1
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Mittal K, Cooper GW, Lee BP, Su Y, Skinner KT, Shim J, Jonus HC, Kim WJ, Doshi M, Almanza D, Kynnap BD, Christie AL, Yang X, Cowley GS, Leeper BA, Morton CL, Dwivedi B, Lawrence T, Rupji M, Keskula P, Meyer S, Clinton CM, Bhasin M, Crompton BD, Tseng YY, Boehm JS, Ligon KL, Root DE, Murphy AJ, Weinstock DM, Gokhale PC, Spangle JM, Rivera MN, Mullen EA, Stegmaier K, Goldsmith KC, Hahn WC, Hong AL. Targeting TRIP13 in favorable histology Wilms tumor with nuclear export inhibitors synergizes with doxorubicin. Commun Biol 2024; 7:426. [PMID: 38589567 PMCID: PMC11001930 DOI: 10.1038/s42003-024-06140-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/03/2024] [Indexed: 04/10/2024] Open
Abstract
Wilms tumor (WT) is the most common renal malignancy of childhood. Despite improvements in the overall survival, relapse occurs in ~15% of patients with favorable histology WT (FHWT). Half of these patients will succumb to their disease. Identifying novel targeted therapies remains challenging in part due to the lack of faithful preclinical in vitro models. Here we establish twelve patient-derived WT cell lines and demonstrate that these models faithfully recapitulate WT biology using genomic and transcriptomic techniques. We then perform loss-of-function screens to identify the nuclear export gene, XPO1, as a vulnerability. We find that the FDA approved XPO1 inhibitor, KPT-330, suppresses TRIP13 expression, which is required for survival. We further identify synergy between KPT-330 and doxorubicin, a chemotherapy used in high-risk FHWT. Taken together, we identify XPO1 inhibition with KPT-330 as a potential therapeutic option to treat FHWTs and in combination with doxorubicin, leads to durable remissions in vivo.
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Affiliation(s)
- Karuna Mittal
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Garrett W Cooper
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Benjamin P Lee
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Yongdong Su
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Katie T Skinner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jenny Shim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Hunter C Jonus
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Won Jun Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mihir Doshi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diego Almanza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bryan D Kynnap
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amanda L Christie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xiaoping Yang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Brittaney A Leeper
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Bhakti Dwivedi
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Taylor Lawrence
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Manali Rupji
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Paula Keskula
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie Meyer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine M Clinton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Manoj Bhasin
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Brian D Crompton
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yuen-Yi Tseng
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew J Murphy
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Merck & Co., Rahway, NJ, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jennifer M Spangle
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Miguel N Rivera
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth A Mullen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kimberly Stegmaier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kelly C Goldsmith
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Andrew L Hong
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA.
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.
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2
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Marino-Enriquez A, Novotny JP, Gulhan DC, Klooster I, Tran AV, Kasbo M, Lundberg MZ, Ou WB, Tao DL, Pilco-Janeta DF, Mao VY, Zenke FT, Leeper BA, Gokhale PC, Cowley GS, Baker LH, Ballman KV, Root DE, Albers J, Park PJ, George S, Fletcher JA. Hyper-Dependence on NHEJ Enables Synergy between DNA-PK Inhibitors and Low-Dose Doxorubicin in Leiomyosarcoma. Clin Cancer Res 2023; 29:5128-5139. [PMID: 37773632 PMCID: PMC10841464 DOI: 10.1158/1078-0432.ccr-23-0998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/18/2023] [Accepted: 09/27/2023] [Indexed: 10/01/2023]
Abstract
PURPOSE Leiomyosarcoma (LMS) is an aggressive sarcoma for which standard chemotherapies achieve response rates under 30%. There are no effective targeted therapies against LMS. Most LMS are characterized by chromosomal instability (CIN), resulting in part from TP53 and RB1 co-inactivation and DNA damage repair defects. We sought to identify therapeutic targets that could exacerbate intrinsic CIN and DNA damage in LMS, inducing lethal genotoxicity. EXPERIMENTAL DESIGN We performed clinical targeted sequencing in 287 LMS and genome-wide loss-of-function screens in 3 patient-derived LMS cell lines, to identify LMS-specific dependencies. We validated candidate targets by biochemical and cell-response assays in vitro and in seven mouse models. RESULTS Clinical targeted sequencing revealed a high burden of somatic copy-number alterations (median fraction of the genome altered =0.62) and demonstrated homologous recombination deficiency signatures in 35% of LMS. Genome-wide short hairpin RNA screens demonstrated PRKDC (DNA-PKcs) and RPA2 essentiality, consistent with compensatory nonhomologous end joining (NHEJ) hyper-dependence. DNA-PK inhibitor combinations with unconventionally low-dose doxorubicin had synergistic activity in LMS in vitro models. Combination therapy with peposertib and low-dose doxorubicin (standard or liposomal formulations) inhibited growth of 5 of 7 LMS mouse models without toxicity. CONCLUSIONS Combinations of DNA-PK inhibitors with unconventionally low, sensitizing, doxorubicin dosing showed synergistic effects in LMS in vitro and in vivo models, without discernable toxicity. These findings underscore the relevance of DNA damage repair alterations in LMS pathogenesis and identify dependence on NHEJ as a clinically actionable vulnerability in LMS.
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Affiliation(s)
- Adrian Marino-Enriquez
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jan Philipp Novotny
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Doga C. Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Isabella Klooster
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Antuan V. Tran
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Macy Kasbo
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Meijun Z. Lundberg
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Wen-Bin Ou
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Derrick L. Tao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel F. Pilco-Janeta
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Sarcoma Translational Research Laboratory, Vall d’Hebron Institute of Oncology, Autonomous University of Barcelona, Barcelona, Spain
| | - Victor Y. Mao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Frank T. Zenke
- Research Unit Oncology, the healthcare business of Merck KGaA, Darmstadt, Germany
| | - Brittaney A. Leeper
- Experimental Therapeutics Core and the Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Prafulla C. Gokhale
- Experimental Therapeutics Core and the Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Karla V. Ballman
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, New York
| | - David E. Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joachim Albers
- Research Unit Oncology, the healthcare business of Merck KGaA, Darmstadt, Germany
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Suzanne George
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jonathan A. Fletcher
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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3
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Eller C, Heydmann L, Colpitts CC, El Saghire H, Piccioni F, Jühling F, Majzoub K, Pons C, Bach C, Lucifora J, Lupberger J, Nassal M, Cowley GS, Fujiwara N, Hsieh SY, Hoshida Y, Felli E, Pessaux P, Sureau C, Schuster C, Root DE, Verrier ER, Baumert TF. A genome-wide gain-of-function screen identifies CDKN2C as a HBV host factor. Nat Commun 2020; 11:2707. [PMID: 32483149 PMCID: PMC7264273 DOI: 10.1038/s41467-020-16517-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 05/03/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic HBV infection is a major cause of liver disease and cancer worldwide. Approaches for cure are lacking, and the knowledge of virus-host interactions is still limited. Here, we perform a genome-wide gain-of-function screen using a poorly permissive hepatoma cell line to uncover host factors enhancing HBV infection. Validation studies in primary human hepatocytes identified CDKN2C as an important host factor for HBV replication. CDKN2C is overexpressed in highly permissive cells and HBV-infected patients. Mechanistic studies show a role for CDKN2C in inducing cell cycle G1 arrest through inhibition of CDK4/6 associated with the upregulation of HBV transcription enhancers. A correlation between CDKN2C expression and disease progression in HBV-infected patients suggests a role in HBV-induced liver disease. Taken together, we identify a previously undiscovered clinically relevant HBV host factor, allowing the development of improved infectious model systems for drug discovery and the study of the HBV life cycle.
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Affiliation(s)
- Carla Eller
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Laura Heydmann
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Che C Colpitts
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Houssein El Saghire
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Federica Piccioni
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Frank Jühling
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Karim Majzoub
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Caroline Pons
- Inserm, U1052, Cancer Research Center of Lyon (CRCL), Université de Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard, Lyon, France
| | - Charlotte Bach
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Julie Lucifora
- Inserm, U1052, Cancer Research Center of Lyon (CRCL), Université de Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard, Lyon, France
| | - Joachim Lupberger
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Glenn S Cowley
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Naoto Fujiwara
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sen-Yung Hsieh
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emanuele Felli
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000, Strasbourg, France
| | - Patrick Pessaux
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000, Strasbourg, France
| | - Camille Sureau
- Laboratoire de Virologie Moléculaire, INTS, Paris, France
| | - Catherine Schuster
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Eloi R Verrier
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France.
| | - Thomas F Baumert
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France.
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000, Strasbourg, France.
- Institut Universitaire de France (IUF), Paris, France.
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4
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Bandopadhayay P, Piccioni F, O'Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin JR, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun 2019; 10:2400. [PMID: 31160565 PMCID: PMC6546744 DOI: 10.1038/s41467-019-10307-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/25/2019] [Indexed: 12/26/2022] Open
Abstract
BET-bromodomain inhibition (BETi) has shown pre-clinical promise for MYC-amplified medulloblastoma. However, the mechanisms for its action, and ultimately for resistance, have not been fully defined. Here, using a combination of expression profiling, genome-scale CRISPR/Cas9-mediated loss of function and ORF/cDNA driven rescue screens, and cell-based models of spontaneous resistance, we identify bHLH/homeobox transcription factors and cell-cycle regulators as key genes mediating BETi's response and resistance. Cells that acquire drug tolerance exhibit a more neuronally differentiated cell-state and expression of lineage-specific bHLH/homeobox transcription factors. However, they do not terminally differentiate, maintain expression of CCND2, and continue to cycle through S-phase. Moreover, CDK4/CDK6 inhibition delays acquisition of resistance. Therefore, our data provide insights about the mechanisms underlying BETi effects and the appearance of resistance and support the therapeutic use of combined cell-cycle inhibitors with BETi in MYC-amplified medulloblastoma.
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Affiliation(s)
- Pratiti Bandopadhayay
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | - Ryan O'Rourke
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Patricia Ho
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Elizabeth M Gonzalez
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Graham Buchan
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Kenin Qian
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Gabrielle Gionet
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Emily Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Margo Coxon
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | | | - Lisa Brenan
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Frank Dubois
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Ofer Shapira
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Noah F Greenwald
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, USA
| | - Melanie Pages
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Amanda Balboni Iniguez
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Brenton R Paolella
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Alice Meng
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Claire Sinai
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Giovanni Roti
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine and Surgery, Hematology and BMT, University of Parma, Parma, Italy
| | - Neekesh V Dharia
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | | | - Prasidda Khadka
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Adam Tracy
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Hong L Tiv
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Boston, USA
| | - Andrew L Hong
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Shannon Coy
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - Rumana Rashid
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, USA
| | - Glenn S Cowley
- Broad Institute of MIT and Harvard, Cambridge, USA
- Discovery Science, Janssen Research and Development (Johnson & Johnson), Spring House, PA, USA
| | - Fred C Lam
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Yenarae Lee
- Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
| | | | - James E Bradner
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Michael B Yaffe
- Broad Institute of MIT and Harvard, Cambridge, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Center for Child and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jun Qi
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pathology, Boston Children's Hospital, Boston, USA
| | - Mark W Kieran
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Sandro Santagata
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Boston, USA
| | | | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Kimberly Stegmaier
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | - Rameen Beroukhim
- Broad Institute of MIT and Harvard, Cambridge, USA.
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA.
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA.
- Department of Medicine, Harvard Medical School, Boston, USA.
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5
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Nandakumar SK, McFarland SK, Mateyka LM, Lareau CA, Ulirsch JC, Ludwig LS, Agarwal G, Engreitz JM, Przychodzen B, McConkey M, Cowley GS, Doench JG, Maciejewski JP, Ebert BL, Root DE, Sankaran VG. Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis. eLife 2019; 8:44080. [PMID: 31070582 PMCID: PMC6534380 DOI: 10.7554/elife.44080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 12/02/2018] [Accepted: 05/08/2019] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified thousands of variants associated with human diseases and traits. However, the majority of GWAS-implicated variants are in non-coding regions of the genome and require in depth follow-up to identify target genes and decipher biological mechanisms. Here, rather than focusing on causal variants, we have undertaken a pooled loss-of-function screen in primary hematopoietic cells to interrogate 389 candidate genes contained in 75 loci associated with red blood cell traits. Using this approach, we identify 77 genes at 38 GWAS loci, with most loci harboring 1-2 candidate genes. Importantly, the hit set was strongly enriched for genes validated through orthogonal genetic approaches. Genes identified by this approach are enriched in specific and relevant biological pathways, allowing regulators of human erythropoiesis and modifiers of blood diseases to be defined. More generally, this functional screen provides a paradigm for gene-centric follow up of GWAS for a variety of human diseases and traits.
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Affiliation(s)
- Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Sean K McFarland
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Laura M Mateyka
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Biochemistry Center (BZH), Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Caleb A Lareau
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Program in Biological and Medical Sciences, Harvard Medical School, Boston, United States
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Program in Biological and Medical Sciences, Harvard Medical School, Boston, United States
| | - Leif S Ludwig
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Gaurav Agarwal
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,University of Oxford, Oxford, United Kingdom.,Harvard Stem Cell Institute, Cambridge, United States
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, United States.,Harvard Society of Fellows, Harvard University, Cambridge, United States
| | - Bartlomiej Przychodzen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, United States
| | - Marie McConkey
- Division of Hematology, Brigham and Women's Hospital, Boston, United States
| | - Glenn S Cowley
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, United States
| | - Benjamin L Ebert
- Broad Institute of MIT and Harvard, Cambridge, United States.,Division of Hematology, Brigham and Women's Hospital, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Harvard Stem Cell Institute, Cambridge, United States
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6
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Oser MG, Fonseca R, Chakraborty AA, Brough R, Spektor A, Jennings RB, Flaifel A, Novak JS, Gulati A, Buss E, Younger ST, McBrayer SK, Cowley GS, Bonal DM, Nguyen QD, Brulle-Soumare L, Taylor P, Cairo S, Ryan CJ, Pease EJ, Maratea K, Travers J, Root DE, Signoretti S, Pellman D, Ashton S, Lord CJ, Barry ST, Kaelin WG. Cells Lacking the RB1 Tumor Suppressor Gene Are Hyperdependent on Aurora B Kinase for Survival. Cancer Discov 2019; 9:230-247. [PMID: 30373918 PMCID: PMC6368871 DOI: 10.1158/2159-8290.cd-18-0389] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/22/2018] [Accepted: 10/05/2018] [Indexed: 12/26/2022]
Abstract
Small cell lung cancer (SCLC) accounts for 15% of lung cancers and is almost always linked to inactivating RB1 and TP53 mutations. SCLC frequently responds, albeit briefly, to chemotherapy. The canonical function of the RB1 gene product RB1 is to repress the E2F transcription factor family. RB1 also plays both E2F-dependent and E2F-independent mitotic roles. We performed a synthetic lethal CRISPR/Cas9 screen in an RB1 -/- SCLC cell line that conditionally expresses RB1 to identify dependencies that are caused by RB1 loss and discovered that RB1 -/- SCLC cell lines are hyperdependent on multiple proteins linked to chromosomal segregation, including Aurora B kinase. Moreover, we show that an Aurora B kinase inhibitor is efficacious in multiple preclinical SCLC models at concentrations that are well tolerated in mice. These results suggest that RB1 loss is a predictive biomarker for sensitivity to Aurora B kinase inhibitors in SCLC and perhaps other RB1 -/- cancers. SIGNIFICANCE: SCLC is rarely associated with actionable protooncogene mutations. We did a CRISPR/Cas9-based screen that showed that RB1 -/- SCLC are hyperdependent on AURKB, likely because both genes control mitotic fidelity, and confirmed that Aurora B kinase inhibitors are efficacious against RB1 -/- SCLC tumors in mice at nontoxic doses.See related commentary by Dick and Li, p. 169.This article is highlighted in the In This Issue feature, p. 151.
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Affiliation(s)
- Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Raquel Fonseca
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Abhishek A Chakraborty
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Alexander Spektor
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Rebecca B Jennings
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Abdallah Flaifel
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jesse S Novak
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aditi Gulati
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Elizabeth Buss
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Scott T Younger
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Samuel K McBrayer
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Dennis M Bonal
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Paula Taylor
- IMED Oncology, AstraZeneca, Cheshire, United Kingdom
| | | | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Republic of Ireland
| | | | - Kim Maratea
- IMED Drug Safety and Metabolism, AstraZeneca, Boston, Massachusetts
| | - Jon Travers
- IMED Oncology, AstraZeneca, Cheshire, United Kingdom
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - David Pellman
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Susan Ashton
- IMED Oncology, AstraZeneca, Cheshire, United Kingdom
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Simon T Barry
- IMED Oncology, AstraZeneca, Cambridge, United Kingdom
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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7
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Sharifnia T, Wawer MJ, Chen T, Huang QY, Weir BA, Sizemore A, Lawlor MA, Goodale A, Cowley GS, Vazquez F, Ott CJ, Francis JM, Sassi S, Cogswell P, Sheppard HE, Zhang T, Gray NS, Clarke PA, Blagg J, Workman P, Sommer J, Hornicek F, Root DE, Hahn WC, Bradner JE, Wong KK, Clemons PA, Lin CY, Kotz JD, Schreiber SL. Small-molecule targeting of brachyury transcription factor addiction in chordoma. Nat Med 2019; 25:292-300. [PMID: 30664779 PMCID: PMC6633917 DOI: 10.1038/s41591-018-0312-3] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [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] [Received: 01/22/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Chordoma is a primary bone cancer with no approved therapy1. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors2,3. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation. In other cancer types, transcriptional CDK inhibitors have been observed to downregulate highly expressed, enhancer-associated oncogenic transcription factors4,5. In chordoma, we find that T is associated with a 1.5-Mb region containing 'super-enhancers' and is the most highly expressed super-enhancer-associated transcription factor. Notably, transcriptional CDK inhibition leads to preferential and concentration-dependent downregulation of cellular brachyury protein levels in all models tested. In vivo, CDK7/12/13-inhibitor treatment substantially reduces tumor growth. Together, these data demonstrate small-molecule targeting of brachyury transcription factor addiction in chordoma, identify a mechanism of T gene regulation that underlies this therapeutic strategy, and provide a blueprint for applying systematic genetic and chemical screening approaches to discover vulnerabilities in genomically quiet cancers.
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Affiliation(s)
| | | | - Ting Chen
- New York University Langone Medical Center, New York, NY, USA
| | - Qing-Yuan Huang
- New York University Langone Medical Center, New York, NY, USA
- Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Barbara A Weir
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Janssen R&D, Cambridge, MA, USA
| | - Ann Sizemore
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew A Lawlor
- Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital, Charlestown, MA, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Janssen R&D, Spring House, PA, USA
| | | | - Christopher J Ott
- Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital, Charlestown, MA, USA
| | - Joshua M Francis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Gritstone Oncology, Cambridge, MA, USA
| | - Slim Sassi
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | | | - Francis Hornicek
- Massachusetts General Hospital, Boston, MA, USA
- UCLA Medical Center, Santa Monica, CA, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Dana-Farber Cancer Institute, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Kwok K Wong
- New York University Langone Medical Center, New York, NY, USA
| | | | | | - Joanne D Kotz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Jnana Therapeutics, Boston, MA, USA.
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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8
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Sievers QL, Gasser JA, Cowley GS, Fischer ES, Ebert BL. Genome-wide screen identifies cullin-RING ligase machinery required for lenalidomide-dependent CRL4 CRBN activity. Blood 2018; 132:1293-1303. [PMID: 30042095 PMCID: PMC6148446 DOI: 10.1182/blood-2018-01-821769] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [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] [Received: 01/05/2018] [Accepted: 07/02/2018] [Indexed: 12/20/2022] Open
Abstract
Lenalidomide mediates the ubiquitination and degradation of Ikaros family zinc finger protein 1 (IKZF1), IKZF3, and casein kinase 1α (CK1α) by facilitating their interaction with cereblon (CRBN), the substrate receptor for the CRL4CRBN E3 ubiquitin ligase. Through this mechanism, lenalidomide is a clinically effective treatment of multiple myeloma and myelodysplastic syndrome (MDS) with deletion of chromosome 5q [del(5q) MDS]. To identify the cellular machinery required for lenalidomide-induced CRL4CRBN activity, we performed a positive selection, genome-scale clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) screen in a lenalidomide-sensitive myeloma cell line. CRBN was the top-ranking gene, with all CRBN-targeting guide RNAs (gRNAs) ranking as the 6 highest-scoring gRNAs. A counterscreen using an IKZF3 degron reporter to assay lenalidomide-induced protein degradation highlighted regulators of cullin-RING ligase neddylation and 2 E2 ubiquitin-conjugating enzymes as necessary for efficient lenalidomide-induced protein degradation. We demonstrated that loss of UBE2M or members of the constitutive photomorphogenesis 9 (COP9) signalosome results in altered neddylation of cullin 4A and impairs lenalidomide-dependent CRL4CRBN activity. Additionally, we established that UBE2D3 and UBE2G1 play distinct roles in substrate ubiquitination by CRL4CRBN, with UBE2D3 acting to prime targets via monoubiquitination and UBE2G1 functioning to extend polyubiquitin chains with lysine 48 linkages. The validation of UBE2D3 and UBE2G1 highlights the functional capacity of CRISPR-Cas9 screening to identify E2 ubiquitin-conjugating enzyme and E3 ubiquitin ligase complex pairings. More broadly, these findings establish key proteins required for lenalidomide-dependent CRL4CRBN function in myeloma and inform potential mechanisms of drug resistance.
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Affiliation(s)
- Quinlan L Sievers
- Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Hematology, Brigham and Women's Hospital, and
- MD/PhD Program, Harvard Medical School, Boston, MA
| | - Jessica A Gasser
- Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Hematology, Brigham and Women's Hospital, and
| | | | - Eric S Fischer
- Department of Chemical Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA; and
| | - Benjamin L Ebert
- Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Hematology, Brigham and Women's Hospital, and
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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9
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Chen L, Alexe G, Dharia NV, Ross L, Iniguez AB, Conway AS, Wang EJ, Veschi V, Lam N, Qi J, Gustafson WC, Nasholm N, Vazquez F, Weir BA, Cowley GS, Ali LD, Pantel S, Jiang G, Harrington WF, Lee Y, Goodale A, Lubonja R, Krill-Burger JM, Meyers RM, Tsherniak A, Root DE, Bradner JE, Golub TR, Roberts CW, Hahn WC, Weiss WA, Thiele CJ, Stegmaier K. CRISPR-Cas9 screen reveals a MYCN-amplified neuroblastoma dependency on EZH2. J Clin Invest 2017; 128:446-462. [PMID: 29202477 DOI: 10.1172/jci90793] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/24/2017] [Indexed: 12/26/2022] Open
Abstract
Pharmacologically difficult targets, such as MYC transcription factors, represent a major challenge in cancer therapy. For the childhood cancer neuroblastoma, amplification of the oncogene MYCN is associated with high-risk disease and poor prognosis. Here, we deployed genome-scale CRISPR-Cas9 screening of MYCN-amplified neuroblastoma and found a preferential dependency on genes encoding the polycomb repressive complex 2 (PRC2) components EZH2, EED, and SUZ12. Genetic and pharmacological suppression of EZH2 inhibited neuroblastoma growth in vitro and in vivo. Moreover, compared with neuroblastomas without MYCN amplification, MYCN-amplified neuroblastomas expressed higher levels of EZH2. ChIP analysis showed that MYCN binds at the EZH2 promoter, thereby directly driving expression. Transcriptomic and epigenetic analysis, as well as genetic rescue experiments, revealed that EZH2 represses neuronal differentiation in neuroblastoma in a PRC2-dependent manner. Moreover, MYCN-amplified and high-risk primary tumors from patients with neuroblastoma exhibited strong repression of EZH2-regulated genes. Additionally, overexpression of IGFBP3, a direct EZH2 target, suppressed neuroblastoma growth in vitro and in vivo. We further observed strong synergy between histone deacetylase inhibitors and EZH2 inhibitors. Together, these observations demonstrate that MYCN upregulates EZH2, leading to inactivation of a tumor suppressor program in neuroblastoma, and support testing EZH2 inhibitors in patients with MYCN-amplified neuroblastoma.
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Affiliation(s)
- Liying Chen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Linda Ross
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA
| | - Amanda Balboni Iniguez
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
| | - Amy Saur Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA
| | - Emily Jue Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA
| | - Veronica Veschi
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Norris Lam
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - W Clay Gustafson
- Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | - Nicole Nasholm
- Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | | | | | | | - Levi D Ali
- Broad Institute, Cambridge, Massachusetts, USA
| | | | | | | | - Yenarae Lee
- Broad Institute, Cambridge, Massachusetts, USA
| | - Amy Goodale
- Broad Institute, Cambridge, Massachusetts, USA
| | | | | | | | | | | | - James E Bradner
- Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Todd R Golub
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Charles Wm Roberts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.,Comprehensive Cancer Center and Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - William C Hahn
- Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - William A Weiss
- Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA.,Department of Neurology, Neurological Surgery, Brain Tumor Research Center, UCSF, San Francisco, California, USA
| | - Carol J Thiele
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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10
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Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, Dharia NV, Montgomery PG, Cowley GS, Pantel S, Goodale A, Lee Y, Ali LD, Jiang G, Lubonja R, Harrington WF, Strickland M, Wu T, Hawes DC, Zhivich VA, Wyatt MR, Kalani Z, Chang JJ, Okamoto M, Stegmaier K, Golub TR, Boehm JS, Vazquez F, Root DE, Hahn WC, Tsherniak A. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet 2017. [PMID: 29083409 DOI: 10.1038/ng.3984.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The CRISPR-Cas9 system has revolutionized gene editing both at single genes and in multiplexed loss-of-function screens, thus enabling precise genome-scale identification of genes essential for proliferation and survival of cancer cells. However, previous studies have reported that a gene-independent antiproliferative effect of Cas9-mediated DNA cleavage confounds such measurement of genetic dependency, thereby leading to false-positive results in copy number-amplified regions. We developed CERES, a computational method to estimate gene-dependency levels from CRISPR-Cas9 essentiality screens while accounting for the copy number-specific effect. In our efforts to define a cancer dependency map, we performed genome-scale CRISPR-Cas9 essentiality screens across 342 cancer cell lines and applied CERES to this data set. We found that CERES decreased false-positive results and estimated sgRNA activity for both this data set and previously published screens performed with different sgRNA libraries. We further demonstrate the utility of this collection of screens, after CERES correction, for identifying cancer-type-specific vulnerabilities.
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Affiliation(s)
- Robin M Meyers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jordan G Bryan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Barbara A Weir
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ann E Sizemore
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Han Xu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Neekesh V Dharia
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | | | - Glenn S Cowley
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sasha Pantel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yenarae Lee
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Levi D Ali
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Guozhi Jiang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rakela Lubonja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Ting Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Derek C Hawes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Victor A Zhivich
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Meghan R Wyatt
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Zohra Kalani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jaime J Chang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael Okamoto
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kimberly Stegmaier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Francisca Vazquez
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Aviad Tsherniak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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11
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Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, Dharia NV, Montgomery PG, Cowley GS, Pantel S, Goodale A, Lee Y, Ali LD, Jiang G, Lubonja R, Harrington WF, Strickland M, Wu T, Hawes DC, Zhivich VA, Wyatt MR, Kalani Z, Chang JJ, Okamoto M, Stegmaier K, Golub TR, Boehm JS, Vazquez F, Root DE, Hahn WC, Tsherniak A. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet 2017; 49:1779-1784. [PMID: 29083409 PMCID: PMC5709193 DOI: 10.1038/ng.3984] [Citation(s) in RCA: 1096] [Impact Index Per Article: 156.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023]
Abstract
The CRISPR-Cas9 system has revolutionized gene editing both on single genes and in multiplexed loss-of-function screens, enabling precise genome-scale identification of genes essential to proliferation and survival of cancer cells1,2. However, previous studies reported that a gene-independent anti-proliferative effect of Cas9-mediated DNA cleavage confounds such measurement of genetic dependency, leading to false positive results in copy number amplified regions3,4. We developed CERES, a computational method to estimate gene dependency levels from CRISPR-Cas9 essentiality screens while accounting for the copy-number-specific effect. As part of our efforts to define a cancer dependency map, we performed genome-scale CRISPR-Cas9 essentiality screens across 342 cancer cell lines and applied CERES to this dataset. We found that CERES reduced false positive results and estimated sgRNA activity for both this dataset and previously published screens performed with different sgRNA libraries. Here, we demonstrate the utility of this collection of screens, upon CERES correction, in revealing cancer-type-specific vulnerabilities.
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Affiliation(s)
- Robin M Meyers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jordan G Bryan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Barbara A Weir
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ann E Sizemore
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Han Xu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Neekesh V Dharia
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | | | - Glenn S Cowley
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sasha Pantel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yenarae Lee
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Levi D Ali
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Guozhi Jiang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rakela Lubonja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Ting Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Derek C Hawes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Victor A Zhivich
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Meghan R Wyatt
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Zohra Kalani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jaime J Chang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael Okamoto
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kimberly Stegmaier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Francisca Vazquez
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Aviad Tsherniak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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12
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Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Syst 2017; 5:485-497.e3. [PMID: 28988802 DOI: 10.1016/j.cels.2017.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 06/18/2017] [Accepted: 09/07/2017] [Indexed: 12/18/2022]
Abstract
We report the results of a DREAM challenge designed to predict relative genetic essentialities based on a novel dataset testing 98,000 shRNAs against 149 molecularly characterized cancer cell lines. We analyzed the results of over 3,000 submissions over a period of 4 months. We found that algorithms combining essentiality data across multiple genes demonstrated increased accuracy; gene expression was the most informative molecular data type; the identity of the gene being predicted was far more important than the modeling strategy; well-predicted genes and selected molecular features showed enrichment in functional categories; and frequently selected expression features correlated with survival in primary tumors. This study establishes benchmarks for gene essentiality prediction, presents a community resource for future comparison with this benchmark, and provides insights into factors influencing the ability to predict gene essentiality from functional genetic screens. This study also demonstrates the value of releasing pre-publication data publicly to engage the community in an open research collaboration.
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Affiliation(s)
- Mehmet Gönen
- Department of Industrial Engineering, College of Engineering, Koç University, İstanbul, Turkey; School of Medicine, Koç University, İstanbul, Turkey; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | | | - Glenn S Cowley
- Genetic Perturbation Platform, The Broad Institute, Boston, MA, USA; Janssen R&D US, Spring House, PA, USA
| | - Francisca Vazquez
- Cancer Program, The Broad Institute, Boston, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Alok Jaiswal
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Masayuki Karasuyama
- Department of Computer Science, Nagoya Institute of Technology, Nagoya, Japan
| | - Vladislav Uzunangelov
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA; Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Sara Howell
- Cancer Program, The Broad Institute, Boston, MA, USA; Brandeis University, Waltham, MA, USA
| | - Daniel Marbach
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Antti Airola
- Department of Information Technology, University of Turku, Turku, Finland
| | - Adrian Bivol
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Kerstin Bunte
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland; School of Computer Science, The University of Birmingham, Birmingham, UK
| | - Daniel Carlin
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Sahil Chopra
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Alden Deran
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Kyle Ellrott
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | | | - Kiley Graim
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Samuel Kaski
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland; Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Suleiman A Khan
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Yulia Newton
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Sam Ng
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Tapio Pahikkala
- Department of Information Technology, University of Turku, Turku, Finland
| | - Evan Paull
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Artem Sokolov
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Hao Tang
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jing Tang
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaowei Zhan
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA; Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Fan Zhu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | | | - Tero Aittokallio
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland; Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Hiroshi Mamitsuka
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Joshua M Stuart
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Jesse S Boehm
- Cancer Program, The Broad Institute, Boston, MA, USA
| | - David E Root
- Genetic Perturbation Platform, The Broad Institute, Boston, MA, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gustavo Stolovitzky
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - William C Hahn
- Cancer Program, The Broad Institute, Boston, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Adam A Margolin
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR, USA.
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13
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Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, Gill S, Harrington WF, Pantel S, Krill-Burger JM, Meyers RM, Ali L, Goodale A, Lee Y, Jiang G, Hsiao J, Gerath WFJ, Howell S, Merkel E, Ghandi M, Garraway LA, Root DE, Golub TR, Boehm JS, Hahn WC. Defining a Cancer Dependency Map. Cell 2017; 170:564-576.e16. [PMID: 28753430 DOI: 10.1016/j.cell.2017.06.010] [Citation(s) in RCA: 1405] [Impact Index Per Article: 200.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/09/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022]
Abstract
Most human epithelial tumors harbor numerous alterations, making it difficult to predict which genes are required for tumor survival. To systematically identify cancer dependencies, we analyzed 501 genome-scale loss-of-function screens performed in diverse human cancer cell lines. We developed DEMETER, an analytical framework that segregates on- from off-target effects of RNAi. 769 genes were differentially required in subsets of these cell lines at a threshold of six SDs from the mean. We found predictive models for 426 dependencies (55%) by nonlinear regression modeling considering 66,646 molecular features. Many dependencies fall into a limited number of classes, and unexpectedly, in 82% of models, the top biomarkers were expression based. We demonstrated the basis behind one such predictive model linking hypermethylation of the UBB ubiquitin gene to a dependency on UBC. Together, these observations provide a foundation for a cancer dependency map that facilitates the prioritization of therapeutic targets.
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Affiliation(s)
- Aviad Tsherniak
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Francisca Vazquez
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Phil G Montgomery
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Barbara A Weir
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Gregory Kryukov
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Stanley Gill
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | | | - Sasha Pantel
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | | | - Robin M Meyers
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Levi Ali
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Yenarae Lee
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Guozhi Jiang
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Jessica Hsiao
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | | | - Sara Howell
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Erin Merkel
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Mahmoud Ghandi
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Levi A Garraway
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, USA
| | - David E Root
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Todd R Golub
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, USA
| | - Jesse S Boehm
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA, USA.
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14
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Chakraborty AA, Nakamura E, Qi J, Creech A, Jaffe JD, Paulk J, Novak JS, Nagulapalli K, McBrayer SK, Cowley GS, Pineda J, Song J, Wang YE, Carr SA, Root DE, Signoretti S, Bradner JE, Kaelin WG. HIF activation causes synthetic lethality between the VHL tumor suppressor and the EZH1 histone methyltransferase. Sci Transl Med 2017; 9:eaal5272. [PMID: 28701475 PMCID: PMC6039096 DOI: 10.1126/scitranslmed.aal5272] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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] [Received: 12/05/2016] [Accepted: 06/10/2017] [Indexed: 12/13/2022]
Abstract
Inactivation of the von Hippel-Lindau tumor suppressor protein (pVHL) is the signature lesion in the most common form of kidney cancer, clear cell renal cell carcinoma (ccRCC). pVHL loss causes the transcriptional activation of hypoxia-inducible factor (HIF) target genes, including many genes that encode histone lysine demethylases. Moreover, chromatin regulators are frequently mutated in this disease. We found that ccRCC displays increased H3K27 acetylation and a shift toward mono- or unmethylated H3K27 caused by an HIF-dependent increase in H3K27 demethylase activity. Using a focused short hairpin RNA library, as well as CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) and a pharmacological inhibitor, we discovered that pVHL-defective ccRCC cells are hyperdependent on the H3K27 methyltransferase EZH1 for survival. Therefore, targeting EZH1 could be therapeutically useful in ccRCC.
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Affiliation(s)
- Abhishek A Chakraborty
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Eijiro Nakamura
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Amanda Creech
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jacob D Jaffe
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Jesse S Novak
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kshithija Nagulapalli
- Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Samuel K McBrayer
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Glenn S Cowley
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Javier Pineda
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Jiaxi Song
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yaoyu E Wang
- Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Steven A Carr
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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15
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Hsu JHR, Hubbell-Engler B, Adelmant G, Huang J, Joyce CE, Vazquez F, Weir BA, Montgomery P, Tsherniak A, Giacomelli AO, Perry JA, Trowbridge J, Fujiwara Y, Cowley GS, Xie H, Kim W, Novina CD, Hahn WC, Marto JA, Orkin SH. PRMT1-Mediated Translation Regulation Is a Crucial Vulnerability of Cancer. Cancer Res 2017; 77:4613-4625. [PMID: 28655788 DOI: 10.1158/0008-5472.can-17-0216] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/10/2017] [Accepted: 06/21/2017] [Indexed: 12/20/2022]
Abstract
Through an shRNA screen, we identified the protein arginine methyltransferase Prmt1 as a vulnerable intervention point in murine p53/Rb-null osteosarcomas, the human counterpart of which lacks effective therapeutic options. Depletion of Prmt1 in p53-deficient cells impaired tumor initiation and maintenance in vitro and in vivo Mechanistic studies reveal that translation-associated pathways were enriched for Prmt1 downstream targets, implicating Prmt1 in translation control. In particular, loss of Prmt1 led to a decrease in arginine methylation of the translation initiation complex, thereby disrupting its assembly and inhibiting translation. p53/Rb-null cells were sensitive to p53-induced translation stress, and analysis of human cancer cell line data from Project Achilles further revealed that Prmt1 and translation-associated pathways converged on the same functional networks. We propose that targeted therapy against Prmt1 and its associated translation-related pathways offer a mechanistic rationale for treatment of osteosarcomas and other cancers that exhibit dependencies on translation stress response. Cancer Res; 77(17); 4613-25. ©2017 AACR.
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Affiliation(s)
- Jessie Hao-Ru Hsu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
| | - Benjamin Hubbell-Engler
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
| | - Guillaume Adelmant
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Jialiang Huang
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts
| | - Cailin E Joyce
- Department of Cancer Immunology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Barbara A Weir
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Aviad Tsherniak
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Andrew O Giacomelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer A Perry
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Yuko Fujiwara
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
| | - Glenn S Cowley
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Huafeng Xie
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
| | - Woojin Kim
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
| | - Carl D Novina
- Department of Cancer Immunology, Dana-Farber Cancer Institute, Boston, Massachusetts.,The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - William C Hahn
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jarrod A Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts. .,Howard Hughes Medical Institute, Boston, Massachusetts
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16
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Vu LP, Prieto C, Amin EM, Chhangawala S, Krivtsov A, Calvo-Vidal MN, Chou T, Chow A, Minuesa G, Park SM, Barlowe TS, Taggart J, Tivnan P, Deering RP, Chu LP, Kwon JA, Meydan C, Perales-Paton J, Arshi A, Gönen M, Famulare C, Patel M, Paietta E, Tallman MS, Lu Y, Glass J, Garret-Bakelman FE, Melnick A, Levine R, Al-Shahrour F, Järås M, Hacohen N, Hwang A, Garippa R, Lengner CJ, Armstrong SA, Cerchietti L, Cowley GS, Root D, Doench J, Leslie C, Ebert BL, Kharas MG. Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells. Nat Genet 2017; 49:866-875. [PMID: 28436985 PMCID: PMC5508533 DOI: 10.1038/ng.3854] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [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: 10/30/2016] [Accepted: 03/31/2017] [Indexed: 12/15/2022]
Abstract
The identity of the RNA-binding proteins (RBPs) that govern cancer stem cells remains poorly characterized. The MSI2 RBP is a central regulator of translation of cancer stem cell programs. Through proteomic analysis of the MSI2-interacting RBP network and functional shRNA screening, we identified 24 genes required for in vivo leukemia. Syncrip was the most differentially required gene between normal and myeloid leukemia cells. SYNCRIP depletion increased apoptosis and differentiation while delaying leukemogenesis. Gene expression profiling of SYNCRIP-depleted cells demonstrated a loss of the MLL and HOXA9 leukemia stem cell program. SYNCRIP and MSI2 interact indirectly though shared mRNA targets. SYNCRIP maintains HOXA9 translation, and MSI2 or HOXA9 overexpression rescued the effects of SYNCRIP depletion. Altogether, our data identify SYNCRIP as a new RBP that controls the myeloid leukemia stem cell program. We propose that targeting these RBP complexes might provide a novel therapeutic strategy in leukemia.
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Affiliation(s)
- Ly P Vu
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Camila Prieto
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
| | - Elianna M Amin
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sagar Chhangawala
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA.,Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrei Krivtsov
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - M Nieves Calvo-Vidal
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medical College, New York, New York, USA
| | - Timothy Chou
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Arthur Chow
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gerard Minuesa
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sun Mi Park
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Trevor S Barlowe
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James Taggart
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Patrick Tivnan
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Lisa P Chu
- Division of Hematology, Brigham and Woman's Hospital, Boston, Massachusetts, USA
| | | | - Cem Meydan
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
| | - Javier Perales-Paton
- Translational Bioinformatics Unit, Clinical Research Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Arora Arshi
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christopher Famulare
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Minal Patel
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Elisabeth Paietta
- Department of Medicine, Montefiore Medical Center, Bronx, New York, USA
| | - Martin S Tallman
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Hospital, New York, New York, USA
| | - Yuheng Lu
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jacob Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Hospital, New York, New York, USA
| | - Francine E Garret-Bakelman
- Department of Medicine and Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA.,Division of Hematology and Medical Oncology, Departments of Medicine and Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Ari Melnick
- Division of Hematology and Medical Oncology, Departments of Medicine and Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Fatima Al-Shahrour
- Translational Bioinformatics Unit, Clinical Research Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Marcus Järås
- Department of Clinical Genetics, Lund University, Lund, Sweden
| | - Nir Hacohen
- Harvard Medical School, Boston, Massachusetts, USA
| | - Alexia Hwang
- RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ralph Garippa
- RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christopher J Lengner
- Department of Animal Biology, Department of Cell and Developmental Biology, and Institute for Regenerative Medicine, Schools of Veterinary Medicine and Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Leandro Cerchietti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Glenn S Cowley
- Discovery Sciences, Janssen Research and Development, Spring House, Pennsylvania, USA
| | - David Root
- Broad Institute, Boston, Massachusetts, USA
| | | | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin L Ebert
- Division of Hematology, Brigham and Woman's Hospital, Boston, Massachusetts, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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17
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Paolella BR, Gibson WJ, Urbanski LM, Alberta JA, Zack TI, Bandopadhayay P, Nichols CA, Agarwalla PK, Brown MS, Lamothe R, Yu Y, Choi PS, Obeng EA, Heckl D, Wei G, Wang B, Tsherniak A, Vazquez F, Weir BA, Root DE, Cowley GS, Buhrlage SJ, Stiles CD, Ebert BL, Hahn WC, Reed R, Beroukhim R. Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. eLife 2017; 6. [PMID: 28177281 PMCID: PMC5357138 DOI: 10.7554/elife.23268] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [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: 11/14/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent. One of these, the pre-mRNA splicing factor SF3B1, is also frequently mutated in cancer. We validated SF3B1 as a CYCLOPS gene and found that human cancer cells harboring partial SF3B1 copy-loss lack a reservoir of SF3b complex that protects cells with normal SF3B1 copy number from cell death upon partial SF3B1 suppression. These data provide a catalog of copy-number associated gene dependencies and identify partial copy-loss of wild-type SF3B1 as a novel, non-driver cancer gene dependency.
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Affiliation(s)
- Brenton R Paolella
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - William J Gibson
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Laura M Urbanski
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - John A Alberta
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Travis I Zack
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Pratiti Bandopadhayay
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Caitlin A Nichols
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Pankaj K Agarwalla
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Meredith S Brown
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Rebecca Lamothe
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Yong Yu
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Peter S Choi
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Esther A Obeng
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Dirk Heckl
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Guo Wei
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Belinda Wang
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Francisca Vazquez
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Barbara A Weir
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Glenn S Cowley
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Charles D Stiles
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Benjamin L Ebert
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - William C Hahn
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
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18
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Meyers RM, Aguirre AJ, Weir BA, Vazquez F, Zhang CZ, Ben-David U, Cook A, Ha G, Harrington WF, Doshi M, Gill S, Xu H, Ali LD, Jiang G, Pantel S, Lee Y, Goodale A, Cherniack AD, Oh C, Kryukov G, Cowley GS, Garraway LA, Stegmaier K, Roberts CW, Golub TR, Meyerson M, Root DE, Tsherniak A, Hahn WC. Abstract B39: Genomic copy number alterations introduce a gene-independent viability bias in CRISPR-Cas9 knock-out screens of cancer cell lines. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.pmccavuln16-b39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Recent studies have demonstrated the power of CRISPR-Cas9 screening methods for identifying genetic vulnerabilities in cancer cells. As part of a larger effort to generate a comprehensive catalog of vulnerabilities, we performed CRISPR-Cas9 genome-scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation and survival. We found a strong correlation between gene copy number and cell viability after Cas9-targeting. Copy number alterations are extremely prevalent in human cancers and frequently lead to overexpression of driver oncogenes and potential vulnerabilities. Therefore, we sought to identify such genes by investigating the relationship of genomic copy number with essentiality from our screening data.
As expected, known oncogenes scored as essential in cell lines harboring amplifications of these genes. However, the scores of all other genes in these amplified regions were also strongly enriched for apparent essentiality, even among unexpressed genes. Furthermore, the infection of cells with sgRNAs targeting Cas9 to non-coding intergenic sequences within regions of high copy number gain also induced this negative effect on cell viability. We observed this effect across multiple different chromosomal structural alterations, including tandem duplications, breakage-fusion-bridge structures, and arm-level gains. More broadly, we found a striking global correlation between cell viability in response to Cas9-targeting and the genomic copy number of the targeted site, even among low-level copy number gain and loss. For example, Cas9-targeting of genes with two copies resulted in, on average, decreased viability relative to Cas9-targeting of genes with only one copy. By examining sgRNAs that target multiple genomic sites, but not within any amplified loci, we found that this cell response to Cas9-targeting correlated strongly with the total number of target sites.
Together, these observations indicate that genome targeting by CRISPR-Cas9 elicits a gene-independent anti-proliferative cell response with a severity proportional to the total number of discrete genomic loci targeted. This effect has important practical implications for interpretation of CRISPR-Cas9 screening data and confounds the use of this technology for identification of essential genes in amplified regions. This result illustrates the sensitivity of cancer cells to site-specific DNA damage, which may provide a path to novel therapeutic strategies. Targeting non-essential genes or non-coding intergenic sequences within regions of copy number amplification may reveal cancer-specific vulnerabilities.
Citation Format: Robin M. Meyers, Andrew J. Aguirre, Barbara A. Weir, Francisca Vazquez, Cheng-Zhong Zhang, Uri Ben-David, April Cook, Gavin Ha, William F. Harrington, Mihir Doshi, Stanley Gill, Han Xu, Levi D. Ali, Guozhi Jiang, Sasha Pantel, Yenarae Lee, Amy Goodale, Andrew D. Cherniack, Coyin Oh, Gregory Kryukov, Glenn S. Cowley, Levi A. Garraway, Kimberly Stegmaier, Charles W. Roberts, Todd R. Golub, Matthew Meyerson, David E. Root, Aviad Tsherniak, William C. Hahn. Genomic copy number alterations introduce a gene-independent viability bias in CRISPR-Cas9 knock-out screens of cancer cell lines. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr B39.
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Affiliation(s)
| | | | | | | | | | | | | | - Gavin Ha
- 1Broad Institute, Cambridge, MA,
| | | | | | | | - Han Xu
- 1Broad Institute, Cambridge, MA,
| | | | | | | | | | | | | | - Coyin Oh
- 1Broad Institute, Cambridge, MA,
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19
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Aguirre AJ, Shao W, Xu H, Weir B, Vazquez F, Meyers R, Zhang CZ, Doshi M, Cowley GS, Ewachiw T, Rasheed Z, Golub TR, Stegmaier K, Roberts CW, Garraway LA, Meyerson M, Tsherniak A, Root DE, Espenshade PJ, Hahn WC. Abstract PR05: Genome-scale CRISPR-Cas9 screening to identify essential genes and pathways in pancreatic cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.panca16-pr05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Loss-of-function genetic screens in cancer cell lines permit the systematic interrogation of genes and pathways involved in cell proliferation and viability. The CRISPR-Cas9 system enables effective genome editing for perturbation of gene function. To identify genes that are essential for cancer cell proliferation and survival, we have optimized an approach for efficient genome-scale CRISPR-Cas9 pooled screening and performed negative-selection knock-out screens in 43 human cancer cell lines with diverse genetic and phenotypic features, including 8 pancreatic cancer cell lines. We report that CRISPR-Cas9 efficacy varies depending on the cell context and propose methods to effectively identify differential cancer dependencies across cell lines. Additionally, we identify a strong correlation between genomic copy number and perceived gene dependency, and further elucidate a gene-independent effect of CRISPR-Cas9 cutting. Using these screening data, we performed a detailed interrogation of gene and pathway dependencies in pancreatic cancer. Through integrative analysis of CRISPR-Cas9 screening results with RNA-interference and small molecule screening data, as well as DNA and RNA sequencing, we identified a high-confidence set of recurrently essential genes in pancreatic cancer, including several with associated biomarkers. Moreover, through pathway analyses of CRISPR-Cas9 screening data, we have identified a number of essential biologic processes including key metabolic and cell signaling pathways that may represent potential therapeutic avenues. In particular, we characterize the sterol regulatory element binding protein (SREBP) signaling pathway as a recurrent vulnerability in pancreatic cancer and credential this pathway as a potential therapeutic target.
This abstract is also being presented as Poster A13
Citation Format: Andrew J. Aguirre, Wei Shao, Han Xu, Barbara Weir, Francisca Vazquez, Robin Meyers, Cheng-Zhong Zhang, Mihir Doshi, Glenn S. Cowley, Theodore Ewachiw, Zeshaan Rasheed, Todd R. Golub, Kimberly Stegmaier, Charles W. Roberts, Levi A. Garraway, Matthew Meyerson, Aviad Tsherniak, David E. Root, Peter J. Espenshade, William C. Hahn.{Authors}. Genome-scale CRISPR-Cas9 screening to identify essential genes and pathways in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr PR05.
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Affiliation(s)
| | - Wei Shao
- 2Johns Hopkins University School of Medicine, Baltimore, MD,
| | - Han Xu
- 3Broad Institute of Harvard and MIT, Cambridge, MA,
| | - Barbara Weir
- 3Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | - Robin Meyers
- 3Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | - Mihir Doshi
- 3Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | | | - Zeshaan Rasheed
- 2Johns Hopkins University School of Medicine, Baltimore, MD,
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20
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Aguirre AJ, Meyers RM, Weir BA, Vazquez F, Zhang CZ, Ben-David U, Cook A, Ha G, Harrington WF, Doshi MB, Kost-Alimova M, Gill S, Xu H, Ali LD, Jiang G, Pantel S, Lee Y, Goodale A, Cherniack AD, Oh C, Kryukov G, Cowley GS, Garraway LA, Stegmaier K, Roberts CW, Golub TR, Meyerson M, Root DE, Tsherniak A, Hahn WC. Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting. Cancer Discov 2016; 6:914-29. [PMID: 27260156 PMCID: PMC4972686 DOI: 10.1158/2159-8290.cd-16-0154] [Citation(s) in RCA: 361] [Impact Index Per Article: 45.1] [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] [Received: 02/04/2016] [Accepted: 05/31/2016] [Indexed: 01/01/2023]
Abstract
UNLABELLED The CRISPR/Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome-scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy-number gain, CRISPR/Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G2 cell-cycle arrest. By examining single-guide RNAs that map to multiple genomic sites, we found that this cell response to CRISPR/Cas9 editing correlated strongly with the number of target loci. These observations indicate that genome targeting by CRISPR/Cas9 elicits a gene-independent antiproliferative cell response. This effect has important practical implications for the interpretation of CRISPR/Cas9 screening data and confounds the use of this technology for the identification of essential genes in amplified regions. SIGNIFICANCE We found that the number of CRISPR/Cas9-induced DNA breaks dictates a gene-independent antiproliferative response in cells. These observations have practical implications for using CRISPR/Cas9 to interrogate cancer gene function and illustrate that cancer cells are highly sensitive to site-specific DNA damage, which may provide a path to novel therapeutic strategies. Cancer Discov; 6(8); 914-29. ©2016 AACR.See related commentary by Sheel and Xue, p. 824See related article by Munoz et al., p. 900This article is highlighted in the In This Issue feature, p. 803.
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Affiliation(s)
- Andrew J Aguirre
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Robin M Meyers
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Barbara A Weir
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Francisca Vazquez
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Cheng-Zhong Zhang
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Uri Ben-David
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - April Cook
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gavin Ha
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Mihir B Doshi
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Stanley Gill
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Han Xu
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Levi D Ali
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Guozhi Jiang
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sasha Pantel
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yenarae Lee
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Coyin Oh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gregory Kryukov
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Levi A Garraway
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts. Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Kimberly Stegmaier
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Harvard Medical School, Boston, Massachusetts. Boston Children's Hospital, Boston, Massachusetts
| | - Charles W Roberts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts. St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Todd R Golub
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Harvard Medical School, Boston, Massachusetts. Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Harvard Medical School, Boston, Massachusetts. Department of Pathology, Harvard Medical School, Boston, Massachusetts. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts.
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21
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Hong AL, Tseng YY, Cowley GS, Jonas O, Cheah JH, Kynnap BD, Doshi MB, Oh C, Meyer SC, Church AJ, Gill S, Bielski CM, Keskula P, Imamovic A, Howell S, Kryukov GV, Clemons PA, Tsherniak A, Vazquez F, Crompton BD, Shamji AF, Rodriguez-Galindo C, Janeway KA, Roberts CWM, Stegmaier K, van Hummelen P, Cima MJ, Langer RS, Garraway LA, Schreiber SL, Root DE, Hahn WC, Boehm JS. Integrated genetic and pharmacologic interrogation of rare cancers. Nat Commun 2016; 7:11987. [PMID: 27329820 PMCID: PMC4917959 DOI: 10.1038/ncomms11987] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [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] [Received: 02/05/2016] [Accepted: 05/18/2016] [Indexed: 02/06/2023] Open
Abstract
Identifying therapeutic targets in rare cancers remains challenging due to the paucity of established models to perform preclinical studies. As a proof-of-concept, we developed a patient-derived cancer cell line, CLF-PED-015-T, from a paediatric patient with a rare undifferentiated sarcoma. Here, we confirm that this cell line recapitulates the histology and harbours the majority of the somatic genetic alterations found in a metastatic lesion isolated at first relapse. We then perform pooled CRISPR-Cas9 and RNAi loss-of-function screens and a small-molecule screen focused on druggable cancer targets. Integrating these three complementary and orthogonal methods, we identify CDK4 and XPO1 as potential therapeutic targets in this cancer, which has no known alterations in these genes. These observations establish an approach that integrates new patient-derived models, functional genomics and chemical screens to facilitate the discovery of targets in rare cancers.
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Affiliation(s)
- Andrew L. Hong
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Yuen-Yi Tseng
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Glenn S. Cowley
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Oliver Jonas
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Jaime H. Cheah
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Bryan D. Kynnap
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Mihir B. Doshi
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Coyin Oh
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Stephanie C. Meyer
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Alanna J. Church
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Shubhroz Gill
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Craig M. Bielski
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Paula Keskula
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Alma Imamovic
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Sara Howell
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Gregory V. Kryukov
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
| | - Paul A. Clemons
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Francisca Vazquez
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Brian D. Crompton
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Alykhan F. Shamji
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Carlos Rodriguez-Galindo
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Katherine A. Janeway
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Charles W. M. Roberts
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Kimberly Stegmaier
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Paul van Hummelen
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Michael J. Cima
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Robert S. Langer
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Levi A. Garraway
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Stuart L. Schreiber
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - David E. Root
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - William C. Hahn
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
| | - Jesse S. Boehm
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
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22
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Puram RV, Kowalczyk MS, de Boer CG, Schneider RK, Miller PG, McConkey M, Tothova Z, Tejero H, Heckl D, Järås M, Chen MC, Li H, Tamayo A, Cowley GS, Rozenblatt-Rosen O, Al-Shahrour F, Regev A, Ebert BL. Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML. Cell 2016; 165:303-16. [PMID: 27058663 PMCID: PMC4826477 DOI: 10.1016/j.cell.2016.03.015] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [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] [Received: 10/04/2015] [Revised: 01/04/2016] [Accepted: 03/09/2016] [Indexed: 01/09/2023]
Abstract
Leukemia stem cells (LSCs) have the capacity to self-renew and propagate disease upon serial transplantation in animal models, and elimination of this cell population is required for curative therapies. Here, we describe a series of pooled, in vivo RNAi screens to identify essential transcription factors (TFs) in a murine model of acute myeloid leukemia (AML) with genetically and phenotypically defined LSCs. These screens reveal the heterodimeric, circadian rhythm TFs Clock and Bmal1 as genes required for the growth of AML cells in vitro and in vivo. Disruption of canonical circadian pathway components produces anti-leukemic effects, including impaired proliferation, enhanced myeloid differentiation, and depletion of LSCs. We find that both normal and malignant hematopoietic cells harbor an intact clock with robust circadian oscillations, and genetic knockout models reveal a leukemia-specific dependence on the pathway. Our findings establish a role for the core circadian clock genes in AML.
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Affiliation(s)
- Rishi V Puram
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA
| | | | - Carl G de Boer
- Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA
| | - Rebekka K Schneider
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Peter G Miller
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Marie McConkey
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zuzana Tothova
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Héctor Tejero
- Translational Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Dirk Heckl
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatric Hematology and Oncology, Hanover Medical School, Hanover 30625, Germany
| | - Marcus Järås
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Michelle C Chen
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hubo Li
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Alfred Tamayo
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Glenn S Cowley
- Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA
| | | | - Fatima Al-Shahrour
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Translational Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Aviv Regev
- Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Benjamin L Ebert
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
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23
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Hong AL, Cowley GS, Tseng YY, Cheah JH, Jonas O, Doshi MB, Kynnap BD, Oh C, Meyer S, Clemons P, Burger M, Vazquez F, Weir B, Kryukov GV, Church A, Imamovic A, Tsherniak A, Bielski C, Crompton B, Mullen E, Roberts C, Rodriguez-Galindo C, Janeway KA, Stegmaier K, Hummelen PV, Langer R, Garraway LA, Schreiber SL, Root DE, Boehm JS, Hahn WC. Abstract B38: Developing a functional genomics platform to interrogate rare pediatric cancers. Cancer Res 2016. [DOI: 10.1158/1538-7445.pedca15-b38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Of pediatric solid tumors, as many as 10% of tumors are categorized as rare. Many of these rare tumors lack standard effective known therapy. The ability to identify vulnerabilities for many rare tumors has been significantly limited by the lack of in vitro and in vivo models. Furthermore, current approaches to study such vulnerabilities are usually limited to a specific compound or target. Our objectives were 1) to develop a platform to collect tumor samples and generate in vitro models and 2) to develop systematic and orthogonal approaches focused on currently known druggable cancer targets to identify vulnerabilities in these difficult to treat cancers. We have developed a proof of concept cell line from a patient who succumbed to progressive undifferentiated sarcoma treated on an aggressive multi-therapy regimen. This cell line, in its early passages, has novel gene fusions that match that of the primary tumor. Furthermore, even at early passages, this cell line was amenable to high throughput functional screens. Using a targeted pooled shRNA screen (employing matched seed controls) and an analogous CRISPR screen we identified dependencies to XPO1 and CDK4. In parallel, compounds against these targets were identified in a small molecule compound screen. These targetable dependencies were further validated in vivo with a micro-dosing device. These observations identify new targets in this rare malignancy. Furthermore, this suggests that the interrogation of patient derived cell lines facilitates the identification of testable therapeutic approaches.
Citation Format: Andrew L. Hong, Glenn S. Cowley, Yuen-Yi Tseng, Jaime H. Cheah, Oliver Jonas, Mihir B. Doshi, Bryan D. Kynnap, Coyin Oh, Stephanie Meyer, Paul Clemons, Michael Burger, Francisca Vazquez, Barbara Weir, Gregory V. Kryukov, Alanna Church, Alma Imamovic, Aviad Tsherniak, Craig Bielski, Brian Crompton, Elizabeth Mullen, Charles Roberts, Carlos Rodriguez-Galindo, Katherine A. Janeway, Kimberly Stegmaier, Paul van Hummelen, Robert Langer, Levi A. Garraway, Stuart L. Schreiber, David E. Root, Jesse S. Boehm, William C. Hahn. Developing a functional genomics platform to interrogate rare pediatric cancers. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B38.
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Affiliation(s)
| | | | | | - Jaime H. Cheah
- 3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA,
| | - Oliver Jonas
- 3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA,
| | | | | | - Coyin Oh
- 2Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | - Paul Clemons
- 2Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | | | - Barbara Weir
- 2Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | | | | | | | | | | | | | | | | | | | | | | | - Robert Langer
- 3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA,
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24
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Kryukov GV, Wilson FH, Ruth JR, Paulk J, Tsherniak A, Marlow SE, Vazquez F, Weir BA, Fitzgerald ME, Tanaka M, Bielski CM, Scott JM, Dennis C, Cowley GS, Boehm JS, Root DE, Golub TR, Clish CB, Bradner JE, Hahn WC, Garraway LA. MTAP deletion confers enhanced dependency on the PRMT5 arginine methyltransferase in cancer cells. Science 2016; 351:1214-8. [PMID: 26912360 DOI: 10.1126/science.aad5214] [Citation(s) in RCA: 312] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/01/2016] [Indexed: 12/19/2022]
Abstract
The discovery of cancer dependencies has the potential to inform therapeutic strategies and to identify putative drug targets. Integrating data from comprehensive genomic profiling of cancer cell lines and from functional characterization of cancer cell dependencies, we discovered that loss of the enzyme methylthioadenosine phosphorylase (MTAP) confers a selective dependence on protein arginine methyltransferase 5 (PRMT5) and its binding partner WDR77. MTAP is frequently lost due to its proximity to the commonly deleted tumor suppressor gene, CDKN2A. We observed increased intracellular concentrations of methylthioadenosine (MTA, the metabolite cleaved by MTAP) in cells harboring MTAP deletions. Furthermore, MTA specifically inhibited PRMT5 enzymatic activity. Administration of either MTA or a small-molecule PRMT5 inhibitor showed a modest preferential impairment of cell viability for MTAP-null cancer cell lines compared with isogenic MTAP-expressing counterparts. Together, our findings reveal PRMT5 as a potential vulnerability across multiple cancer lineages augmented by a common "passenger" genomic alteration.
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Affiliation(s)
- Gregory V Kryukov
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Frederick H Wilson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason R Ruth
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviad Tsherniak
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sara E Marlow
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Francisca Vazquez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Barbara A Weir
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Minoru Tanaka
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Craig M Bielski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justin M Scott
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Courtney Dennis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Glenn S Cowley
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse S Boehm
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Todd R Golub
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clary B Clish
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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25
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Whittaker SR, Cowley GS, Wagner S, Luo F, Root DE, Garraway LA. Abstract C72: Combined pan-RAF and MEK inhibition overcomes multiple resistance mechanisms to selective RAF inhibitors. Mol Cancer Ther 2015. [DOI: 10.1158/1535-7163.targ-15-c72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Background
RAF and MEK inhibitors are efficacious in BRAF mutant melanoma but not in BRAF mutant colorectal cancer (CRC). To understand the underlying mechanisms of this difference we performed an RNA interference screen to identify loss of function events that sensitize CRC cells to RAF inhibition by PLX4720.
Methods
A pooled lentiviral library encoding 90,000 shRNAs, targeting 16,500 genes was transduced into the PLX4720-resistant, BRAF mutant RKO CRC cell line. The shRNA-infected cells were split into two experimental arms treated with either PLX4720 or DMSO. After 16 population doublings, the abundance of each shRNA was determined by PCR amplification and deep sequencing of the barcoded shRNA pool. The log-fold change in shRNA reads in the drug-treated condition was calculated relative to the vehicle control. RNAi gene enrichment (RIGER) was employed to rank genes that promoted sensitivity to PLX4720. Candidate genes were validated individually and their effects on cell proliferation, survival and MAPK pathway inhibition assessed.
Results
Genes involved in maintaining MAPK pathway activity scored prominently in our screen. Knockdown of MET, SHP2, SHOC2 and CRAF by shRNA sensitized cells to PLX4720. Efforts to suppress cell proliferation via single agent pan-RAF or MEK inhibition were more effective across melanoma and colorectal cancer cell lines than PLX4720. Strikingly, combined pan-RAF and MEK inhibition elicited a synergistic response in cell lines showing intrinsic resistance to PLX4720 associated with NF1 or KRAS mutation.
Conclusions
Resistance to BRAF inhibition is mediated by reactivation of the MAPK pathway in a CRAF-dependent manner. Pan-RAF inhibitors synergize with MEK inhibitors to suppress proliferation and induce apoptosis in both BRAF mutant, PLX4720-resistant cell lines and also in KRAS mutant cell lines. Pan-RAF inhibitors are progressing into clinical trials and our data support their use in combination with MEK inhibitors.
Citation Format: Steven R. Whittaker, Glenn S. Cowley, Steve Wagner, Flora Luo, David E. Root, Levi A. Garraway. Combined pan-RAF and MEK inhibition overcomes multiple resistance mechanisms to selective RAF inhibitors. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C72.
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Affiliation(s)
| | | | - Steve Wagner
- 1The Institute of Cancer Research, London, United Kingdom
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26
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Whittaker SR, Cowley GS, Wagner S, Luo F, Root DE, Garraway LA. Combined Pan-RAF and MEK Inhibition Overcomes Multiple Resistance Mechanisms to Selective RAF Inhibitors. Mol Cancer Ther 2015; 14:2700-11. [PMID: 26351322 DOI: 10.1158/1535-7163.mct-15-0136-t] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 08/30/2015] [Indexed: 12/19/2022]
Abstract
RAF and MEK inhibitors are effective in BRAF-mutant melanoma but not in BRAF-mutant colorectal cancer. To gain additional insights into this difference, we performed a genome-scale pooled shRNA enhancer screen in a BRAF-mutant, RAF inhibitor-resistant colorectal cancer cell line exposed to the selective RAF inhibitor PLX4720. We identified multiple genes along the receptor tyrosine kinase (RTK)/mitogen-activated protein kinase (MAPK) signaling axis that, when suppressed, either genetically or pharmacologically, sensitized cells to the selective RAF inhibitor through sustained inhibition of MAPK signaling. Strikingly, CRAF was a key mediator of resistance that could be overcome by the use of pan-RAF inhibitors in combination with a MEK inhibitor. Furthermore, the combination of pan-RAF and MEK inhibitors displayed strong synergy in melanoma and colorectal cancer cell lines with RAS-activating events such as RTK activation, KRAS mutation, or NF1 loss-of-function mutations. Combinations of selective RAF inhibitors, such as PLX4720 or dabrafenib, with MEK inhibitors did not incur such profound synergy, suggesting that inhibition of CRAF by pan-RAF inhibitors plays a key role in determining cellular response. Importantly, in contrast to the modest activity seen with single-agent treatment, dual pan-RAF and MEK inhibition results in the induction of apoptosis, greatly enhancing efficacy. Notably, combined pan-RAF and MEK inhibition can overcome intrinsic and acquired resistance to single-agent RAF/MEK inhibition, supporting dual pan-RAF and MEK inhibition as a novel therapeutic strategy for BRAF- and KRAS-mutant cancers.
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Affiliation(s)
- Steven R Whittaker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. The Broad Institute, Cambridge, Massachusetts. Division of Cancer Therapeutics, Institute of Cancer Research, London, United Kingdom
| | | | - Steve Wagner
- Division of Cancer Therapeutics, Institute of Cancer Research, London, United Kingdom
| | - Flora Luo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. The Broad Institute, Cambridge, Massachusetts
| | | | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. The Broad Institute, Cambridge, Massachusetts. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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27
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Filone CM, Dower K, Cowley GS, Hensley LE, Connor JH. Probing the virus host interaction in high containment: an approach using pooled short hairpin RNA. Assay Drug Dev Technol 2015; 13:34-43. [PMID: 25646658 DOI: 10.1089/adt.2014.613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The study of viruses in high containment offers unique challenges for technology-intense approaches. These approaches include high-throughput screening for small-molecule antivirals and genetic perturbation-based screens for host factors required for viral replication. Here, we describe the use of whole-genome scale pooled short hairpin RNA (shRNA) libraries to screen for host factors necessary for viral infection at BSL2, and the transition of this technique into the BSL4 environment. Pooled screening provides a unique way to circumvent many of the technological challenges associated with other high-throughput screening approaches in high containment. Our pooled screening approach identified host factors involved in the replication of orthopoxviruses (Vaccinia and Monkeypox) and filoviruses (Ebola and Marburg) under conditions that enable straightforward screen-to-follow-up approaches.
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Affiliation(s)
- Claire Marie Filone
- 1 National Emerging Infectious Diseases Laboratory, Boston University School of Medicine , Boston, Massachusetts
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28
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Place CS, Cowley GS, Root DE, Garraway LA. Abstract 3429: Synthetic lethal RNAi screens to nominate potential therapeutic combinations for uveal melanoma. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Uveal melanoma (UM) is the most common form of ocular cancer in adults and metastatic disease currently has no effective therapy. Over 80% of UM tumors harbor activating mutations in the heterotrimeric G protein α subunits GNAQ or GNA11. These mutations induce protein kinase C (PKC) and the MAP kinase pathway, which signals through RAF, MEK, and ERK. Clinical trials of MEK and PKC inhibitors are underway to treat UM, however, novel therapeutic strategies may be required for effective treatment. To identify rational combination therapies in the context of MEK or PKC inhibition, we performed a pooled, genome-wide synthetic lethal RNA interference screen. Candidate genes whose silencing sensitizes GNAQ/11-mutant UM cells to MEK or PKC inhibition were nominated and further validated across a panel of cell lines using a custom pool of shRNAs. Several genes scored well across all cell lines. The top MEK inhibitor sensitizer was BRAF, thereby highlighting the importance of MAPK signaling in UM. Several non-MAPK pathway genes were also nominated and may represent novel pathways for the development of combination therapies.
Citation Format: Chelsea S. Place, Glenn S. Cowley, David E. Root, Levi A. Garraway. Synthetic lethal RNAi screens to nominate potential therapeutic combinations for uveal melanoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3429. doi:10.1158/1538-7445.AM2014-3429
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Affiliation(s)
| | | | - David E. Root
- 2The Broad Institute of Harvard and MIT, Cambridge, MA
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29
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Järås M, Miller PG, Chu LP, Puram RV, Fink EC, Schneider RK, Al-Shahrour F, Peña P, Breyfogle LJ, Hartwell KA, McConkey ME, Cowley GS, Root DE, Kharas MG, Mullally A, Ebert BL. Csnk1a1 inhibition has p53-dependent therapeutic efficacy in acute myeloid leukemia. ACTA ACUST UNITED AC 2014; 211:605-12. [PMID: 24616378 PMCID: PMC3978274 DOI: 10.1084/jem.20131033] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [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] [Indexed: 11/04/2022]
Abstract
Despite extensive insights into the underlying genetics and biology of acute myeloid leukemia (AML), overall survival remains poor and new therapies are needed. We found that casein kinase 1 α (Csnk1a1), a serine-threonine kinase, is essential for AML cell survival in vivo. Normal hematopoietic stem and progenitor cells (HSPCs) were relatively less affected by shRNA-mediated knockdown of Csnk1a1. To identify downstream mediators of Csnk1a1 critical for leukemia cells, we performed an in vivo pooled shRNA screen and gene expression profiling. We found that Csnk1a1 knockdown results in decreased Rps6 phosphorylation, increased p53 activity, and myeloid differentiation. Consistent with these observations, p53-null leukemias were insensitive to Csnk1a1 knockdown. We further evaluated whether D4476, a casein kinase 1 inhibitor, would exhibit selective antileukemic effects. Treatment of leukemia stem cells (LSCs) with D4476 showed highly selective killing of LSCs over normal HSPCs. In summary, these findings demonstrate that Csnk1a1 inhibition causes reduced Rps6 phosphorylation and activation of p53, resulting in selective elimination of leukemia cells, revealing Csnk1a1 as a potential therapeutic target for the treatment of AML.
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Affiliation(s)
- Marcus Järås
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
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30
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Filone CM, Caballero IS, Dower K, Mendillo ML, Cowley GS, Santagata S, Rozelle DK, Yen J, Rubins KH, Hacohen N, Root DE, Hensley LE, Connor J. The master regulator of the cellular stress response (HSF1) is critical for orthopoxvirus infection. PLoS Pathog 2014; 10:e1003904. [PMID: 24516381 PMCID: PMC3916389 DOI: 10.1371/journal.ppat.1003904] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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] [Received: 06/14/2013] [Accepted: 12/12/2013] [Indexed: 12/17/2022] Open
Abstract
The genus Orthopoxviridae contains a diverse group of human pathogens including monkeypox, smallpox and vaccinia. These viruses are presumed to be less dependent on host functions than other DNA viruses because they have large genomes and replicate in the cytoplasm, but a detailed understanding of the host factors required by orthopoxviruses is lacking. To address this topic, we performed an unbiased, genome-wide pooled RNAi screen targeting over 17,000 human genes to identify the host factors that support orthopoxvirus infection. We used secondary and tertiary assays to validate our screen results. One of the strongest hits was heat shock factor 1 (HSF1), the ancient master regulator of the cytoprotective heat-shock response. In investigating the behavior of HSF1 during vaccinia infection, we found that HSF1 was phosphorylated, translocated to the nucleus, and increased transcription of HSF1 target genes. Activation of HSF1 was supportive for virus replication, as RNAi knockdown and HSF1 small molecule inhibition prevented orthopoxvirus infection. Consistent with its role as a transcriptional activator, inhibition of several HSF1 targets also blocked vaccinia virus replication. These data show that orthopoxviruses co-opt host transcriptional responses for their own benefit, thereby effectively extending their functional genome to include genes residing within the host DNA. The dependence on HSF1 and its chaperone network offers multiple opportunities for antiviral drug development.
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Affiliation(s)
- Claire Marie Filone
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- United States Army Medical Research Institute of Infectious Diseases, Virology Division, Fort Detrick, Maryland, United States of America
- * E-mail:
| | - Ignacio S. Caballero
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ken Dower
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Marc L. Mendillo
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Glenn S. Cowley
- The Broad Institute, Cambridge Massachusetts, United States of America
| | - Sandro Santagata
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Daniel K. Rozelle
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Judy Yen
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Kathleen H. Rubins
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Nir Hacohen
- The Broad Institute, Cambridge Massachusetts, United States of America
| | - David E. Root
- The Broad Institute, Cambridge Massachusetts, United States of America
| | - Lisa E. Hensley
- United States Army Medical Research Institute of Infectious Diseases, Virology Division, Fort Detrick, Maryland, United States of America
| | - John Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
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31
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Zhou P, Shaffer DR, Alvarez Arias DA, Nakazaki Y, Pos W, Torres AJ, Cremasco V, Dougan SK, Cowley GS, Elpek K, Brogdon J, Lamb J, Turley SJ, Ploegh HL, Root DE, Love JC, Dranoff G, Hacohen N, Cantor H, Wucherpfennig KW. In vivo discovery of immunotherapy targets in the tumour microenvironment. Nature 2014; 506:52-7. [PMID: 24476824 DOI: 10.1038/nature12988] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 12/31/2013] [Indexed: 02/07/2023]
Abstract
Recent clinical trials showed that targeting of inhibitory receptors on T cells induces durable responses in a subset of cancer patients, despite advanced disease. However, the regulatory switches controlling T-cell function in immunosuppressive tumours are not well understood. Here we show that such inhibitory mechanisms can be systematically discovered in the tumour microenvironment. We devised an in vivo pooled short hairpin RNA (shRNA) screen in which shRNAs targeting negative regulators became highly enriched in murine tumours by releasing a block on T-cell proliferation upon tumour antigen recognition. Such shRNAs were identified by deep sequencing of the shRNA cassette from T cells infiltrating tumour or control tissues. One of the target genes was Ppp2r2d, a regulatory subunit of the PP2A phosphatase family. In tumours, Ppp2r2d knockdown inhibited T-cell apoptosis and enhanced T-cell proliferation as well as cytokine production. Key regulators of immune function can therefore be discovered in relevant tissue microenvironments.
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Affiliation(s)
- Penghui Zhou
- 1] Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [2]
| | - Donald R Shaffer
- 1] Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [2] [3] Jounce Therapeutics, Cambridge, Massachusetts 02138, USA
| | | | - Yukoh Nakazaki
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Wouter Pos
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Alexis J Torres
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | | | - Stephanie K Dougan
- Whitehead Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Glenn S Cowley
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kutlu Elpek
- 1] Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [2] Jounce Therapeutics, Cambridge, Massachusetts 02138, USA
| | - Jennifer Brogdon
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - John Lamb
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | | | - Hidde L Ploegh
- Whitehead Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - J Christopher Love
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Glenn Dranoff
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Harvey Cantor
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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32
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Li L, Shen C, Nakamura E, Ando K, Signoretti S, Beroukhim R, Cowley GS, Lizotte P, Liberzon E, Bair S, Root DE, Tamayo P, Tsherniak A, Cheng SC, Tabak B, Jacobsen A, Hakimi AA, Schultz N, Ciriello G, Sander C, Hsieh JJ, Kaelin WG. SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer. Cancer Cell 2013; 24:738-50. [PMID: 24332042 PMCID: PMC3910168 DOI: 10.1016/j.ccr.2013.10.025] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 09/02/2013] [Accepted: 10/31/2013] [Indexed: 12/22/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer and is often linked to loss of chromosome 3p, which harbors the VHL tumor suppressor gene, loss of chromosome 14q, which includes HIF1A, and gain of chromosome 5q. The relevant target(s) on chromosome 5q is not known. Here, we show that 5q amplification leads to overexpression of the SQSTM1 oncogene in ccRCC lines and tumors. Overexpression of SQSTM1 in ccRCC lines promoted resistance to redox stress and increased soft agar growth, while downregulation of SQSTM1 decreased resistance to redox stress, impaired cellular fitness, and decreased tumor formation. Therefore, the selection pressure to amplify 5q in ccRCC is driven, at least partly, by SQSTM1.
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Affiliation(s)
- Lianjie Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chuan Shen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eijiro Nakamura
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kiyohiro Ando
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Patrick Lizotte
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ella Liberzon
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Steven Bair
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Pablo Tamayo
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Su-Chun Cheng
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Barbara Tabak
- Department of Cancer Biology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Anders Jacobsen
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 16605, USA
| | - A Ari Hakimi
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 16605, USA
| | - Nikolaus Schultz
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 16605, USA
| | - Giovanni Ciriello
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 16605, USA
| | - Chris Sander
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 16605, USA
| | - James J Hsieh
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 16605, USA; Department of Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 16605, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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33
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Whittaker SR, Luo F, Hsiao J, Cowley GS, Root DE, Garraway LA. Abstract B108: A genome-scale shRNA synthetic lethal screen identifies enhancers of sensitivity to RAF inhibition. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.targ-13-b108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Genome-scale RNA interference screens have identified a dependency on BRAF for the proliferation of BRAF-mutant colorectal cancer (CRC) cell lines. Despite this, small molecule RAF inhibitors, such as vemurafenib, have been unsuccessful in clinical trials of patients with CRC, with a response rate of only 5%. CRC cell lines demonstrate intrinsic resistance to RAF inhibitors, in some cases through EGFR or MET activity. We designed a genome-scale RNA interference screen to identify loss of function events that could synergize with pharmacologic RAF inhibition. We transduced a pooled lentiviral library encoding 90,000 shRNAs targeting over 16,500 genes into the RKO CRC cell line, which displays robust resistance to PLX470. The shRNA-infected population was divided into two experimental arms, one treated with DMSO, the other treated with PLX4720. Following 16 population doublings, the abundance of each hairpin was assessed by PCR amplification of barcoded hairpin DNA, followed by massively parallel paired-end sequencing. The log-fold change in shRNA abundance between the PLX4720- and DMSO-treated controls was determined and RNAi gene enrichment (RIGER) used to rank individual shRNAs and nominate candidate genes that were required for survival of RKO cells exposed to PLX4720. Top-ranking genes that displayed synthetic lethality with RAF inhibition were validated in an arrayed secondary screen. shRNAs targeting MET scored highly, consistent with recent reports implicating HGF-MET signaling in resistance to BRAF inhibition, validating our approach. Furthermore, we describe the characterization of additional genes that sensitize cells to inhibition of BRAF. Ultimately, these studies aim to nominate pharmacologically targetable events that mediate RAF-inhibitor resistance in colorectal cancers.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B108.
Citation Format: Steven R. Whittaker, Flora Luo, Jessica Hsiao, Glenn S. Cowley, David E. Root, Levi A. Garraway. A genome-scale shRNA synthetic lethal screen identifies enhancers of sensitivity to RAF inhibition. [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 B108.
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34
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Miller PG, Al-Shahrour F, Hartwell KA, Chu LP, Järås M, Puram RV, Puissant A, Callahan KP, Ashton J, McConkey ME, Poveromo LP, Cowley GS, Kharas MG, Labelle M, Shterental S, Fujisaki J, Silberstein L, Alexe G, Al-Hajj MA, Shelton CA, Armstrong SA, Root DE, Scadden DT, Hynes RO, Mukherjee S, Stegmaier K, Jordan CT, Ebert BL. In Vivo RNAi screening identifies a leukemia-specific dependence on integrin beta 3 signaling. Cancer Cell 2013; 24:45-58. [PMID: 23770013 PMCID: PMC3746037 DOI: 10.1016/j.ccr.2013.05.004] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 02/19/2013] [Accepted: 05/02/2013] [Indexed: 01/05/2023]
Abstract
We used an in vivo small hairpin RNA (shRNA) screening approach to identify genes that are essential for MLL-AF9 acute myeloid leukemia (AML). We found that Integrin Beta 3 (Itgb3) is essential for murine leukemia cells in vivo and for human leukemia cells in xenotransplantation studies. In leukemia cells, Itgb3 knockdown impaired homing, downregulated LSC transcriptional programs, and induced differentiation via the intracellular kinase Syk. In contrast, loss of Itgb3 in normal hematopoietic stem and progenitor cells did not affect engraftment, reconstitution, or differentiation. Finally, using an Itgb3 knockout mouse model, we confirmed that Itgb3 is dispensable for normal hematopoiesis but is required for leukemogenesis. Our results establish the significance of the Itgb3 signaling pathway as a potential therapeutic target in AML.
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Affiliation(s)
- Peter G Miller
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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35
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Liu Y, Marks K, Cowley GS, Carretero J, Liu Q, Nieland TJF, Xu C, Cohoon TJ, Gao P, Zhang Y, Chen Z, Altabef AB, Tchaicha JH, Wang X, Choe S, Driggers EM, Zhang J, Bailey ST, Sharpless NE, Hayes DN, Patel NM, Janne PA, Bardeesy N, Engelman JA, Manning BD, Shaw RJ, Asara JM, Scully R, Kimmelman A, Byers LA, Gibbons DL, Wistuba II, Heymach JV, Kwiatkowski DJ, Kim WY, Kung AL, Gray NS, Root DE, Cantley LC, Wong KK. Metabolic and functional genomic studies identify deoxythymidylate kinase as a target in LKB1-mutant lung cancer. Cancer Discov 2013; 3:870-9. [PMID: 23715154 DOI: 10.1158/2159-8290.cd-13-0015] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The LKB1/STK11 tumor suppressor encodes a serine/threonine kinase, which coordinates cell growth, polarity, motility, and metabolism. In non-small cell lung carcinoma, LKB1 is somatically inactivated in 25% to 30% of cases, often concurrently with activating KRAS mutations. Here, we used an integrative approach to define novel therapeutic targets in KRAS-driven LKB1-mutant lung cancers. High-throughput RNA interference screens in lung cancer cell lines from genetically engineered mouse models driven by activated KRAS with or without coincident Lkb1 deletion led to the identification of Dtymk, encoding deoxythymidylate kinase (DTYMK), which catalyzes dTTP biosynthesis, as synthetically lethal with Lkb1 deficiency in mouse and human lung cancer lines. Global metabolite profiling showed that Lkb1-null cells had a striking decrease in multiple nucleotide metabolites as compared with the Lkb1-wild-type cells. Thus, LKB1-mutant lung cancers have deficits in nucleotide metabolism that confer hypersensitivity to DTYMK inhibition, suggesting that DTYMK is a potential therapeutic target in this aggressive subset of tumors.
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Affiliation(s)
- Yan Liu
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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36
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Whittaker SR, Luo F, Hsiao J, Cowley GS, Root DE, Garraway LA. Abstract B27: Probing synthetic lethal interactions with RAF inhibition in BRAF-mutant colorectal cancer. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.pms-b27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Large-scale RNA interference screens have indicated that BRAF-mutant colorectal cancer (CRC) cell lines are dependent upon BRAF expression for proliferation. However, small molecule RAF inhibitors, such as vemurafenib, have so far failed to exhibit robust activity in clinical trials of patients with CRC, with a response rate of only 5%. Commensurate with this, CRC cell lines demonstrate intrinsic resistance to RAF inhibitors. Therefore, we designed an RNA interference screen to identify loss of function events that could synergize with pharmacologic RAF inhibition. We transduced a pooled lentiviral library encoding 90,000 shRNAs targeting over 16,500 genes into RAF-inhibitor-resistant RKO CRC cells. The shRNA-infected population was divided into two experimental arms, one treated with DMSO, the other treated with PLX4720. Following 16 population doublings, the abundance of each hairpin was assessed by PCR amplification of barcoded hairpin DNA, followed by massively parallel paired-end sequencing. The log-fold change in shRNA abundance between the PLX4720- and DMSO-treated controls was determined and RNAi gene enrichment (RIGER) used to rank individual shRNAs and nominate candidate genes that were required for survival of RKO cells exposed to PLX4720. We validated the 40 top-ranking genes that displayed synthetic lethality with RAF inhibition in an arrayed secondary screen. shRNAs targeting MET scored highly, consistent with recent reports implicating HGF-MET signaling in resistance to BRAF inhibition, validating our approach. Furthermore, we describe the characterization of additional genes that sensitize cells to inhibition of BRAF, suggesting novel therapeutic opportunities. By integrating these findings with other genomic and functional studies we aim to identify clinically actionable events that cause RAF-inhibitor resistance in colorectal cancers.
Citation Format: Steven R. Whittaker, Flora Luo, Jessica Hsiao, Glenn S. Cowley, David E. Root, Levi A. Garraway. Probing synthetic lethal interactions with RAF inhibition in BRAF-mutant colorectal cancer. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B27.
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Affiliation(s)
| | - Flora Luo
- 2Dana-Farber Cancer Institute, Boston, MA
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37
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Losman JA, Looper RE, Koivunen P, Lee S, Schneider RK, McMahon C, Cowley GS, Root DE, Ebert BL, Kaelin WG. (R)-2-hydroxyglutarate is sufficient to promote leukemogenesis and its effects are reversible. Science 2013; 339:1621-5. [PMID: 23393090 PMCID: PMC3836459 DOI: 10.1126/science.1231677] [Citation(s) in RCA: 566] [Impact Index Per Article: 51.5] [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: 01/17/2023]
Abstract
Mutations in IDH1 and IDH2, the genes coding for isocitrate dehydrogenases 1 and 2, are common in several human cancers, including leukemias, and result in overproduction of the (R)-enantiomer of 2-hydroxyglutarate [(R)-2HG]. Elucidation of the role of IDH mutations and (R)-2HG in leukemogenesis has been hampered by a lack of appropriate cell-based models. Here, we show that a canonical IDH1 mutant, IDH1 R132H, promotes cytokine independence and blocks differentiation in hematopoietic cells. These effects can be recapitulated by (R)-2HG, but not (S)-2HG, despite the fact that (S)-2HG more potently inhibits enzymes, such as the 5'-methylcytosine hydroxylase TET2, that have previously been linked to the pathogenesis of IDH mutant tumors. We provide evidence that this paradox relates to the ability of (S)-2HG, but not (R)-2HG, to inhibit the EglN prolyl hydroxylases. Additionally, we show that transformation by (R)-2HG is reversible.
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Affiliation(s)
- Julie-Aurore Losman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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38
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Whittaker SR, Theurillat JP, Van Allen E, Wagle N, Hsiao J, Cowley GS, Schadendorf D, Root DE, Garraway LA. A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition. Cancer Discov 2013; 3:350-62. [PMID: 23288408 DOI: 10.1158/2159-8290.cd-12-0470] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RAF inhibitors such as vemurafenib and dabrafenib block BRAF-mediated cell proliferation and achieve meaningful clinical benefit in the vast majority of patients with BRAF(V600E)-mutant melanoma. However, some patients do not respond to this regimen, and nearly all progress to therapeutic resistance. We used a pooled RNA interference screen targeting more than 16,500 genes to discover loss-of-function events that could drive resistance to RAF inhibition. The highest ranking gene was NF1, which encodes neurofibromin, a tumor suppressor that inhibits RAS activity. NF1 loss mediates resistance to RAF and mitogen-activated protein kinase (MAPK) kinase kinase (MEK) inhibitors through sustained MAPK pathway activation. However, cells lacking NF1 retained sensitivity to the irreversible RAF inhibitor AZ628 and an ERK inhibitor. NF1 mutations were observed in BRAF-mutant tumor cells that are intrinsically resistant to RAF inhibition and in melanoma tumors obtained from patients exhibiting resistance to vemurafenib, thus showing the clinical potential for NF1-driven resistance to RAF/MEK-targeted therapies.
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Affiliation(s)
- Steven R Whittaker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
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39
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Rosenbluh J, Nijhawan D, Cox AG, Li X, Neal JT, Schafer EJ, Zack TI, Wang X, Tsherniak A, Schinzel AC, Shao DD, Schumacher SE, Weir BA, Vazquez F, Cowley GS, Root DE, Mesirov JP, Beroukhim R, Kuo CJ, Goessling W, Hahn WC. β-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis. Cell 2012; 151:1457-73. [PMID: 23245941 DOI: 10.1016/j.cell.2012.11.026] [Citation(s) in RCA: 590] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 09/23/2012] [Accepted: 11/13/2012] [Indexed: 12/20/2022]
Abstract
Wnt/β-catenin signaling plays a key role in the pathogenesis of colon and other cancers; emerging evidence indicates that oncogenic β-catenin regulates several biological processes essential for cancer initiation and progression. To decipher the role of β-catenin in transformation, we classified β-catenin activity in 85 cancer cell lines in which we performed genome-scale loss-of-function screens and found that β-catenin active cancers are dependent on a signaling pathway involving the transcriptional regulator YAP1. Specifically, we found that YAP1 and the transcription factor TBX5 form a complex with β-catenin. Phosphorylation of YAP1 by the tyrosine kinase YES1 leads to localization of this complex to the promoters of antiapoptotic genes, including BCL2L1 and BIRC5. A small-molecule inhibitor of YES1 impeded the proliferation of β-catenin-dependent cancers in both cell lines and animal models. These observations define a β-catenin-YAP1-TBX5 complex essential to the transformation and survival of β-catenin-driven cancers.
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Affiliation(s)
- Joseph Rosenbluh
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
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Nijhawan D, Zack TI, Ren Y, Strickland MR, Lamothe R, Schumacher SE, Tsherniak A, Besche HC, Rosenbluh J, Shehata S, Cowley GS, Weir BA, Goldberg AL, Mesirov JP, Root DE, Bhatia SN, Beroukhim R, Hahn WC. Cancer vulnerabilities unveiled by genomic loss. Cell 2012; 150:842-54. [PMID: 22901813 PMCID: PMC3429351 DOI: 10.1016/j.cell.2012.07.023] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [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] [Received: 05/27/2012] [Revised: 07/21/2012] [Accepted: 07/26/2012] [Indexed: 01/22/2023]
Abstract
Due to genome instability, most cancers exhibit loss of regions containing tumor suppressor genes and collateral loss of other genes. To identify cancer-specific vulnerabilities that are the result of copy number losses, we performed integrated analyses of genome-wide copy number and RNAi profiles and identified 56 genes for which gene suppression specifically inhibited the proliferation of cells harboring partial copy number loss of that gene. These CYCLOPS (copy number alterations yielding cancer liabilities owing to partial loss) genes are enriched for spliceosome, proteasome, and ribosome components. One CYCLOPS gene, PSMC2, encodes an essential member of the 19S proteasome. Normal cells express excess PSMC2, which resides in a complex with PSMC1, PSMD2, and PSMD5 and acts as a reservoir protecting cells from PSMC2 suppression. Cells harboring partial PSMC2 copy number loss lack this complex and die after PSMC2 suppression. These observations define a distinct class of cancer-specific liabilities resulting from genome instability.
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Affiliation(s)
- Deepak Nijhawan
- Departments of Cancer Biology and Medical Oncology, Dana Farber Cancer Institute
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Travis I. Zack
- Departments of Cancer Biology and Medical Oncology, Dana Farber Cancer Institute
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Biophysics Program, Harvard University
| | - Yin Ren
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Rebecca Lamothe
- Departments of Cancer Biology and Medical Oncology, Dana Farber Cancer Institute
| | - Steven E. Schumacher
- Departments of Cancer Biology and Medical Oncology, Dana Farber Cancer Institute
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | | | - Henrike C. Besche
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115
| | - Joseph Rosenbluh
- Departments of Cancer Biology and Medical Oncology, Dana Farber Cancer Institute
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shyemaa Shehata
- Departments of Cancer Biology and Medical Oncology, Dana Farber Cancer Institute
| | | | | | - Alfred L. Goldberg
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115
| | | | - David E. Root
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Sangeeta N. Bhatia
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Rameen Beroukhim
- Departments of Cancer Biology and Medical Oncology, Dana Farber Cancer Institute
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - William C. Hahn
- Departments of Cancer Biology and Medical Oncology, Dana Farber Cancer Institute
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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Ren Y, Cheung HW, von Maltzhan G, Agrawal A, Cowley GS, Weir BA, Boehm JS, Tamayo P, Karst AM, Liu JF, Hirsch MS, Mesirov JP, Drapkin R, Root DE, Lo J, Fogal V, Ruoslahti E, Hahn WC, Bhatia SN. Targeted tumor-penetrating siRNA nanocomplexes for credentialing the ovarian cancer oncogene ID4. Sci Transl Med 2012; 4:147ra112. [PMID: 22896676 PMCID: PMC3633234 DOI: 10.1126/scitranslmed.3003778] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [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: 12/22/2022]
Abstract
The comprehensive characterization of a large number of cancer genomes will eventually lead to a compendium of genetic alterations in specific cancers. Unfortunately, the number and complexity of identified alterations complicate endeavors to identify biologically relevant mutations critical for tumor maintenance because many of these targets are not amenable to manipulation by small molecules or antibodies. RNA interference provides a direct way to study putative cancer targets; however, specific delivery of therapeutics to the tumor parenchyma remains an intractable problem. We describe a platform for the discovery and initial validation of cancer targets, composed of a systematic effort to identify amplified and essential genes in human cancer cell lines and tumors partnered with a novel modular delivery technology. We developed a tumor-penetrating nanocomplex (TPN) that comprised small interfering RNA (siRNA) complexed with a tandem tumor-penetrating and membrane-translocating peptide, which enabled the specific delivery of siRNA deep into the tumor parenchyma. We used TPN in vivo to evaluate inhibitor of DNA binding 4 (ID4) as a novel oncogene. Treatment of ovarian tumor-bearing mice with ID4-specific TPN suppressed growth of established tumors and significantly improved survival. These observations not only credential ID4 as an oncogene in 32% of high-grade ovarian cancers but also provide a framework for the identification, validation, and understanding of potential therapeutic cancer targets.
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Affiliation(s)
- Yin Ren
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hiu Wing Cheung
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Geoffrey von Maltzhan
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Amit Agrawal
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | | | | | - Pablo Tamayo
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Alison M. Karst
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Joyce F. Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Michelle S. Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jill P. Mesirov
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Electrical Engineering and Computer Science and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ronny Drapkin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David E. Root
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Justin Lo
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Valentina Fogal
- Center for Nanomedicine, Sanford-Burnham Medical Research Institute, University of California, Santa Barbara, CA 93106-9610
- Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Erkki Ruoslahti
- Center for Nanomedicine, Sanford-Burnham Medical Research Institute, University of California, Santa Barbara, CA 93106-9610
- Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - William C. Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Sangeeta N. Bhatia
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Electrical Engineering and Computer Science and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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Liu Y, Cowley GS, Cohoon TJ, Root DE, Kwok-kin W. Abstract LB-260: Identification of DTYMK and CHEK1 as therapeutic targets in LKB1 mutant non-small cell lung cancer. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-lb-260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
The LKB1 tumor suppressor encodes a key metabolic sensor that integrates cell growth and metabolism. LKB1 is mutationally inactivated in multiple adult malignancies, including >20% of lung cancers, often simultaneously with activating KRAS mutations. LKB1 mutations are an important predictor of poor outcome and resistance to current therapeutic approaches. We employed an integrative approach to define novel therapeutic targets in Lkb1 mutant lung cancers. Matched cell lines from genetically engineered mouse models of cancer driven by activated Kras alone or in combination with Lkb1 deletion, were employed in high-throughput RNAi, kinase inhibitor, and metabolite screens. These screens identified knockdown of either Dtymk (deoxythymidylate kinase) or Chek1 (checkpoint kinase 1) as synthetically lethal with Lkb1 deficiency in both mouse and human lung cancer cell lines, and revealed that Lkb1 inactivation conferred marked sensitivity to treatment with CHEK1 inhibitors. Lkb1 deficient cells had a distinct metabolic profile, characterized by striking decreases in multiple nucleotide metabolites. Knockdown of DTYMK inhibited dTTP biosynthesis and, consequently, DNA synthesis, and knockdown of CHEK1 caused accumulation of DNA damage. We hypothesize that Lkb1 loss enhances dependence on these enzymes due to broad defects in nucleotide metabolism. Our studies support the development of therapies target DTYMK and CHEK1 in LKB1 mutant non-small cell lung cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-260. doi:1538-7445.AM2012-LB-260
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Affiliation(s)
- Yan Liu
- 1Dana Farber Cancer Institute, Boston, MA
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Ketela T, Heisler LE, Brown KR, Ammar R, Kasimer D, Surendra A, Ericson E, Blakely K, Karamboulas D, Smith AM, Durbic T, Arnoldo A, Cheung-Ong K, Koh JLY, Gopal S, Cowley GS, Yang X, Grenier JK, Giaever G, Root DE, Moffat J, Nislow C. A comprehensive platform for highly multiplexed mammalian functional genetic screens. BMC Genomics 2011; 12:213. [PMID: 21548937 PMCID: PMC3115879 DOI: 10.1186/1471-2164-12-213] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [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: 11/04/2010] [Accepted: 05/06/2011] [Indexed: 11/15/2022] Open
Abstract
Background Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP) is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens. Results Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens. Conclusion Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray) based deconvolution methods.
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Affiliation(s)
- Troy Ketela
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
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Walker JA, Tchoudakova AV, McKenney PT, Brill S, Wu D, Cowley GS, Hariharan IK, Bernards A. Reduced growth of Drosophila neurofibromatosis 1 mutants reflects a non-cell-autonomous requirement for GTPase-Activating Protein activity in larval neurons. Genes Dev 2006; 20:3311-23. [PMID: 17114577 PMCID: PMC1686607 DOI: 10.1101/gad.1466806] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Neurofibromatosis type 1 (NF1) is among the most common genetic disorders of humans and is caused by loss of neurofibromin, a large and highly conserved protein whose only known function is to serve as a GTPase-Activating Protein (GAP) for Ras. However, most Drosophila NF1 mutant phenotypes, including an overall growth deficiency, are not readily modified by manipulating Ras signaling strength, but are rescued by increasing signaling through the cAMP-dependent protein kinase A pathway. This has led to suggestions that NF1 has distinct Ras- and cAMP-related functions. Here we report that the Drosophila NF1 growth defect reflects a non-cell-autonomous requirement for NF1 in larval neurons that express the R-Ras ortholog Ras2, that NF1 is a GAP for Ras1 and Ras2, and that a functional NF1-GAP catalytic domain is both necessary and sufficient for rescue. Moreover, a Drosophila p120RasGAP ortholog, when expressed in the appropriate cells, can substitute for NF1 in growth regulation. Our results show that loss of NF1 can give rise to non-cell-autonomous developmental defects, implicate aberrant Ras-mediated signaling in larval neurons as the primary cause of the NF1 growth deficiency, and argue against the notion that neurofibromin has separable Ras- and cAMP-related functions.
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Affiliation(s)
- James A Walker
- Massachusetts General Hospital Center for Cancer Research and Harvard Medical School, Charlestown, Massachusetts 02129, USA
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Cowley GS, Murthy AE, Parry DM, Schneider G, Korf B, Upadhyaya M, Harper P, MacCollin M, Bernards A, Gusella JF. Genetic variation in the 3' untranslated region of the neurofibromatosis 1 gene: application to unequal allelic expression. Somat Cell Mol Genet 1998; 24:107-19. [PMID: 9919310 DOI: 10.1023/b:scam.0000007113.28381.53] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a common genetic disorder caused by inactivation of neurofibromin, a protein capable of modulating signal transduction by activating Ras-GTPase activity. We have used cDNA cloning and Northern blot analysis to confirm the NF1 gene produces alternatively polyadenylated mRNAs with 3' untranslated regions (3' UTR) that show striking evolutionary conservation. Scanning of the 3'UTRs for genetic variation revealed three common sequence polymorphisms (> 30% heterozygosity), one less informative polymorphism (approximately 5% heterozygosity) and one rare variant (1/144 chromosomes). These differences were used to examine relative levels of expression of normal and mutant NF1 alleles in lymphoblast cell lines and in one case, autopsy tissue, from patients with NF1. Unequal allelic expression (up to 4-fold) was observed in a subset of both sporadic and familial NF1 cases. Where linkage phase could be determined, the allele segregating with the disorder displayed a relative reduction in expression. However, the magnitude of this effect was variable suggesting the operation of additional, non-genetic factors in determining the degree of relative expression of the mutant allele.
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Affiliation(s)
- G S Cowley
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown 02129, USA
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Abstract
The neurofibromatosis type 1 (NF1) tumor suppressor protein is thought to restrict cell proliferation by functioning as a Ras-specific guanosine triphosphatase-activating protein. However, Drosophila homozygous for null mutations of an NF1 homolog showed no obvious signs of perturbed Ras1-mediated signaling. Loss of NF1 resulted in a reduction in size of larvae, pupae, and adults. This size defect was not modified by manipulating Ras1 signaling but was restored by expression of activated adenosine 3', 5'-monophosphate-dependent protein kinase (PKA). Thus, NF1 and PKA appear to interact in a pathway that controls the overall growth of Drosophila.
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Affiliation(s)
- I The
- Massachusetts General Hospital Cancer Center and Harvard Medical School Building 149, 13th Street, Charlestown, MA 02129, USA
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Basson CT, Cowley GS, Solomon SD, Weissman B, Poznanski AK, Traill TA, Seidman JG, Seidman CE. The clinical and genetic spectrum of the Holt-Oram syndrome (heart-hand syndrome). N Engl J Med 1994; 330:885-91. [PMID: 8114858 DOI: 10.1056/nejm199403313301302] [Citation(s) in RCA: 233] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND The Holt-Oram syndrome is an autosomal dominant condition characterized by skeletal abnormalities that are frequently accompanied by congenital cardiac defects. The cause of these disparate clinical features is unknown. To identify the chromosomal location of the Holt-Oram syndrome gene, we performed clinical and genetic studies. METHODS Two large families with the Holt-Oram syndrome were evaluated by radiography of the hands, electrocardiography, and transthoracic echocardiography. Genetic-linkage analyses were performed with polymorphic DNA loci dispersed throughout the genome to identify a locus that was inherited with the Holt-Oram syndrome in family members. RESULTS A total of 19 members of Family A had Holt-Oram syndrome with mild-to-moderate skeletal deformities, including triphalangeal thumbs and carpal-bone dysmorphism. All affected members of Family A had moderate-to-severe congenital cardiac abnormalities, such as ventricular or atrial septal defects or atrioventricular-canal defects. Eighteen members of a second kindred (Family B) had Holt-Oram syndrome with moderate-to-severe skeletal deformities, including phocomelia. Twelve of the affected members had no cardiac defects; six had only atrial septal defects. Genetic analyses demonstrated linkage of the disease in each family to polymorphic loci on the long arm of chromosome 12 (combined multipoint lod score, 16.8). These data suggest odds greater than 10(16):1 that the genetic defect for Holt-Oram syndrome is present on the long arm of chromosome 12 (12q2). CONCLUSIONS Mutations in a gene on chromosome 12q2 can produce a wide range of disease phenotypes characteristic of the Holt-Oram syndrome. This gene has an important role in both skeletal and cardiac development.
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Affiliation(s)
- C T Basson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
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Olsson JE, Gordon JW, Pawlyk BS, Roof D, Hayes A, Molday RS, Mukai S, Cowley GS, Berson EL, Dryja TP. Transgenic mice with a rhodopsin mutation (Pro23His): a mouse model of autosomal dominant retinitis pigmentosa. Neuron 1992; 9:815-30. [PMID: 1418997 DOI: 10.1016/0896-6273(92)90236-7] [Citation(s) in RCA: 316] [Impact Index Per Article: 9.9] [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: 12/26/2022]
Abstract
We inserted into the germline of mice either a mutant or wild-type allele from a patient with retinitis pigmentosa and a missense mutation (P23H) in the rhodopsin gene. All three lines of transgenic mice with the mutant allele developed photoreceptor degeneration; the one with the least severe retinal photoreceptor degeneration had the lowest transgene expression, which was one-sixth the level of endogenous murine rod opsin. Of two lines of mice with the wild-type allele, one expressed approximately equal amounts of transgenic and murine opsin and maintained normal retinal function and structure. The other expressed approximately 5 times more transgenic than murine opsin and developed a retinal degeneration similar to that found in mice carrying a mutant allele, presumably due to the overexpression of this protein. Our findings help to establish the pathogenicity of mutant human P23H rod opsin and suggest that overexpression of wild-type human rod opsin leads to a remarkably similar photoreceptor degeneration.
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Affiliation(s)
- J E Olsson
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston 02114
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Rosenfeld PJ, Cowley GS, McGee TL, Sandberg MA, Berson EL, Dryja TP. A null mutation in the rhodopsin gene causes rod photoreceptor dysfunction and autosomal recessive retinitis pigmentosa. Nat Genet 1992; 1:209-13. [PMID: 1303237 DOI: 10.1038/ng0692-209] [Citation(s) in RCA: 299] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mutations within the rhodopsin gene are known to give rise to autosomal dominant retinitis pigmentosa (RP), a common hereditary form of retinal degeneration. We now describe a patient with autosomal recessive RP who is homozygous for a nonsense mutation at codon 249 within exon 4 of the rhodopsin gene. This null mutation, the first gene defect identified in autosomal recessive retinitis pigmentosa, should result in a functionally inactive rhodopsin protein that is missing the sixth and seventh transmembrane domains including the 11-cis-retinal attachment site. We also found a different null mutation carried heterozygously by an unrelated unaffected individual. Heterozygous carriers of either mutation had normal ophthalmologic examinations but their electroretinograms revealed an abnormality in rod photoreceptor function.
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Affiliation(s)
- P J Rosenfeld
- Howe Laboratory, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston 02114
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50
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Dryja TP, Hahn LB, Cowley GS, McGee TL, Berson EL. Mutation spectrum of the rhodopsin gene among patients with autosomal dominant retinitis pigmentosa. Proc Natl Acad Sci U S A 1991; 88:9370-4. [PMID: 1833777 PMCID: PMC52716 DOI: 10.1073/pnas.88.20.9370] [Citation(s) in RCA: 250] [Impact Index Per Article: 7.6] [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: 12/29/2022] Open
Abstract
We searched for point mutations in every exon of the rhodopsin gene in 150 patients from separate families with autosomal dominant retinitis pigmentosa. Including the 4 mutations we reported previously, we found a total of 17 different mutations that correlate with the disease. Each of these mutations is a single-base substitution corresponding to a single amino acid substitution. Based on current models for the structure of rhodopsin, 3 of the 17 mutant amino acids are normally located on the cytoplasmic side of the protein, 6 in transmembrane domains, and 8 on the intradiscal side. Forty-three of the 150 patients (29%) carry 1 of these mutations, and no patient has more than 1 mutation. In every family with a mutation so far analyzed, the mutation cosegregates with the disease. We found one instance of a mutation in an affected patient that was absent in both unaffected parents (i.e., a new germ-line mutation), indicating that some "isolate" cases of retinitis pigmentosa carry a mutation of the rhodopsin gene.
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Affiliation(s)
- T P Dryja
- Howe Laboratory of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston
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