1
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Weinstein HN, Hu K, Fish L, Chen YA, Allegakoen P, Hui KSF, Pham JH, Baco MB, Song H, Giacomelli AO, Vazquez F, Ghandi M, Goodarzi H, Huang FW. RPL22 is a tumor suppressor in MSI-high cancers and a key splicing regulator of MDM4. bioRxiv 2023:2023.12.10.570873. [PMID: 38106152 PMCID: PMC10723389 DOI: 10.1101/2023.12.10.570873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Microsatellite instability high (MSI-H) tumors are malignant tumors that, despite harboring a high mutational burden, often have intact TP53. One of the most frequent mutations in MSI-H tumors is a frameshift mutation in RPL22, a ribosomal protein. Here, we identified RPL22 as a modulator of MDM4 splicing through an alternative splicing switch in exon 6. RPL22 loss increases MDM4 exon 6 inclusion, cell proliferation, and augments resistance to the MDM inhibitor Nutlin-3a. RPL22 represses expression of its paralog, RPL22L1, by mediating the splicing of a cryptic exon corresponding to a truncated transcript. Therefore, damaging mutations in RPL22 drive oncogenic MDM4 induction and reveal a common splicing circuit in MSI-H tumors that may inform therapeutic targeting of the MDM4-p53 axis and oncogenic RPL22L1 induction.
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Affiliation(s)
- Hannah N.W. Weinstein
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | - Kevin Hu
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | - Lisa Fish
- Department of Biochemistry and Biophysics, University of California; San Francisco, USA
| | - Yih-An Chen
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | - Paul Allegakoen
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | - Keliana S. F. Hui
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | - Julia H. Pham
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | | | - Hanbing Song
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | | | | | | | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California; San Francisco, USA
| | - Franklin W. Huang
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
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2
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Dai C, Rennhack JP, Arnoff TE, Thaker M, Younger ST, Doench JG, Huang AY, Yang A, Aguirre AJ, Wang B, Mun E, O'Connell JT, Huang Y, Labella K, Talamas JA, Li J, Ilic N, Hwang J, Hong AL, Giacomelli AO, Gjoerup O, Root DE, Hahn WC. SMAD4 represses FOSL1 expression and pancreatic cancer metastatic colonization. Cell Rep 2021; 36:109443. [PMID: 34320363 PMCID: PMC8350598 DOI: 10.1016/j.celrep.2021.109443] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 04/20/2020] [Revised: 04/26/2021] [Accepted: 07/02/2021] [Indexed: 02/07/2023] Open
Abstract
Metastasis is a complex and poorly understood process. In pancreatic cancer, loss of the transforming growth factor (TGF)-β/BMP effector SMAD4 is correlated with changes in altered histopathological transitions, metastatic disease, and poor prognosis. In this study, we use isogenic cancer cell lines to identify SMAD4 regulated genes that contribute to the development of metastatic colonization. We perform an in vivo screen identifying FOSL1 as both a SMAD4 target and sufficient to drive colonization to the lung. The targeting of these genes early in treatment may provide a therapeutic benefit.
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Affiliation(s)
- Chao Dai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan P Rennhack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Taylor E Arnoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maneesha Thaker
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott T Younger
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - August Yue Huang
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Annan Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Belinda Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Evan Mun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Northeastern University, Boston, MA 02115, USA
| | - Joyce T O'Connell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ying Huang
- Molecular Pathology Core Lab, Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Katherine Labella
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jessica A Talamas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ji Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nina Ilic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justin Hwang
- Masonic Cancer Center and Department of Medicine, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Andrew L Hong
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Andrew O Giacomelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Ole Gjoerup
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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3
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Howard TP, Oberlick EM, Rees MG, Arnoff TE, Pham MT, Brenan L, DoCarmo M, Hong AL, Kugener G, Chou HC, Drosos Y, Mathias KM, Ramos P, Seashore-Ludlow B, Giacomelli AO, Wang X, Freeman BB, Blankenship K, Hoffmann L, Tiv HL, Gokhale PC, Johannessen CM, Stewart EA, Schreiber SL, Hahn WC, Roberts CWM. Rhabdoid Tumors Are Sensitive to the Protein-Translation Inhibitor Homoharringtonine. Clin Cancer Res 2020; 26:4995-5006. [PMID: 32631955 DOI: 10.1158/1078-0432.ccr-19-2717] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 05/30/2020] [Accepted: 06/29/2020] [Indexed: 12/31/2022]
Abstract
PURPOSE Rhabdoid tumors are devastating pediatric cancers in need of improved therapies. We sought to identify small molecules that exhibit in vitro and in vivo efficacy against preclinical models of rhabdoid tumor. EXPERIMENTAL DESIGN We screened eight rhabdoid tumor cell lines with 481 small molecules and compared their sensitivity with that of 879 other cancer cell lines. Genome-scale CRISPR-Cas9 inactivation screens in rhabdoid tumors were analyzed to confirm target vulnerabilities. Gene expression and CRISPR-Cas9 data were queried across cell lines and primary rhabdoid tumors to discover biomarkers of small-molecule sensitivity. Molecular correlates were validated by manipulating gene expression. Subcutaneous rhabdoid tumor xenografts were treated with the most effective drug to confirm in vitro results. RESULTS Small-molecule screening identified the protein-translation inhibitor homoharringtonine (HHT), an FDA-approved treatment for chronic myelogenous leukemia (CML), as the sole drug to which all rhabdoid tumor cell lines were selectively sensitive. Validation studies confirmed the sensitivity of rhabdoid tumor to HHT was comparable with that of CML cell lines. Low expression of the antiapoptotic gene BCL2L1, which encodes Bcl-XL, was the strongest predictor of HHT sensitivity, and HHT treatment consistently depleted Mcl-1, the synthetic-lethal antiapoptotic partner of Bcl-XL. Rhabdoid tumor cell lines and primary-tumor samples expressed low BCL2L1, and overexpression of BCL2L1 induced resistance to HHT in rhabdoid tumor cells. Furthermore, HHT treatment inhibited rhabdoid tumor cell line and patient-derived xenograft growth in vivo. CONCLUSIONS Rhabdoid tumor cell lines and xenografts are highly sensitive to HHT, at least partially due to their low expression of BCL2L1. HHT may have therapeutic potential against rhabdoid tumors.
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Affiliation(s)
- Thomas P Howard
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Elaine M Oberlick
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Matthew G Rees
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Taylor E Arnoff
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Minh-Tam Pham
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lisa Brenan
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Mariana DoCarmo
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Andrew L Hong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Pediatrics, Emory University, Atlanta, Georgia
| | | | - Hsien-Chao Chou
- Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yiannis Drosos
- Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kaeli M Mathias
- Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Pilar Ramos
- Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Andrew O Giacomelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Xiaofeng Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | - Burgess B Freeman
- Preclinical Pharmacokinetics Shared Resource, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kaley Blankenship
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Lauren Hoffmann
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hong L Tiv
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Prafulla C Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Elizabeth A Stewart
- Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee. .,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Charles W M Roberts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
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4
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Schauer NJ, Liu X, Magin RS, Doherty LM, Chan WC, Ficarro SB, Hu W, Roberts RM, Iacob RE, Stolte B, Giacomelli AO, Perera S, McKay K, Boswell SA, Weisberg EL, Ray A, Chauhan D, Dhe-Paganon S, Anderson KC, Griffin JD, Li J, Hahn WC, Sorger PK, Engen JR, Stegmaier K, Marto JA, Buhrlage SJ. Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism. Sci Rep 2020; 10:5324. [PMID: 32210275 PMCID: PMC7093416 DOI: 10.1038/s41598-020-62076-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [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: 01/14/2019] [Accepted: 02/25/2020] [Indexed: 12/21/2022] Open
Abstract
Ubiquitin specific peptidase 7 (USP7) is a deubiquitinating enzyme (DUB) that removes ubiquitin tags from specific protein substrates in order to alter their degradation rate and sub-cellular localization. USP7 has been proposed as a therapeutic target in several cancers because it has many reported substrates with a role in cancer progression, including FOXO4, MDM2, N-Myc, and PTEN. The multi-substrate nature of USP7, combined with the modest potency and selectivity of early generation USP7 inhibitors, has presented a challenge in defining predictors of response to USP7 and potential patient populations that would benefit most from USP7-targeted drugs. Here, we describe the structure-guided development of XL177A, which irreversibly inhibits USP7 with sub-nM potency and selectivity across the human proteome. Evaluation of the cellular effects of XL177A reveals that selective USP7 inhibition suppresses cancer cell growth predominantly through a p53-dependent mechanism: XL177A specifically upregulates p53 transcriptional targets transcriptome-wide, hotspot mutations in TP53 but not any other genes predict response to XL177A across a panel of ~500 cancer cell lines, and TP53 knockout rescues XL177A-mediated growth suppression of TP53 wild-type (WT) cells. Together, these findings suggest TP53 mutational status as a biomarker for response to USP7 inhibition. We find that Ewing sarcoma and malignant rhabdoid tumor (MRT), two pediatric cancers that are sensitive to other p53-dependent cytotoxic drugs, also display increased sensitivity to XL177A.
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Affiliation(s)
- Nathan J Schauer
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Robert S Magin
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Laura M Doherty
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wanyi Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rebekka M Roberts
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Björn Stolte
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Andrew O Giacomelli
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Kyle McKay
- Department of Chemistry, University of Vermont, Burlington, VT, USA
| | - Sarah A Boswell
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arghya Ray
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dharminder Chauhan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ken C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James D Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, VT, USA
| | - William C Hahn
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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5
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Boettcher S, Miller PG, Sharma R, McConkey M, Leventhal M, Krivtsov AV, Giacomelli AO, Wong W, Kim J, Chao S, Kurppa KJ, Yang X, Milenkowic K, Piccioni F, Root DE, Rücker FG, Flamand Y, Neuberg D, Lindsley RC, Jänne PA, Hahn WC, Jacks T, Döhner H, Armstrong SA, Ebert BL. A dominant-negative effect drives selection of TP53 missense mutations in myeloid malignancies. Science 2020; 365:599-604. [PMID: 31395785 DOI: 10.1126/science.aax3649] [Citation(s) in RCA: 227] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022]
Abstract
TP53, which encodes the tumor suppressor p53, is the most frequently mutated gene in human cancer. The selective pressures shaping its mutational spectrum, dominated by missense mutations, are enigmatic, and neomorphic gain-of-function (GOF) activities have been implicated. We used CRISPR-Cas9 to generate isogenic human leukemia cell lines of the most common TP53 missense mutations. Functional, DNA-binding, and transcriptional analyses revealed loss of function but no GOF effects. Comprehensive mutational scanning of p53 single-amino acid variants demonstrated that missense variants in the DNA-binding domain exert a dominant-negative effect (DNE). In mice, the DNE of p53 missense variants confers a selective advantage to hematopoietic cells on DNA damage. Analysis of clinical outcomes in patients with acute myeloid leukemia showed no evidence of GOF for TP53 missense mutations. Thus, a DNE is the primary unit of selection for TP53 missense mutations in myeloid malignancies.
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Affiliation(s)
- Steffen Boettcher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Peter G Miller
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rohan Sharma
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marie McConkey
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Leventhal
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrei V Krivtsov
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew O Giacomelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,The Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Waihay Wong
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jesi Kim
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sherry Chao
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Department of Biomedical Informatics, Harvard University, Boston, MA 02115, USA
| | - Kari J Kurppa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xiaoping Yang
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Kirsten Milenkowic
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Federica Piccioni
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Frank G Rücker
- Department of Internal Medicine III, University of Ulm, 89081 Ulm, Germany
| | - Yael Flamand
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hartmut Döhner
- Department of Internal Medicine III, University of Ulm, 89081 Ulm, Germany
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. .,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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6
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Hwang JH, Seo JH, Beshiri ML, Wankowicz S, Liu D, Cheung A, Li J, Qiu X, Hong AL, Botta G, Golumb L, Richter C, So J, Sandoval GJ, Giacomelli AO, Ly SH, Han C, Dai C, Pakula H, Sheahan A, Piccioni F, Gjoerup O, Loda M, Sowalsky AG, Ellis L, Long H, Root DE, Kelly K, Van Allen EM, Freedman ML, Choudhury AD, Hahn WC. CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer. Cell Rep 2019; 29:2355-2370.e6. [PMID: 31747605 PMCID: PMC6886683 DOI: 10.1016/j.celrep.2019.10.068] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 05/17/2019] [Revised: 08/08/2019] [Accepted: 10/15/2019] [Indexed: 12/24/2022] Open
Abstract
Androgen-receptor (AR) inhibitors, including enzalutamide, are used for treatment of all metastatic castration-resistant prostate cancers (mCRPCs). However, some patients develop resistance or never respond. We find that the transcription factor CREB5 confers enzalutamide resistance in an open reading frame (ORF) expression screen and in tumor xenografts. CREB5 overexpression is essential for an enzalutamide-resistant patient-derived organoid. In AR-expressing prostate cancer cells, CREB5 interactions enhance AR activity at a subset of promoters and enhancers upon enzalutamide treatment, including MYC and genes involved in the cell cycle. In mCRPC, we found recurrent amplification and overexpression of CREB5. Our observations identify CREB5 as one mechanism that drives resistance to AR antagonists in prostate cancers.
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Affiliation(s)
- Justin H Hwang
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ji-Heui Seo
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael L Beshiri
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stephanie Wankowicz
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Liu
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander Cheung
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ji Li
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xintao Qiu
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew L Hong
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ginevra Botta
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lior Golumb
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jonathan So
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gabriel J Sandoval
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Andrew O Giacomelli
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Seav Huong Ly
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Celine Han
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chao Dai
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Anjali Sheahan
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Ole Gjoerup
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Massimo Loda
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Adam G Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Leigh Ellis
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Henry Long
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kathleen Kelly
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Eliezer M Van Allen
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Atish D Choudhury
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Brigham and Women's Hospital, Boston, MA, USA.
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7
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Howard TP, Arnoff TE, Song MR, Giacomelli AO, Wang X, Hong AL, Dharia NV, Wang S, Vazquez F, Pham MT, Morgan AM, Wachter F, Bird GH, Kugener G, Oberlick EM, Rees MG, Tiv H, Hwang JH, Walsh KH, Cook A, Krill-Burger JM, Tsherniak A, Gokhale PC, Park PJ, Stegmaier K, Walensky LD, Hahn WC, Roberts CW. Abstract 2867: MDM2 and MDM4 are therapeutic vulnerabilities in malignant rhabdoid tumors. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2867] [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
Malignant rhabdoid tumors (MRT) are aggressive cancers of early childhood that are largely resistant to traditional therapies. MRT exhibit a remarkably low mutation rate, with no recurrent mutations beyond the defining biallelic inactivating mutation in SMARCB1, a core subunit of the SWI/SNF (BAF) chromatin-remodeling complex. Thus, MRT do not display traditional oncogenic mutations that are amenable to targeted therapies, limiting their use for this disease. In order to nominate new drug targets for MRT, we screened MRT cell lines with large-scale RNAi, CRISPR-Cas9, and small-molecule libraries. The most significant vulnerabilities consistent across all three screens were MDM2 and MDM4, the major negative regulators of p53. We found that MRT cell lines are more sensitive than other p53 wild-type cancer cell lines to both idasanutlin (MDM2-specific) and ATSP-7041 (MDM2/4-dual) in vitro. Both inhibitors induced substantial activation of the p53 pathway in MRT cell lines, which responded with permanent apoptotic or senescent cell fate decisions. CRISPR-Cas9-mediated inactivation of TP53 caused a significant resistance to these compounds, confirming that on-target mechanisms were responsible for MRT sensitivity. We found that loss of SMARCB1 sensitizes MRT cells to idasanutlin by shifting the p53 response towards apoptosis. In MRT xenograft studies, both idasanutlin and ATSP-7041 slowed tumor growth. Most strikingly, an idasanutlin pulse of only five days was sufficient to induce sizable regression of all tumors, which remained complete and durable in 50% of mice. Finally, gene expression analysis of primary MRT predicts that, like cell lines and xenografts, MRT in patients are likely to be sensitive to MDM2 inhibition. Collectively, these studies describe a genetic link between SWI/SNF complex mutations and p53, while providing evidence to support the use of MDM2 and MDM2/4 inhibitors that have already entered clinical trials for the treatment of this devastating pediatric cancer.
Citation Format: Thomas P. Howard, Taylor E. Arnoff, Melinda R. Song, Andrew O. Giacomelli, Xiaofeng Wang, Andrew L. Hong, Neekesh V. Dharia, Su Wang, Francisca Vazquez, Minh-Tam Pham, Ann M. Morgan, Franziska Wachter, Gregory H. Bird, Guillaume Kugener, Elaine M. Oberlick, Matthew G. Rees, Hong Tiv, Justin H. Hwang, Katherine H. Walsh, April Cook, John M. Krill-Burger, Aviad Tsherniak, Prafulla C. Gokhale, Peter J. Park, Kimberly Stegmaier, Loren D. Walensky, William C. Hahn, Charles W. Roberts. MDM2 and MDM4 are therapeutic vulnerabilities in malignant rhabdoid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2867.
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Affiliation(s)
| | | | | | | | | | | | | | - Su Wang
- 3Harvard Medical School, Boston, MA
| | | | | | | | | | | | | | | | | | - Hong Tiv
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - April Cook
- 1Dana-Farber Cancer Institute, Boston, MA
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8
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Howard TP, Arnoff TE, Song MR, Giacomelli AO, Wang X, Hong AL, Dharia NV, Wang S, Vazquez F, Pham MT, Morgan AM, Wachter F, Bird GH, Kugener G, Oberlick EM, Rees MG, Tiv HL, Hwang JH, Walsh KH, Cook A, Krill-Burger JM, Tsherniak A, Gokhale PC, Park PJ, Stegmaier K, Walensky LD, Hahn WC, Roberts CWM. MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer Res 2019; 79:2404-2414. [PMID: 30755442 DOI: 10.1158/0008-5472.can-18-3066] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/28/2018] [Accepted: 02/07/2019] [Indexed: 12/21/2022]
Abstract
Malignant rhabdoid tumors (MRT) are highly aggressive pediatric cancers that respond poorly to current therapies. In this study, we screened several MRT cell lines with large-scale RNAi, CRISPR-Cas9, and small-molecule libraries to identify potential drug targets specific for these cancers. We discovered MDM2 and MDM4, the canonical negative regulators of p53, as significant vulnerabilities. Using two compounds currently in clinical development, idasanutlin (MDM2-specific) and ATSP-7041 (MDM2/4-dual), we show that MRT cells were more sensitive than other p53 wild-type cancer cell lines to inhibition of MDM2 alone as well as dual inhibition of MDM2/4. These compounds caused significant upregulation of the p53 pathway in MRT cells, and sensitivity was ablated by CRISPR-Cas9-mediated inactivation of TP53. We show that loss of SMARCB1, a subunit of the SWI/SNF (BAF) complex mutated in nearly all MRTs, sensitized cells to MDM2 and MDM2/4 inhibition by enhancing p53-mediated apoptosis. Both MDM2 and MDM2/4 inhibition slowed MRT xenograft growth in vivo, with a 5-day idasanutlin pulse causing marked regression of all xenografts, including durable complete responses in 50% of mice. Together, these studies identify a genetic connection between mutations in the SWI/SNF chromatin-remodeling complex and the tumor suppressor gene TP53 and provide preclinical evidence to support the targeting of MDM2 and MDM4 in this often-fatal pediatric cancer. SIGNIFICANCE: This study identifies two targets, MDM2 and MDM4, as vulnerabilities in a deadly pediatric cancer and provides preclinical evidence that compounds inhibiting these proteins have therapeutic potential.
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Affiliation(s)
- Thomas P Howard
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Taylor E Arnoff
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Melinda R Song
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew O Giacomelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Xiaofeng Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Andrew L Hong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Su Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | | | - Minh-Tam Pham
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ann M Morgan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Franziska Wachter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gregory H Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Elaine M Oberlick
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Matthew G Rees
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Hong L Tiv
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Justin H Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Katherine H Walsh
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - April Cook
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Prafulla C Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Charles W M Roberts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Oncology, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee
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9
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Giacomelli AO, Yang X, Lintner RE, McFarland JM, Duby M, Kim J, Howard TP, Takeda DY, Ly SH, Kim E, Gannon HS, Hurhula B, Sharpe T, Goodale A, Fritchman B, Steelman S, Vazquez F, Tsherniak A, Aguirre AJ, Doench JG, Piccioni F, Roberts CWM, Meyerson M, Getz G, Johannessen CM, Root DE, Hahn WC. Mutational processes shape the landscape of TP53 mutations in human cancer. Nat Genet 2018; 50:1381-1387. [PMID: 30224644 PMCID: PMC6168352 DOI: 10.1038/s41588-018-0204-y] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [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: 11/22/2017] [Accepted: 07/26/2018] [Indexed: 12/11/2022]
Abstract
Unlike most tumor suppressor genes, the most common genetic alterations in TP53 are missense mutations1,2. Mutant p53 protein is often abundantly expressed in cancers, and specific allelic variants exhibit dominant-negative or gain-of-function activities in experimental models3–8. To gain a systematic view of p53 function, we interrogated loss-of-function screens conducted in hundreds of human cancer cell lines and performed TP53 saturation mutagenesis screens in an isogenic pair of TP53-wild-type and -null cell lines. We found that loss or dominant-negative inhibition of p53 function reliably enhanced cellular fitness. By integrating these data with the COSMIC mutational signatures database9,10, we developed a statistical model that describes the TP53 mutational spectrum as a function of the baseline probability of acquiring each mutation and the fitness advantage conferred by attenuation of p53 activity. Collectively, these observations show that widely-acting and tissue-specific mutational processes combine with phenotypic selection to dictate the frequencies of recurrent TP53 mutations.
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Affiliation(s)
- Andrew O Giacomelli
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoping Yang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Marc Duby
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thomas P Howard
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - David Y Takeda
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Seav Huong Ly
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eejung Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hugh S Gannon
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brian Hurhula
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ted Sharpe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Francisca Vazquez
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Andrew J Aguirre
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Charles W M Roberts
- Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Massachusetts General Hospital Center for Cancer Research, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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10
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Li J, Choi PS, Chaffer CL, Labella K, Hwang JH, Giacomelli AO, Kim JW, Ilic N, Doench JG, Ly SH, Dai C, Hagel K, Hong AL, Gjoerup O, Goel S, Ge JY, Root DE, Zhao JJ, Brooks AN, Weinberg RA, Hahn WC. An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. eLife 2018; 7:37184. [PMID: 30059005 PMCID: PMC6103745 DOI: 10.7554/elife.37184] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [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: 04/01/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing of mRNA precursors represents a key gene expression regulatory step and permits the generation of distinct protein products with diverse functions. In a genome-scale expression screen for inducers of the epithelial-to-mesenchymal transition (EMT), we found a striking enrichment of RNA-binding proteins. We validated that QKI and RBFOX1 were necessary and sufficient to induce an intermediate mesenchymal cell state and increased tumorigenicity. Using RNA-seq and eCLIP analysis, we found that QKI and RBFOX1 coordinately regulated the splicing and function of the actin-binding protein FLNB, which plays a causal role in the regulation of EMT. Specifically, the skipping of FLNB exon 30 induced EMT by releasing the FOXC1 transcription factor. Moreover, skipping of FLNB exon 30 is strongly associated with EMT gene signatures in basal-like breast cancer patient samples. These observations identify a specific dysregulation of splicing, which regulates tumor cell plasticity and is frequently observed in human cancer. As the human body develops, countless cells change from one state into another. Two important cell states are known as epithelial and mesenchymal. Cells in the epithelial state tend to be tightly connected and form barriers, like skin cells. Mesenchymal state cells are loosely organized, move around more and make up connective tissues. Some cells alternate between these states via an epithelial-to-mesenchymal transition (EMT for short) and back again. Without this transition, certain organs would not develop and wounds would not heal. Yet, cancer cells also use this transition to spread to distant sites of the body. Such cancers are often the most aggressive, and therefore the most deadly. The epithelial-to-mesenchymal transition is dynamically regulated in a reversible manner. For example, the genes for some proteins might only be active in the epithelial state and further reinforce this state by turning on other ‘epithelial genes’. Alternatively, there might be differences in the processing of mRNA molecules – the intermediate molecules between DNA and protein – that result in the production of different proteins in epithelial and mesenchymal cells. Li, Choi et al. wanted to know which of the thousands of human genes can endow epithelial state cells with mesenchymal characteristics. A better understanding of the switch could help to prevent cancers undergoing an epithelial-to-mesenchymal transition. From a large-scale experiment in human breast cancer cells, Li, Choi et al. found that a group of proteins that bind and modify mRNA molecules are important for the epithelial-to-mesenchymal transition. Two proteins in particular promoted the transition, most likely by binding to the mRNA of a third protein called FLNB and removing a small piece of it. FLNB normally works to prevent the epithelial-to-mesenchymal transition, but the smaller protein encoded by the shorter mRNA promoted the transition by turning on ‘mesenchymal genes’. This switching between different FLNB proteins happens in some of the more aggressive breast cancers, which also contain mesenchymal cells. Finding out which FLNB protein is made in a given cancer may provide an indication of its aggressiveness. Also, looking for drugs that can target the mRNA-binding proteins or FLNB may one day lead to new treatments for some of the most aggressive breast cancers.
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Affiliation(s)
- Ji Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Peter S Choi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Christine L Chaffer
- Whitehead Institute for Biomedical Research and MIT, Cambridge, United States.,Garvan Institute of Medical Research, Sydney, Australia
| | - Katherine Labella
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States
| | - Justin H Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Andrew O Giacomelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jong Wook Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Nina Ilic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Seav Huong Ly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Chao Dai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Kimberly Hagel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States
| | - Andrew L Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Ole Gjoerup
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Shom Goel
- Harvard Medical School, Boston, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, United States
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jean J Zhao
- Harvard Medical School, Boston, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Angela N Brooks
- University of California, Santa Cruz, Santa Cruz, United States
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research and MIT, Cambridge, United States
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
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11
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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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12
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Abazeed ME, Adams DJ, Hurov KE, Tamayo P, Creighton CJ, Sonkin D, Giacomelli AO, Du C, Fries DF, Wong KK, Mesirov JP, Loeffler JS, Schreiber SL, Hammerman PS, Meyerson M. Integrative radiogenomic profiling of squamous cell lung cancer. Cancer Res 2013; 73:6289-98. [PMID: 23980093 PMCID: PMC3856255 DOI: 10.1158/0008-5472.can-13-1616] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Radiotherapy is one of the mainstays of anticancer treatment, but the relationship between the radiosensitivity of cancer cells and their genomic characteristics is still not well defined. Here, we report the development of a high-throughput platform for measuring radiation survival in vitro and its validation in comparison with conventional clonogenic radiation survival analysis. We combined results from this high-throughput assay with genomic parameters in cell lines from squamous cell lung carcinoma, which is standardly treated by radiotherapy, to identify parameters that predict radiation sensitivity. We showed that activation of NFE2L2, a frequent event in lung squamous cancers, confers radiation resistance. An expression-based, in silico screen nominated inhibitors of phosphoinositide 3-kinase (PI3K) as NFE2L2 antagonists. We showed that the selective PI3K inhibitor, NVP-BKM120, both decreased NRF2 protein levels and sensitized NFE2L2 or KEAP1-mutant cells to radiation. We then combined results from this high-throughput assay with single-sample gene set enrichment analysis of gene expression data. The resulting analysis identified pathways implicated in cell survival, genotoxic stress, detoxification, and innate and adaptive immunity as key correlates of radiation sensitivity. The integrative and high-throughput methods shown here for large-scale profiling of radiation survival and genomic features of solid-tumor-derived cell lines should facilitate tumor radiogenomics and the discovery of genotype-selective radiation sensitizers and protective agents.
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Affiliation(s)
| | - Drew J. Adams
- Chemical Biology Program, Broad Institute, Cambridge, MA 02142
| | | | - Pablo Tamayo
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Chad J. Creighton
- Department of Medicine, Baylor College of Medicine, Houston, Texas 77030
| | - Dmitriy Sonkin
- Novartis Institute for Biomedical Research, Cambridge, MA 02139
| | | | | | - Daniel F. Fries
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Kwok-Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
- Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02214
| | | | - Jay S. Loeffler
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Stuart L. Schreiber
- Chemical Biology Program, Broad Institute, Cambridge, MA 02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Howard Hughes Medical Institute, Broad Institute, Cambridge, MA 02142
| | - Peter S. Hammerman
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts 02215
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13
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Hagerstrand D, Tong A, Schumacher SE, Ilic N, Shen RR, Cheung HW, Vazquez F, Shrestha Y, Kim SY, Giacomelli AO, Rosenbluh J, Schinzel AC, Spardy NA, Barbie DA, Mermel CH, Weir BA, Garraway LA, Tamayo P, Mesirov JP, Beroukhim R, Hahn WC. Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers. Cancer Discov 2013; 3:1044-57. [PMID: 23764425 DOI: 10.1158/2159-8290.cd-12-0592] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
UNLABELLED 3q26 is frequently amplified in several cancer types with a common amplified region containing 20 genes. To identify cancer driver genes in this region, we interrogated the function of each of these genes by loss- and gain-of-function genetic screens. Specifically, we found that TLOC1 (SEC62) was selectively required for the proliferation of cell lines with 3q26 amplification. Increased TLOC1 expression induced anchorage-independent growth, and a second 3q26 gene, SKIL (SNON), facilitated cell invasion in immortalized human mammary epithelial cells. Expression of both TLOC1 and SKIL induced subcutaneous tumor growth. Proteomic studies showed that TLOC1 binds to DDX3X, which is essential for TLOC1-induced transformation and affected protein translation. SKIL induced invasion through upregulation of SLUG (SNAI2) expression. Together, these studies identify TLOC1 and SKIL as driver genes at 3q26 and more broadly suggest that cooperating genes may be coamplified in other regions with somatic copy number gain. SIGNIFICANCE These studies identify TLOC1 and SKIL as driver genes in 3q26. These observations provide evidence that regions of somatic copy number gain may harbor cooperating genes of different but complementary functions.
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Affiliation(s)
- Daniel Hagerstrand
- 1Departments of Medical Oncology and 2Cancer Biology; 3Center for Cancer Genome Discovery, Dana-Farber Cancer Institute;4Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; 5Broad Institute of Harvard and MIT, Cambridge, Massachusetts; and 6Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina
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14
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Sachlos E, Risueño RM, Laronde S, Shapovalova Z, Lee JH, Russell J, Malig M, McNicol JD, Fiebig-Comyn A, Graham M, Levadoux-Martin M, Lee JB, Giacomelli AO, Hassell JA, Fischer-Russell D, Trus MR, Foley R, Leber B, Xenocostas A, Brown ED, Collins TJ, Bhatia M. Identification of drugs including a dopamine receptor antagonist that selectively target cancer stem cells. Cell 2012; 149:1284-97. [PMID: 22632761 DOI: 10.1016/j.cell.2012.03.049] [Citation(s) in RCA: 359] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Revised: 01/20/2012] [Accepted: 03/29/2012] [Indexed: 12/22/2022]
Abstract
Selective targeting of cancer stem cells (CSCs) offers promise for a new generation of therapeutics. However, assays for both human CSCs and normal stem cells that are amenable to robust biological screens are limited. Using a discovery platform that reveals differences between neoplastic and normal human pluripotent stem cells (hPSC), we identify small molecules from libraries of known compounds that induce differentiation to overcome neoplastic self-renewal. Surprisingly, thioridazine, an antipsychotic drug, selectively targets the neoplastic cells, and impairs human somatic CSCs capable of in vivo leukemic disease initiation while having no effect on normal blood SCs. The drug antagonizes dopamine receptors that are expressed on CSCs and on breast cancer cells as well. These results suggest that dopamine receptors may serve as a biomarker for diverse malignancies, demonstrate the utility of using neoplastic hPSCs for identifying CSC-targeting drugs, and provide support for the use of differentiation as a therapeutic strategy.
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Affiliation(s)
- Eleftherios Sachlos
- McMaster Stem Cell and Cancer Research Institute, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
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15
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Hallett RM, Kondratyev MK, Giacomelli AO, Nixon AML, Girgis-Gabardo A, Ilieva D, Hassell JA. Small molecule antagonists of the Wnt/β-catenin signaling pathway target breast tumor-initiating cells in a Her2/Neu mouse model of breast cancer. PLoS One 2012; 7:e33976. [PMID: 22470504 PMCID: PMC3314694 DOI: 10.1371/journal.pone.0033976] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 02/20/2012] [Indexed: 12/18/2022] Open
Abstract
Background Recent evidence suggests that human breast cancer is sustained by a minor subpopulation of breast tumor-initiating cells (BTIC), which confer resistance to anticancer therapies and consequently must be eradicated to achieve durable breast cancer cure. Methods/Findings To identify signaling pathways that might be targeted to eliminate BTIC, while sparing their normal stem and progenitor cell counterparts, we performed global gene expression profiling of BTIC- and mammary epithelial stem/progenitor cell- enriched cultures derived from mouse mammary tumors and mammary glands, respectively. Such analyses suggested a role for the Wnt/Beta-catenin signaling pathway in maintaining the viability and or sustaining the self-renewal of BTICs in vitro. To determine whether the Wnt/Beta-catenin pathway played a role in BTIC processes we employed a chemical genomics approach. We found that pharmacological inhibitors of Wnt/β-catenin signaling inhibited sphere- and colony-formation by primary breast tumor cells and primary mammary epithelial cells, as well as by tumorsphere- and mammosphere-derived cells. Serial assays of self-renewal in vitro revealed that the Wnt/Beta-catenin signaling inhibitor PKF118–310 irreversibly affected BTIC, whereas it functioned reversibly to suspend the self-renewal of mammary epithelial stem/progenitor cells. Incubation of primary tumor cells in vitro with PKF118–310 eliminated their capacity to subsequently seed tumor growth after transplant into syngeneic mice. Administration of PKF118–310 to tumor-bearing mice halted tumor growth in vivo. Moreover, viable tumor cells harvested from PKF118–310 treated mice were unable to seed the growth of secondary tumors after transplant. Conclusions These studies demonstrate that inhibitors of Wnt/β-catenin signaling eradicated BTIC in vitro and in vivo and provide a compelling rationale for developing such antagonists for breast cancer therapy.
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Affiliation(s)
| | | | | | | | | | | | - John A. Hassell
- Department of Biochemistry and Biomedical Sciences, Centre for Functional Genomics, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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16
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Hallett RM, Kondratyev MK, Giacomelli AO, Nixon AML, Girgis-Gabardo A, Ilieva D, Hassell JA. Small molecule antagonists of the Wnt/β-catenin signaling pathway target breast tumor-initiating cells in a Her2/Neu mouse model of breast cancer. PLoS One 2012. [PMID: 22470504 DOI: 10.1371/journal.pone.0033976pone-d-11-22474] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Recent evidence suggests that human breast cancer is sustained by a minor subpopulation of breast tumor-initiating cells (BTIC), which confer resistance to anticancer therapies and consequently must be eradicated to achieve durable breast cancer cure. METHODS/FINDINGS To identify signaling pathways that might be targeted to eliminate BTIC, while sparing their normal stem and progenitor cell counterparts, we performed global gene expression profiling of BTIC- and mammary epithelial stem/progenitor cell- enriched cultures derived from mouse mammary tumors and mammary glands, respectively. Such analyses suggested a role for the Wnt/Beta-catenin signaling pathway in maintaining the viability and or sustaining the self-renewal of BTICs in vitro. To determine whether the Wnt/Beta-catenin pathway played a role in BTIC processes we employed a chemical genomics approach. We found that pharmacological inhibitors of Wnt/β-catenin signaling inhibited sphere- and colony-formation by primary breast tumor cells and primary mammary epithelial cells, as well as by tumorsphere- and mammosphere-derived cells. Serial assays of self-renewal in vitro revealed that the Wnt/Beta-catenin signaling inhibitor PKF118-310 irreversibly affected BTIC, whereas it functioned reversibly to suspend the self-renewal of mammary epithelial stem/progenitor cells. Incubation of primary tumor cells in vitro with PKF118-310 eliminated their capacity to subsequently seed tumor growth after transplant into syngeneic mice. Administration of PKF118-310 to tumor-bearing mice halted tumor growth in vivo. Moreover, viable tumor cells harvested from PKF118-310 treated mice were unable to seed the growth of secondary tumors after transplant. CONCLUSIONS These studies demonstrate that inhibitors of Wnt/β-catenin signaling eradicated BTIC in vitro and in vivo and provide a compelling rationale for developing such antagonists for breast cancer therapy.
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Affiliation(s)
- Robin M Hallett
- Department of Biochemistry and Biomedical Sciences, Centre for Functional Genomics, McMaster University, Hamilton, Ontario, Canada
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17
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Kurpios NA, MacNeil L, Shepherd TG, Gludish DW, Giacomelli AO, Hassell JA. The Pea3 Ets transcription factor regulates differentiation of multipotent progenitor cells during mammary gland development. Dev Biol 2008; 325:106-21. [PMID: 18977342 DOI: 10.1016/j.ydbio.2008.09.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 09/29/2008] [Accepted: 09/29/2008] [Indexed: 10/21/2022]
Abstract
The Pea3 Ets transcription factor is overexpressed in breast tumors suggesting that it plays a role in mammary oncogenesis. However, the normal biological function of Pea3 in the mammary gland is not known. Here we report that Pea3 was expressed in the epithelium of the mouse mammary anlagen commensurate with their genesis, and at later times in the nipple and mammary ducts of female embryos. In adult mice Pea3 transcripts peaked at the onset of puberty and early pregnancy, times of active epithelial cell proliferation and differentiation. Pea3 was expressed in all progenitor cap cells and rare body cells of terminal end buds, and in the myoepithelial cells of ducts and alveoli. Analyses of the mammary glands of Pea3-null mice during puberty revealed an increased number of terminal end buds and an increased fraction of proliferating progenitor cells within these structures compared to their wild type littermates. Tissue transplant experiments demonstrated that these phenotypes were intrinsic to the Pea3-null mammary epithelium. During pregnancy, mammary glands isolated from Pea3-null females had impaired alveolar development as revealed by a decreased fraction of alveolar structures. We performed in vitro colony forming assays of mammary epithelial cells and discovered that loss of Pea3 altered the distribution of specific multipotent progenitor cells. Double-immunofluorescence confirmed that multipotential progenitors co-expressing markers of the myoepithelial and luminal epithelial lineage were amplified in the mammary glands of Pea3-null mice by comparison to their wild type counterparts. We propose that Pea3 functions in multipotential progenitors to regulate their lineage-specific differentiation potential.
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Affiliation(s)
- Natasza A Kurpios
- Department of Biochemistry and Biomedical Sciences, Centre for Functional Genomics, McMaster University, Hamilton, Ontario, Canada
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