassil
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Omar M. Lopez
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - D. Lucas Kerr
- Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christina J. Falcon
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Helena A. Yu
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Aaron N. Hata
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Collin M. Blakely
- Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Caroline E. McCoach
- Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Trever G. Bivona
- Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kris C. Wood
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
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5
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Su A, Ling F, Vaganay C, Sodaro G, Benaksas C, Dal Bello R, Forget A, Pardieu B, Lin KH, Rutter JC, Bassil CF, Fortin G, Pasanisi J, Antony-Debré I, Alexe G, Benoist JF, Pruvost A, Pikman Y, Qi J, Schlageter MH, Micol JB, Roti G, Cluzeau T, Dombret H, Preudhomme C, Fenouille N, Benajiba L, Golan HM, Stegmaier K, Lobry C, Wood KC, Itzykson R, Puissant A. The Folate Cycle Enzyme MTHFR Is a Critical Regulator of Cell Response to MYC-Targeting Therapies. Cancer Discov 2020; 10:1894-1911. [PMID: 32826232 DOI: 10.1158/2159-8290.cd-19-0970] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 07/02/2020] [Accepted: 08/18/2020] [Indexed: 01/12/2023]
Abstract
Deciphering the impact of metabolic intervention on response to anticancer therapy may elucidate a path toward improved clinical responses. Here, we identify amino acid-related pathways connected to the folate cycle whose activation predicts sensitivity to MYC-targeting therapies in acute myeloid leukemia (AML). We establish that folate restriction and deficiency of the rate-limiting folate cycle enzyme MTHFR, which exhibits reduced-function polymorphisms in about 10% of Caucasians, induce resistance to MYC targeting by BET and CDK7 inhibitors in cell lines, primary patient samples, and syngeneic mouse models of AML. Furthermore, this effect is abrogated by supplementation with the MTHFR enzymatic product CH3-THF. Mechanistically, folate cycle disturbance reduces H3K27/K9 histone methylation and activates a SPI1 transcriptional program counteracting the effect of BET inhibition. Our data provide a rationale for screening MTHFR polymorphisms and folate cycle status to nominate patients most likely to benefit from MYC-targeting therapies. SIGNIFICANCE: Although MYC-targeting therapies represent a promising strategy for cancer treatment, evidence of predictors of sensitivity to these agents is limited. We pinpoint that folate cycle disturbance and frequent polymorphisms associated with reduced MTHFR activity promote resistance to BET inhibitors. CH3-THF supplementation thus represents a low-risk intervention to enhance their effects.See related commentary by Marando and Huntly, p. 1791.This article is highlighted in the In This Issue feature, p. 1775.
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Affiliation(s)
- Angela Su
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Frank Ling
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Camille Vaganay
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Gaetano Sodaro
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Chaïma Benaksas
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Reinaldo Dal Bello
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Antoine Forget
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Bryann Pardieu
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Kevin H Lin
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Justine C Rutter
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Christopher F Bassil
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Gael Fortin
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Justine Pasanisi
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Iléana Antony-Debré
- INSERM UMR 1287, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,The Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Alain Pruvost
- Paris-Saclay University, CEA, INRAE, Département Médicaments et Technologies pour la santé, SPI, Gif-sur-Yvette, France
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jun Qi
- The Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marie-Hélène Schlageter
- AP-HP, Cellular Biology Department, St Louis Hospital, Paris, France.,INSERM U 1131, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Jean-Baptiste Micol
- INSERM UMR 1287, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France.,Department of Hematology, Gustave Roussy Institute, Villejuif, France
| | - Giovanni Roti
- University of Parma, Department of Medicine and Surgery, Parma, Italy
| | - Thomas Cluzeau
- Department of Hematology, Centre Hospitalier Universitaire, Nice, France
| | | | | | - Nina Fenouille
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Lina Benajiba
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France.,AP-HP, Hematology Department, St Louis Hospital, Paris, France
| | - Hava M Golan
- Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,The Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Camille Lobry
- INSERM UMR 1287, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Raphael Itzykson
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France.
| | - Alexandre Puissant
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France.
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6
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Boros K, Puissant A, Back M, Alexe G, Bassil CF, Sinha P, Tholouli E, Stegmaier K, Byers RJ, Rodig SJ. Increased SYK activity is associated with unfavorable outcome among patients with acute myeloid leukemia. Oncotarget 2016; 6:25575-87. [PMID: 26315286 PMCID: PMC4694851 DOI: 10.18632/oncotarget.4669] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/29/2015] [Indexed: 01/19/2023] Open
Abstract
Recent discoveries have led to the testing of novel targeted therapies for the treatment of acute myeloid leukemia (AML). To better inform the results of clinical trials, there is a need to identify and systematically assess biomarkers of response and pharmacodynamic markers of successful target engagement. Spleen tyrosine kinase (SYK) is a candidate therapeutic target in AML. Small-molecule inhibitors of SYK induce AML differentiation and impair leukemia progression in preclinical studies. However, tools to predict response to SYK inhibition and to routinely evaluate SYK activation in primary patient samples have been lacking. In this study we quantified phosphorylated SYK (P-SYK) in AML cell lines and establish that increasing levels of baseline P-SYK are correlated with an increasing sensitivity to small-molecule inhibitors targeting SYK. In addition, we found that pharmacological inhibition of SYK activity extinguishes P-SYK expression as detected by an immunohistochemical (IHC) test. Quantitative analysis of P-SYK expression by the IHC test in a series of 70 primary bone marrow biopsy specimens revealed a spectrum of P-SYK expression across AML cases and that high P-SYK expression is associated with unfavourable outcome independent of age, cytogenetics, and white blood cell count. This study thus establishes P-SYK as a critical biomarker in AML that identifies tumors sensitive to SYK inhibition, identifies an at-risk patient population, and allows for the monitoring of target inhibition during treatment.
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Affiliation(s)
- Katalin Boros
- Department of Histopathology, Manchester Royal Infirmary, Manchester, UK
| | - Alexandre Puissant
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA.,INSERM U1065, Team 2, C3M, Nice, France
| | - Morgan Back
- The Medical School, The University of Manchester, Manchester, UK
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Christopher F Bassil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Papiya Sinha
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Eleni Tholouli
- Department of Haematology, Manchester Royal Infirmary, Manchester, UK
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Richard J Byers
- Institute of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
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7
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Pikman Y, Puissant A, Alexe G, Furman A, Chen LM, Frumm SM, Ross L, Fenouille N, Bassil CF, Lewis CA, Ramos A, Gould J, Stone RM, DeAngelo DJ, Galinsky I, Clish CB, Kung AL, Hemann MT, Vander Heiden MG, Banerji V, Stegmaier K. Targeting MTHFD2 in acute myeloid leukemia. J Biophys Biochem Cytol 2016. [DOI: 10.1083/jcb.2141oia135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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8
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Pikman Y, Puissant A, Alexe G, Furman A, Chen LM, Frumm SM, Ross L, Fenouille N, Bassil CF, Lewis CA, Ramos A, Gould J, Stone RM, DeAngelo DJ, Galinsky I, Clish CB, Kung AL, Hemann MT, Vander Heiden MG, Banerji V, Stegmaier K. Targeting MTHFD2 in acute myeloid leukemia. J Exp Med 2016; 213:1285-306. [PMID: 27325891 PMCID: PMC4925018 DOI: 10.1084/jem.20151574] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/09/2016] [Indexed: 12/31/2022] Open
Abstract
Drugs targeting metabolism have formed the backbone of therapy for some cancers. We sought to identify new such targets in acute myeloid leukemia (AML). The one-carbon folate pathway, specifically methylenetetrahydrofolate dehydrogenase-cyclohydrolase 2 (MTHFD2), emerged as a top candidate in our analyses. MTHFD2 is the most differentially expressed metabolic enzyme in cancer versus normal cells. Knockdown of MTHFD2 in AML cells decreased growth, induced differentiation, and impaired colony formation in primary AML blasts. In human xenograft and MLL-AF9 mouse leukemia models, MTHFD2 suppression decreased leukemia burden and prolonged survival. Based upon primary patient AML data and functional genomic screening, we determined that FLT3-ITD is a biomarker of response to MTHFD2 suppression. Mechanistically, MYC regulates the expression of MTHFD2, and MTHFD2 knockdown suppresses the TCA cycle. This study supports the therapeutic targeting of MTHFD2 in AML.
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Affiliation(s)
- Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215
| | - Alexandre Puissant
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215 Institut National de la Santé et de la Recherche Medicale U1065, Team 2, C3M, 06204 Nice, France
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215 Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142 Bioinformatics Graduate Program, Boston University, Boston, MA 02215
| | - Andrew Furman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215
| | - Liying M Chen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215
| | - Stacey M Frumm
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215
| | - Linda Ross
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215
| | - Nina Fenouille
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Christopher F Bassil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215
| | - Caroline A Lewis
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Azucena Ramos
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Joshua Gould
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Ilene Galinsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Clary B Clish
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142
| | - Andrew L Kung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032
| | - Michael T Hemann
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Matthew G Vander Heiden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142 Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Versha Banerji
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215 Research Institute of Oncology and Hematology at CancerCare Manitoba and the University of Manitoba, Winnipeg R3E OV9, Manitoba, Canada
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215 Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142
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9
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Abstract
Epigenetic modifications, including DNA methylation, are critically important mediators of normal cell function over the course of our lives. These modifications therefore also can play prominent roles in the development of disorders and diseases, including ovarian cancer. Genome-wide studies are now beginning to comprehensively decipher the methylome in normal and diseased tissues and cells, providing new insights into the distribution, specificity, and magnitude of modifications that occur and raising questions about these changes at specific loci. Further study of these alterations in specific tissues usually involves targeted approaches, of which there are a number available, all with distinct advantages and disadvantages. Here we provide a brief overview of DNA methylation and some of the methylation alterations that have been identified in ovarian cancer, as well as some of the technical approaches used to study these modifications.
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Affiliation(s)
- Susan K Murphy
- Division of Gynecologic Oncology, Duke University Medical Center, Durham, NC, USA
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10
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Puissant A, Fenouille N, Alexe G, Pikman Y, Bassil CF, Mehta S, Du J, Kazi JU, Luciano F, Rönnstrand L, Kung AL, Aster JC, Galinsky I, Stone RM, DeAngelo DJ, Hemann MT, Stegmaier K. SYK is a critical regulator of FLT3 in acute myeloid leukemia. Cancer Cell 2014; 25:226-42. [PMID: 24525236 PMCID: PMC4106711 DOI: 10.1016/j.ccr.2014.01.022] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 11/14/2013] [Accepted: 01/22/2014] [Indexed: 10/25/2022]
Abstract
Cooperative dependencies between mutant oncoproteins and wild-type proteins are critical in cancer pathogenesis and therapy resistance. Although spleen tyrosine kinase (SYK) has been implicated in hematologic malignancies, it is rarely mutated. We used kinase activity profiling to identify collaborators of SYK in acute myeloid leukemia (AML) and determined that FMS-like tyrosine kinase 3 (FLT3) is transactivated by SYK via direct binding. Highly activated SYK is predominantly found in FLT3-ITD positive AML and cooperates with FLT3-ITD to activate MYC transcriptional programs. FLT3-ITD AML cells are more vulnerable to SYK suppression than FLT3 wild-type counterparts. In a FLT3-ITD in vivo model, SYK is indispensable for myeloproliferative disease (MPD) development, and SYK overexpression promotes overt transformation to AML and resistance to FLT3-ITD-targeted therapy.
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MESH Headings
- Animals
- Antimetabolites, Antineoplastic/pharmacology
- Apoptosis
- Blotting, Western
- Cell Proliferation
- Cell Transformation, Neoplastic
- Cells, Cultured
- Drug Resistance, Neoplasm
- Fluorouracil/pharmacology
- Humans
- Immunoenzyme Techniques
- Intracellular Signaling Peptides and Proteins/antagonists & inhibitors
- Intracellular Signaling Peptides and Proteins/genetics
- Intracellular Signaling Peptides and Proteins/metabolism
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred BALB C
- Mutation/genetics
- Phosphorylation
- Protein Kinase Inhibitors/pharmacology
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Survival Rate
- Syk Kinase
- fms-Like Tyrosine Kinase 3/antagonists & inhibitors
- fms-Like Tyrosine Kinase 3/genetics
- fms-Like Tyrosine Kinase 3/metabolism
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Affiliation(s)
- Alexandre Puissant
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Nina Fenouille
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA; The Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Christopher F Bassil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Swapnil Mehta
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Jinyan Du
- The Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Julhash U Kazi
- Experimental Clinical Chemistry, Department of Laboratory Medicine, Lund University, Medicon Village, 221 00 Lund, Sweden
| | - Frédéric Luciano
- C3M/ INSERM U1065 Team Cell Death, Differentiation, Inflammation and Cancer, 06204 Nice, France
| | - Lars Rönnstrand
- Experimental Clinical Chemistry, Department of Laboratory Medicine, Lund University, Medicon Village, 221 00 Lund, Sweden
| | - Andrew L Kung
- Pediatric Department, Columbia University Medical Center, New York, NY 10032, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Ilene Galinsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Michael T Hemann
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA; The Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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11
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Frumm SM, Fan ZP, Ross KN, Duvall JR, Gupta S, VerPlank L, Suh BC, Holson E, Wagner FF, Smith WB, Paranal RM, Bassil CF, Qi J, Roti G, Kung AL, Bradner JE, Tolliday N, Stegmaier K. Selective HDAC1/HDAC2 inhibitors induce neuroblastoma differentiation. ACTA ACUST UNITED AC 2013; 20:713-25. [PMID: 23706636 DOI: 10.1016/j.chembiol.2013.03.020] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 03/07/2013] [Accepted: 03/22/2013] [Indexed: 01/05/2023]
Abstract
While cytotoxic chemotherapy remains the hallmark of cancer treatment, intensive regimens fall short in many malignancies, including high-risk neuroblastoma. One alternative strategy is to therapeutically promote tumor differentiation. We created a gene expression signature to measure neuroblast maturation, adapted it to a high-throughput platform, and screened a diversity oriented synthesis-generated small-molecule library for differentiation inducers. We identified BRD8430, containing a nine-membered lactam, an ortho-amino anilide functionality, and three chiral centers, as a selective class I histone deacetylase (HDAC) inhibitor (HDAC1 > 2 > 3). Further investigation demonstrated that selective HDAC1/HDAC2 inhibition using compounds or RNA interference induced differentiation and decreased viability in neuroblastoma cell lines. Combined treatment with 13-cis retinoic acid augmented these effects and enhanced activation of retinoic acid signaling. Therefore, by applying a chemical genomic screening approach, we identified selective HDAC1/HDAC2 inhibition as a strategy to induce neuroblastoma differentiation.
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Affiliation(s)
- Stacey M Frumm
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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12
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Puissant A, Frumm SM, Alexe G, Bassil CF, Qi J, Chanthery YH, Nekritz EA, Zeid R, Gustafson WC, Greninger P, Garnett MJ, McDermott U, Benes CH, Kung AL, Weiss WA, Bradner JE, Stegmaier K. Abstract 4622: Targeting MYCN in Neuroblastoma by BET Bromodomain Inhibition. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-4622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
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 (bromodomain and extra-terminal domain) 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 demonstrated downregulation of the MYCN transcriptional program accompanied by suppression of MYCN transcription, and a BET Bromodomain inhibitor was found to displace BRD4 from the MYCN promoter region in neuroblastoma cell lines. Functionally, bromodomain-mediated inhibition of MYCN impaired growth and induced apoptosis in neuroblastoma. BRD4 knock-down phenocopied these effects, establishing BET bromodomains as transcriptional regulators of MYCN. BET inhibition conferred a significant survival advantage in three in vivo neuroblastoma models, providing a compelling rationale for developing BET bromodomain inhibitors in patients with neuroblastoma.
Citation Format: Alexandre Puissant, Stacey M. Frumm, Gabriela Alexe, Christopher F. Bassil, Jun Qi, Yvan H. Chanthery, Erin A. Nekritz, Rhamy Zeid, W. Clay Gustafson, Patricia Greninger, Matthew J. Garnett, Ultan McDermott, Cyril H. Benes, Andrew L. Kung, William A. Weiss, James E. Bradner, Kimberly Stegmaier. Targeting MYCN in Neuroblastoma by BET Bromodomain Inhibition. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4622. doi:10.1158/1538-7445.AM2013-4622
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Affiliation(s)
| | | | | | | | - Jun Qi
- Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Rhamy Zeid
- Dana-Farber Cancer Institute, Boston, MA
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13
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Puissant A, Frumm SM, Alexe G, Bassil CF, Qi J, Chanthery YH, Nekritz EA, Zeid R, Gustafson WC, Greninger P, Garnett MJ, McDermott U, Benes CH, Kung AL, Weiss WA, Bradner JE, Stegmaier K. Targeting MYCN in neuroblastoma by BET bromodomain inhibition. Cancer Discov 2013; 3:308-23. [PMID: 23430699 DOI: 10.1158/2159-8290.cd-12-0418] [Citation(s) in RCA: 475] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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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Affiliation(s)
- Alexandre Puissant
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
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14
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Abstract
Bisulfite pyrosequencing is a sequencing-by-synthesis method used to quantitatively determine the methylation of individual CG cytosines from PCR amplicons of a region up to 115 bases in length. The procedure relies on prior bisulfite conversion of all potentially methylated CG cytosines to either cytosine (methylated) or thymine (unmethylated) and involves the stepwise incorporation of deoxynucleotide triphosphates into the growing strand of nascent DNA. The incorporation of these dNTPs results in the proportional release of pyrophosphate, which is converted into ATP to aid in a subsequent conversion of luciferin to oxyluciferin. The amount of light released in the process is proportional to the number of nucleotides incorporated, and the procedure provides a quantitative portrait of the methylation profile for the amplicon in question.
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Affiliation(s)
- Christopher F Bassil
- Division of Gynecologic Oncology, Duke University Medical Center, Durham, NC, USA
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15
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Abstract
Defining DNA methylation patterns in the genome has become essential for understanding diverse biological processes including the regulation of gene expression, imprinted genes, and X chromosome inactivation and how these patterns are deregulated in human diseases. Methylation-specific (MS)-PCR is a useful tool for qualitative DNA methylation analysis with multiple advantages, including ease of design and execution, sensitivity in the ability to detect small quantities of methylated DNA, and the ability to rapidly screen a large number of samples without the need for purchase of expensive laboratory equipment. This assay requires modification of the genomic DNA by sodium bisulfite and two independent primer sets for PCR amplification, one pair designed to recognize the methylated and the other pair the unmethylated versions of the bisulfite-modified sequence. The amplicons are visualized using ethidium bromide staining following agarose gel electrophoresis. Amplicons of the expected size produced from either primer pair are indicative of the presence of DNA in the original sample with the respective methylation status.
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Affiliation(s)
- Zhiqing Huang
- Division of Gynecologic Oncology, Duke University Medical Center, Durham, NC, USA
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16
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Abstract
Bisulfite sequencing of cloned alleles is a widely used method for capturing the methylation profiles of single alleles. This method combines PCR amplification of the bisulfite-modified DNA with the subcloning of the amplicons into plasmids followed by transformation into bacteria and plating on selective media. The resulting colony forming units are each comprised of bacterial clones containing the same plasmid reflecting a single allele in the original PCR reaction. Following whole cell PCR and sequencing, the results provide highly detailed information about the status of each CG site within an allele. Sequencing of a large number of individual clones can provide quantitative information, assuming unbiased PCR, subcloning and clone selection. The proportion of methylated cytosine at a particular position within the sequenced alleles can be determined by counting the number of alleles showing methylation at the position of interest and dividing this by the total number of clones sequenced.
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Affiliation(s)
- Zhiqing Huang
- Division of Gynecologic Oncology, Duke University Medical Center, Durham, NC, USA
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