1
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Bei Y, Bramé L, Kirchner M, Fritsche-Guenther R, Kunz S, Bhattacharya A, Rusu MC, Gürgen D, Dubios FPB, Köppke JKC, Proba J, Wittstruck N, Sidorova OA, Chamorro González R, Dorado Garcia H, Brückner L, Xu R, Giurgiu M, Rodriguez-Fos E, Yu Q, Spanjaard B, Koche RP, Schmitt CA, Schulte JH, Eggert A, Haase K, Kirwan J, Hagemann AIH, Mertins P, Dörr JR, Henssen AG. Passenger Gene Coamplifications Create Collateral Therapeutic Vulnerabilities in Cancer. Cancer Discov 2024; 14:492-507. [PMID: 38197697 PMCID: PMC10911929 DOI: 10.1158/2159-8290.cd-23-1189] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/10/2023] [Revised: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024]
Abstract
DNA amplifications in cancer do not only harbor oncogenes. We sought to determine whether passenger coamplifications could create collateral therapeutic vulnerabilities. Through an analysis of >3,000 cancer genomes followed by the interrogation of CRISPR-Cas9 loss-of-function screens across >700 cancer cell lines, we determined that passenger coamplifications are accompanied by distinct dependency profiles. In a proof-of-principle study, we demonstrate that the coamplification of the bona fide passenger gene DEAD-Box Helicase 1 (DDX1) creates an increased dependency on the mTOR pathway. Interaction proteomics identified tricarboxylic acid (TCA) cycle components as previously unrecognized DDX1 interaction partners. Live-cell metabolomics highlighted that this interaction could impair TCA activity, which in turn resulted in enhanced mTORC1 activity. Consequently, genetic and pharmacologic disruption of mTORC1 resulted in pronounced cell death in vitro and in vivo. Thus, structurally linked coamplification of a passenger gene and an oncogene can result in collateral vulnerabilities. SIGNIFICANCE We demonstrate that coamplification of passenger genes, which were largely neglected in cancer biology in the past, can create distinct cancer dependencies. Because passenger coamplifications are frequent in cancer, this principle has the potential to expand target discovery in oncology. This article is featured in Selected Articles from This Issue, p. 384.
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Affiliation(s)
- Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Luca Bramé
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Raphaela Fritsche-Guenther
- Core Unit Metabolomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Severine Kunz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
| | - Animesh Bhattacharya
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mara-Camelia Rusu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
| | - Dennis Gürgen
- Experimental Pharmacology and Oncology (EPO), Berlin, Germany
| | - Frank P B Dubios
- Institute of pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia K C Köppke
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jutta Proba
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Nadine Wittstruck
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olga Alexandra Sidorova
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Rocío Chamorro González
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lotte Brückner
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
| | - Robin Xu
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mădălina Giurgiu
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Elias Rodriguez-Fos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Qinghao Yu
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bastiaan Spanjaard
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Clemens A Schmitt
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kerstin Haase
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer Kirwan
- Core Unit Metabolomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anja I H Hagemann
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Mertins
- Core Unit Proteomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jan R Dörr
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
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2
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Ciceri G, Baggiolini A, Cho HS, Kshirsagar M, Benito-Kwiecinski S, Walsh RM, Aromolaran KA, Gonzalez-Hernandez AJ, Munguba H, Koo SY, Xu N, Sevilla KJ, Goldstein PA, Levitz J, Leslie CS, Koche RP, Studer L. An epigenetic barrier sets the timing of human neuronal maturation. Nature 2024; 626:881-890. [PMID: 38297124 PMCID: PMC10881400 DOI: 10.1038/s41586-023-06984-8] [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: 05/17/2022] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
The pace of human brain development is highly protracted compared with most other species1-7. The maturation of cortical neurons is particularly slow, taking months to years to develop adult functions3-5. Remarkably, such protracted timing is retained in cortical neurons derived from human pluripotent stem cells (hPSCs) during in vitro differentiation or upon transplantation into the mouse brain4,8,9. Those findings suggest the presence of a cell-intrinsic clock setting the pace of neuronal maturation, although the molecular nature of this clock remains unknown. Here we identify an epigenetic developmental programme that sets the timing of human neuronal maturation. First, we developed a hPSC-based approach to synchronize the birth of cortical neurons in vitro which enabled us to define an atlas of morphological, functional and molecular maturation. We observed a slow unfolding of maturation programmes, limited by the retention of specific epigenetic factors. Loss of function of several of those factors in cortical neurons enables precocious maturation. Transient inhibition of EZH2, EHMT1 and EHMT2 or DOT1L, at progenitor stage primes newly born neurons to rapidly acquire mature properties upon differentiation. Thus our findings reveal that the rate at which human neurons mature is set well before neurogenesis through the establishment of an epigenetic barrier in progenitor cells. Mechanistically, this barrier holds transcriptional maturation programmes in a poised state that is gradually released to ensure the prolonged timeline of human cortical neuron maturation.
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Affiliation(s)
- Gabriele Ciceri
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Arianna Baggiolini
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute of Oncology Research (IOR), Bellinzona Institutes of Science (BIOS+), Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Hyein S Cho
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meghana Kshirsagar
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Microsoft AI for Good Research, Redmond, WA, USA
| | - Silvia Benito-Kwiecinski
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan M Walsh
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Hermany Munguba
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - So Yeon Koo
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Nan Xu
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaylin J Sevilla
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter A Goldstein
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Agustinus AS, Al-Rawi D, Dameracharla B, Raviram R, Jones BSCL, Stransky S, Scipioni L, Luebeck J, Di Bona M, Norkunaite D, Myers RM, Duran M, Choi S, Weigelt B, Yomtoubian S, McPherson A, Toufektchan E, Keuper K, Mischel PS, Mittal V, Shah SP, Maciejowski J, Storchova Z, Gratton E, Ly P, Landau D, Bakhoum MF, Koche RP, Sidoli S, Bafna V, David Y, Bakhoum SF. Epigenetic dysregulation from chromosomal transit in micronuclei. Nature 2023; 619:176-183. [PMID: 37286593 PMCID: PMC10322720 DOI: 10.1038/s41586-023-06084-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [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: 11/15/2021] [Accepted: 04/14/2023] [Indexed: 06/09/2023]
Abstract
Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers1-4, but whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei5,6 and subsequent rupture of the micronuclear envelope7 profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice, as well as in cancer and non-transformed cells. Some of the changes in histone PTMs occur because of the rupture of the micronuclear envelope, whereas others are inherited from mitotic abnormalities before the micronucleus is formed. Using orthogonal approaches, we demonstrate that micronuclei exhibit extensive differences in chromatin accessibility, with a strong positional bias between promoters and distal or intergenic regions, in line with observed redistributions of histone PTMs. Inducing CIN causes widespread epigenetic dysregulation, and chromosomes that transit in micronuclei experience heritable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, as well as altering genomic copy number, CIN promotes epigenetic reprogramming and heterogeneity in cancer.
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Affiliation(s)
- Albert S Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Duaa Al-Rawi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bhargavi Dameracharla
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | | | - Bailey S C L Jones
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Lorenzo Scipioni
- School of Engineering, University of California, Irvine, Irvine, CA, USA
| | - Jens Luebeck
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | - Melody Di Bona
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Danguole Norkunaite
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Tri-institutional MD-PhD Program, New York, NY, USA
| | - Mercedes Duran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seongmin Choi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shira Yomtoubian
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eléonore Toufektchan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristina Keuper
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Paul S Mischel
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Vivek Mittal
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Maciejowski
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zuzana Storchova
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Enrico Gratton
- School of Engineering, University of California, Irvine, Irvine, CA, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dan Landau
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Mathieu F Bakhoum
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Vineet Bafna
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | - Yael David
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA.
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-institutional PhD Program in Chemical Biology, New York, NY, USA.
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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4
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Zhu C, Soto-Feliciano YM, Morris JP, Huang CH, Koche RP, Ho YJ, Banito A, Chen CWD, Shroff A, Tian S, Livshits G, Chen CC, Fennell M, Armstrong SA, Allis CD, Tschaharganeh DF, Lowe SW. MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer. eLife 2023; 12:80854. [PMID: 37261974 DOI: 10.7554/elife.80854] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 05/31/2023] [Indexed: 06/03/2023] Open
Abstract
Mutations in genes encoding components of chromatin modifying and remodeling complexes are among the most frequently observed somatic events in human cancers. For example, missense and nonsense mutations targeting the mixed lineage leukemia family member 3 (MLL3, encoded by KMT2C) histone methyltransferase occur in a range of solid tumors, and heterozygous deletions encompassing KMT2C occur in a subset of aggressive leukemias. Although MLL3 loss can promote tumorigenesis in mice, the molecular targets and biological processes by which MLL3 suppresses tumorigenesis remain poorly characterized. Here we combined genetic, epigenomic, and animal modeling approaches to demonstrate that one of the mechanisms by which MLL3 links chromatin remodeling to tumor suppression is by co-activating the Cdkn2a tumor suppressor locus. Disruption of Kmt2c cooperates with Myc overexpression in the development of murine hepatocellular carcinoma (HCC), in which MLL3 binding to the Cdkn2a locus is blunted, resulting in reduced H3K4 methylation and low expression levels of the locus-encoded tumor suppressors p16/Ink4a and p19/Arf. Conversely, elevated KMT2C expression increases its binding to the CDKN2A locus and co-activates gene transcription. Endogenous Kmt2c restoration reverses these chromatin and transcriptional effects and triggers Ink4a/Arf-dependent apoptosis. Underscoring the human relevance of this epistasis, we found that genomic alterations in KMT2C and CDKN2A were associated with similar transcriptional profiles in human HCC samples. These results collectively point to a new mechanism for disrupting CDKN2A activity during cancer development and, in doing so, link MLL3 to an established tumor suppressor network.
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Affiliation(s)
- Changyu Zhu
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Yadira M Soto-Feliciano
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - John P Morris
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Chun-Hao Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Yu-Jui Ho
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Ana Banito
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Chun-Wei David Chen
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Aditya Shroff
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Sha Tian
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Geulah Livshits
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Chi-Chao Chen
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Myles Fennell
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, United States
| | | | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
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5
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Chamorro González R, Conrad T, Stöber MC, Xu R, Giurgiu M, Rodriguez-Fos E, Kasack K, Brückner L, van Leen E, Helmsauer K, Dorado Garcia H, Stefanova ME, Hung KL, Bei Y, Schmelz K, Lodrini M, Mundlos S, Chang HY, Deubzer HE, Sauer S, Eggert A, Schulte JH, Schwarz RF, Haase K, Koche RP, Henssen AG. Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells. Nat Genet 2023; 55:880-890. [PMID: 37142849 PMCID: PMC10181933 DOI: 10.1038/s41588-023-01386-y] [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: 12/20/2021] [Accepted: 03/28/2023] [Indexed: 05/06/2023]
Abstract
Extrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe single-cell extrachromosomal circular DNA and transcriptome sequencing (scEC&T-seq), a method for parallel sequencing of circular DNAs and full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, we describe intercellular differences in ecDNA content while investigating their structural heterogeneity and transcriptional impact. Oncogene-containing ecDNAs were clonally present in cancer cells and drove intercellular oncogene expression differences. In contrast, other small circular DNAs were exclusive to individual cells, indicating differences in their selection and propagation. Intercellular differences in ecDNA structure pointed to circular recombination as a mechanism of ecDNA evolution. These results demonstrate scEC&T-seq as an approach to systematically characterize both small and large circular DNA in cancer cells, which will facilitate the analysis of these DNA elements in cancer and beyond.
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Affiliation(s)
- Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Thomas Conrad
- Genomics Technology Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maja C Stöber
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Faculty of Life Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robin Xu
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Mădălina Giurgiu
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Elias Rodriguez-Fos
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Katharina Kasack
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Potsdam, Germany
| | - Lotte Brückner
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Eric van Leen
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Maria E Stefanova
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Yi Bei
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marco Lodrini
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hedwig E Deubzer
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Sascha Sauer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Computational Cancer Biology, Center for Integrated Oncology, Cancer Research Center Cologne Essen Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany.
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany.
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6
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Ogura K, Elkrief A, Bowman AS, Koche RP, de Stanchina E, Benayed R, Mauguen A, Mattar MS, Khodos I, Meyers PA, Healey JH, Tap WD, Hameed M, Zehir A, Shukla N, Sawyers C, Bose R, Slotkin E, Ladanyi M. Prospective Clinical Genomic Profiling of Ewing Sarcoma: ERF and FGFR1 Mutations as Recurrent Secondary Alterations of Potential Biologic and Therapeutic Relevance. JCO Precis Oncol 2022; 6:e2200048. [PMID: 35952322 PMCID: PMC9384944 DOI: 10.1200/po.22.00048] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ewing sarcoma (ES) is a primitive sarcoma defined by EWSR1-ETS fusions as the primary driver alteration. To better define the landscape of cooperating secondary genetic alterations in ES, we analyzed clinical genomic profiling data of 113 patients with ES, a cohort including more adult patients (> 18 years) and more patients with advanced stage at presentation than previous genomic cohorts.
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Affiliation(s)
- Koichi Ogura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Arielle Elkrief
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elisa de Stanchina
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,AstraZeneca Pharmaceuticals, Wilmington, DE
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marissa S Mattar
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Inna Khodos
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - John H Healey
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Surgery, Orthopaedic Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - William D Tap
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,AstraZeneca Pharmaceuticals, Wilmington, DE
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Charles Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,HHMI, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rohit Bose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA.,Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA.,Department of Urology, University of California, San Francisco, San Francisco, CA.,Benioff Initiative for Prostate Cancer Research, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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7
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Li L, Kim JH, Lu W, Williams DM, Kim J, Cope L, Rampal RK, Koche RP, Xian L, Luo LZ, Vasiljevic M, Matson DR, Zhao ZJ, Rogers O, Stubbs MC, Reddy K, Romero AR, Psaila B, Spivak JL, Moliterno AR, Resar LMS. HMGA1 chromatin regulators induce transcriptional networks involved in GATA2 and proliferation during MPN progression. Blood 2022; 139:2797-2815. [PMID: 35286385 PMCID: PMC9074401 DOI: 10.1182/blood.2021013925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Received: 09/03/2021] [Accepted: 02/18/2022] [Indexed: 11/20/2022] Open
Abstract
Myeloproliferative neoplasms (MPNs) transform to myelofibrosis (MF) and highly lethal acute myeloid leukemia (AML), although the actionable mechanisms driving progression remain elusive. Here, we elucidate the role of the high mobility group A1 (HMGA1) chromatin regulator as a novel driver of MPN progression. HMGA1 is upregulated in MPN, with highest levels after transformation to MF or AML. To define HMGA1 function, we disrupted gene expression via CRISPR/Cas9, short hairpin RNA, or genetic deletion in MPN models. HMGA1 depletion in JAK2V617F AML cell lines disrupts proliferation, clonogenicity, and leukemic engraftment. Surprisingly, loss of just a single Hmga1 allele prevents progression to MF in JAK2V617F mice, decreasing erythrocytosis, thrombocytosis, megakaryocyte hyperplasia, and expansion of stem and progenitors, while preventing splenomegaly and fibrosis within the spleen and BM. RNA-sequencing and chromatin immunoprecipitation sequencing revealed HMGA1 transcriptional networks and chromatin occupancy at genes that govern proliferation (E2F, G2M, mitotic spindle) and cell fate, including the GATA2 master regulatory gene. Silencing GATA2 recapitulates most phenotypes observed with HMGA1 depletion, whereas GATA2 re-expression partially rescues leukemogenesis. HMGA1 transactivates GATA2 through sequences near the developmental enhancer (+9.5), increasing chromatin accessibility and recruiting active histone marks. Further, HMGA1 transcriptional networks, including proliferation pathways and GATA2, are activated in human MF and MPN leukemic transformation. Importantly, HMGA1 depletion enhances responses to the JAK2 inhibitor, ruxolitinib, preventing MF and prolonging survival in murine models of JAK2V617F AML. These findings illuminate HMGA1 as a key epigenetic switch involved in MPN transformation and a promising therapeutic target to treat or prevent disease progression.
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Affiliation(s)
- Liping Li
- Division of Hematology, Department of Medicine, and
| | | | - Wenyan Lu
- Division of Hematology, Department of Medicine, and
| | | | - Joseph Kim
- Division of Hematology, Department of Medicine, and
| | - Leslie Cope
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Raajit K Rampal
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Center for Epigenetics Research, Memorial Sloan Kettering Cancer Institute, New York, NY
| | - Richard P Koche
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Center for Epigenetics Research, Memorial Sloan Kettering Cancer Institute, New York, NY
| | | | - Li Z Luo
- Division of Hematology, Department of Medicine, and
| | | | - Daniel R Matson
- Blood Cancer Research Institute, Department of Cell and Regenerative Biology, UW Carbone Cancer Center, University of Wisconsin School of Medicine, Madison, WI
| | - Zhizhuang Joe Zhao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | | | | | - Karen Reddy
- Department of Biologic Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Antonio-Rodriguez Romero
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine and National Institutes of Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, UK; and
| | - Bethan Psaila
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine and National Institutes of Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, UK; and
| | - Jerry L Spivak
- Division of Hematology, Department of Medicine, and
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Linda M S Resar
- Division of Hematology, Department of Medicine, and
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
- Cellular and Molecular Medicine Graduate Program and
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD
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8
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Shakiba M, Zumbo P, Espinosa-Carrasco G, Menocal L, Dündar F, Carson SE, Bruno EM, Sanchez-Rivera FJ, Lowe SW, Camara S, Koche RP, Reuter VP, Socci ND, Whitlock B, Tamzalit F, Huse M, Hellmann MD, Wells DK, Defranoux NA, Betel D, Philip M, Schietinger A. TCR signal strength defines distinct mechanisms of T cell dysfunction and cancer evasion. J Exp Med 2022; 219:212936. [PMID: 34935874 PMCID: PMC8704919 DOI: 10.1084/jem.20201966] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 09/11/2020] [Revised: 07/07/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022] Open
Abstract
T cell receptor (TCR) signal strength is a key determinant of T cell responses. We developed a cancer mouse model in which tumor-specific CD8 T cells (TST cells) encounter tumor antigens with varying TCR signal strength. High-signal-strength interactions caused TST cells to up-regulate inhibitory receptors (IRs), lose effector function, and establish a dysfunction-associated molecular program. TST cells undergoing low-signal-strength interactions also up-regulated IRs, including PD1, but retained a cell-intrinsic functional state. Surprisingly, neither high- nor low-signal-strength interactions led to tumor control in vivo, revealing two distinct mechanisms by which PD1hi TST cells permit tumor escape; high signal strength drives dysfunction, while low signal strength results in functional inertness, where the signal strength is too low to mediate effective cancer cell killing by functional TST cells. CRISPR-Cas9-mediated fine-tuning of signal strength to an intermediate range improved anti-tumor activity in vivo. Our study defines the role of TCR signal strength in TST cell function, with important implications for T cell-based cancer immunotherapies.
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Affiliation(s)
- Mojdeh Shakiba
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY.,Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY
| | | | - Laura Menocal
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY.,Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY
| | - Sandra E Carson
- Department of Biochemistry, Cell and Molecular Biology, Weill Cornell Medicine, New York, NY
| | - Emmanuel M Bruno
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Scott W Lowe
- Cancer Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Steven Camara
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vincent P Reuter
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas D Socci
- Bioinformatics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin Whitlock
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fella Tamzalit
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Morgan Huse
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Matthew D Hellmann
- Parker Institute for Cancer Immunotherapy, San Francisco, CA.,Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, Cornell University, New York, NY
| | - Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | | | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Mary Philip
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
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9
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Quintanal-Villalonga A, Taniguchi H, Hao Y, Chow A, Zhan YA, Chavan SS, Uddin F, Allaj V, Manoj P, Shah NS, Chan JM, Offin M, Ciampricotti M, Ray-Kirton J, Egger J, Bhanot U, Linkov I, Asher M, Roehrl MH, Qiu J, de Stanchina E, Hollmann TJ, Koche RP, Sen T, Poirier JT, Rudin CM. Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy. Cancer Res 2022; 82:472-483. [PMID: 34815254 PMCID: PMC8813890 DOI: 10.1158/0008-5472.can-21-2964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Received: 09/01/2021] [Revised: 10/17/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022]
Abstract
Small cell lung cancer (SCLC) is an aggressive malignancy characterized by early metastasis and extreme lethality. The backbone of SCLC treatment over the past several decades has been platinum-based doublet chemotherapy, with the recent addition of immunotherapy providing modest benefits in a subset of patients. However, nearly all patients treated with systemic therapy quickly develop resistant disease, and there is an absence of effective therapies for recurrent and progressive disease. Here we conducted CRISPR-Cas9 screens using a druggable genome library in multiple SCLC cell lines representing distinct molecular subtypes. This screen nominated exportin-1, encoded by XPO1, as a therapeutic target. XPO1 was highly and ubiquitously expressed in SCLC relative to other lung cancer histologies and other tumor types. XPO1 knockout enhanced chemosensitivity, and exportin-1 inhibition demonstrated synergy with both first- and second-line chemotherapy. The small molecule exportin-1 inhibitor selinexor in combination with cisplatin or irinotecan dramatically inhibited tumor growth in chemonaïve and chemorelapsed SCLC patient-derived xenografts, respectively. Together these data identify exportin-1 as a promising therapeutic target in SCLC, with the potential to markedly augment the efficacy of cytotoxic agents commonly used in treating this disease. SIGNIFICANCE: CRISPR-Cas9 screening nominates exportin-1 as a therapeutic target in SCLC, and exportin-1 inhibition enhances chemotherapy efficacy in patient-derived xenografts, providing a novel therapeutic opportunity in this disease.
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Affiliation(s)
- Alvaro Quintanal-Villalonga
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Hirokazu Taniguchi
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuan Hao
- Perlmutter Cancer Center, New York University Langone Health, New York, New York
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, New York
| | - Andrew Chow
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yingqian A Zhan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shweta S Chavan
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fathema Uddin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Viola Allaj
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Parvathy Manoj
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nisargbhai S Shah
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joseph M Chan
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Offin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Metamia Ciampricotti
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jordana Ray-Kirton
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacklynn Egger
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Umesh Bhanot
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irina Linkov
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marina Asher
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael H Roehrl
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Juan Qiu
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Travis J Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Triparna Sen
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - John T Poirier
- Perlmutter Cancer Center, New York University Langone Health, New York, New York.
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.
- Weill Cornell Medical College, New York, New York
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10
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Quintanal-Villalonga A, Taniguchi H, Zhan YA, Hasan MM, Chavan SS, Meng F, Uddin F, Allaj V, Manoj P, Shah NS, Chan JM, Ciampricotti M, Chow A, Offin M, Ray-Kirton J, Egger JD, Bhanot UK, Linkov I, Asher M, Roehrl MH, Ventura K, Qiu J, de Stanchina E, Chang JC, Rekhtman N, Houck-Loomis B, Koche RP, Yu HA, Sen T, Rudin CM. Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation. J Hematol Oncol 2021; 14:170. [PMID: 34656143 PMCID: PMC8520275 DOI: 10.1186/s13045-021-01186-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 08/16/2021] [Accepted: 10/04/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Lineage plasticity, the ability to transdifferentiate among distinct phenotypic identities, facilitates therapeutic resistance in cancer. In lung adenocarcinomas (LUADs), this phenomenon includes small cell and squamous cell (LUSC) histologic transformation in the context of acquired resistance to targeted inhibition of driver mutations. LUAD-to-LUSC transdifferentiation, occurring in up to 9% of EGFR-mutant patients relapsed on osimertinib, is associated with notably poor prognosis. We hypothesized that multi-parameter profiling of the components of mixed histology (LUAD/LUSC) tumors could provide insight into factors licensing lineage plasticity between these histologies. METHODS We performed genomic, epigenomics, transcriptomics and protein analyses of microdissected LUAD and LUSC components from mixed histology tumors, pre-/post-transformation tumors and reference non-transformed LUAD and LUSC samples. We validated our findings through genetic manipulation of preclinical models in vitro and in vivo and performed patient-derived xenograft (PDX) treatments to validate potential therapeutic targets in a LUAD PDX model acquiring LUSC features after osimertinib treatment. RESULTS Our data suggest that LUSC transdifferentiation is primarily driven by transcriptional reprogramming rather than mutational events. We observed consistent relative upregulation of PI3K/AKT, MYC and PRC2 pathway genes. Concurrent activation of PI3K/AKT and MYC induced squamous features in EGFR-mutant LUAD preclinical models. Pharmacologic inhibition of EZH1/2 in combination with osimertinib prevented relapse with squamous-features in an EGFR-mutant patient-derived xenograft model, and inhibition of EZH1/2 or PI3K/AKT signaling re-sensitized resistant squamous-like tumors to osimertinib. CONCLUSIONS Our findings provide the first comprehensive molecular characterization of LUSC transdifferentiation, suggesting putative drivers and potential therapeutic targets to constrain or prevent lineage plasticity.
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Affiliation(s)
- Alvaro Quintanal-Villalonga
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA.
| | - Hirokazu Taniguchi
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Yingqian A Zhan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Maysun M Hasan
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fanli Meng
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fathema Uddin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Viola Allaj
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Parvathy Manoj
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Nisargbhai S Shah
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Joseph M Chan
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Metamia Ciampricotti
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Andrew Chow
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Michael Offin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Jordana Ray-Kirton
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacklynn D Egger
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
| | - Umesh K Bhanot
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Linkov
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marina Asher
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael H Roehrl
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katia Ventura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan Qiu
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jason C Chang
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natasha Rekhtman
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian Houck-Loomis
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Helena A Yu
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA
- Weill Cornell Medical College, 1275 York Avenue, New York, NY, 10065, USA
| | - Triparna Sen
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA.
- Weill Cornell Medical College, 1275 York Avenue, New York, NY, 10065, USA.
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, 408 East 69th Street, ZRC-1731, New York, NY, 10021, USA.
- Weill Cornell Medical College, 1275 York Avenue, New York, NY, 10065, USA.
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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11
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Baggiolini A, Callahan SJ, Montal E, Weiss JM, Trieu T, Tagore MM, Tischfield SE, Walsh RM, Suresh S, Fan Y, Campbell NR, Perlee SC, Saurat N, Hunter MV, Simon-Vermot T, Huang TH, Ma Y, Hollmann T, Tickoo SK, Taylor BS, Khurana E, Koche RP, Studer L, White RM. Developmental chromatin programs determine oncogenic competence in melanoma. Science 2021; 373:eabc1048. [PMID: 34516843 DOI: 10.1126/science.abc1048] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Arianna Baggiolini
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Scott J Callahan
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Gerstner Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Emily Montal
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joshua M Weiss
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Tuan Trieu
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Mohita M Tagore
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sam E Tischfield
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ryan M Walsh
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shruthy Suresh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yujie Fan
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Nathaniel R Campbell
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Sarah C Perlee
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Gerstner Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nathalie Saurat
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Miranda V Hunter
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Theresa Simon-Vermot
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ting-Hsiang Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yilun Ma
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Travis Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Satish K Tickoo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Barry S Taylor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Joan & Sanford I. Weill Medical College of Cornell University, Cornell University, New York, NY, USA
| | - Ekta Khurana
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lorenz Studer
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Gerstner Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Richard M White
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
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12
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Quintanal-Villalonga A, Taniguchi H, Zhan YA, Hasan MM, Chavan SS, Meng F, Uddin F, Manoj P, Donoghue MTA, Won HH, Chan JM, Ciampricotti M, Chow A, Offin M, Chang JC, Ray-Kirton J, Tischfield SE, Egger J, Bhanot UK, Linkov I, Asher M, Sinha S, Silber J, Iacobuzio-Donahue CA, Roehrl MH, Hollmann TJ, Yu HA, Qiu J, de Stanchina E, Baine MK, Rekhtman N, Poirier JT, Loomis B, Koche RP, Rudin CM, Sen T. Multi-omic analysis of lung tumors defines pathways activated in neuroendocrine transformation. Cancer Discov 2021; 11:3028-3047. [PMID: 34155000 DOI: 10.1158/2159-8290.cd-20-1863] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/30/2021] [Accepted: 06/15/2021] [Indexed: 11/16/2022]
Abstract
Lineage plasticity is implicated in treatment resistance in multiple cancers. In lung adenocarcinomas (LUADs) amenable to targeted therapy, transformation to small cell lung cancer (SCLC) is a recognized resistance mechanism. Defining molecular mechanisms of neuroendocrine (NE) transformation in lung cancer has been limited by a paucity of pre-/post-transformation clinical samples. Detailed genomic, epigenomic, transcriptomic, and protein characterization of combined LUAD/SCLC tumors, as well as pre-/post-transformation samples, support that NE transformation is primarily driven by transcriptional reprogramming rather than mutational events. We identify genomic contexts in which NE transformation is favored, including frequent loss of the 3p chromosome arm. We observed enhanced expression of genes involved in PRC2 complex and PI3K/AKT and NOTCH pathways. Pharmacological inhibition of the PI3K/AKT pathway delayed tumor growth and NE transformation in an EGFR-mutant patient-derived xenograft model. Our findings define a novel landscape of potential drivers and therapeutic vulnerabilities of neuroendocrine transformation in lung cancer.
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Affiliation(s)
| | | | - Yingqian A Zhan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center
| | - Maysun M Hasan
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center
| | | | - Fanli Meng
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center
| | | | | | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center
| | - Helen H Won
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center
| | | | | | - Andrew Chow
- Medicine, Memorial Sloan Kettering Cancer Center
| | | | - Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | | | - Sam E Tischfield
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center
| | | | - Umesh K Bhanot
- Pathology Core Facility, Memorial Sloan Kettering Cancer Center
| | | | - Marina Asher
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | | | | | | | | | | | - Helena A Yu
- Medicine, Memorial Sloan Kettering Cancer Center
| | - Juan Qiu
- Memorial Sloan Kettering Cancer Center
| | | | | | | | - John T Poirier
- Perlmutter Cancer Center, New York University Langone Health
| | - Brian Loomis
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center
| | - Charles M Rudin
- Druckenmiller Center for Lung Cancer Research and Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center
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13
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Marinaccio C, Suraneni P, Celik H, Volk A, Wen QJ, Ling T, Bulic M, Lasho T, Koche RP, Famulare CA, Farnoud N, Stein B, Schieber M, Gurbuxani S, Root DE, Younger ST, Hoffman R, Gangat N, Ntziachristos P, Chandel NS, Levine RL, Rampal RK, Challen GA, Tefferi A, Crispino JD. LKB1/ STK11 Is a Tumor Suppressor in the Progression of Myeloproliferative Neoplasms. Cancer Discov 2021; 11:1398-1410. [PMID: 33579786 PMCID: PMC8178182 DOI: 10.1158/2159-8290.cd-20-1353] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 09/23/2020] [Revised: 12/18/2020] [Accepted: 02/09/2021] [Indexed: 12/30/2022]
Abstract
The myeloproliferative neoplasms (MPN) frequently progress to blast phase disease, an aggressive form of acute myeloid leukemia. To identify genes that suppress disease progression, we performed a focused CRISPR/Cas9 screen and discovered that depletion of LKB1/Stk11 led to enhanced in vitro self-renewal of murine MPN cells. Deletion of Stk11 in a mouse MPN model caused rapid lethality with enhanced fibrosis, osteosclerosis, and an accumulation of immature cells in the bone marrow, as well as enhanced engraftment of primary human MPN cells in vivo. LKB1 loss was associated with increased mitochondrial reactive oxygen species and stabilization of HIF1α, and downregulation of LKB1 and increased levels of HIF1α were observed in human blast phase MPN specimens. Of note, we observed strong concordance of pathways that were enriched in murine MPN cells with LKB1 loss with those enriched in blast phase MPN patient specimens, supporting the conclusion that STK11 is a tumor suppressor in the MPNs. SIGNIFICANCE: Progression of the myeloproliferative neoplasms to acute myeloid leukemia occurs in a substantial number of cases, but the genetic basis has been unclear. We discovered that loss of LKB1/STK11 leads to stabilization of HIF1a and promotes disease progression. This observation provides a potential therapeutic avenue for targeting progression.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
| | | | - Hamza Celik
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Andrew Volk
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Te Ling
- St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Noushin Farnoud
- Center for Hematologic Malignancies, Memorial Sloan Kettering, New York, New York
| | | | | | | | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Scott T Younger
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | | | - Panagiotis Ntziachristos
- Northwestern University, Chicago, Illinois
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | - Ross L Levine
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Raajit K Rampal
- Center for Hematologic Malignancies, Memorial Sloan Kettering, New York, New York
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Grant A Challen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | | | - John D Crispino
- Northwestern University, Chicago, Illinois.
- St. Jude Children's Research Hospital, Memphis, Tennessee
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14
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Takao S, Forbes L, Uni M, Cheng S, Pineda JMB, Tarumoto Y, Cifani P, Minuesa G, Chen C, Kharas MG, Bradley RK, Vakoc CR, Koche RP, Kentsis A. Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia. eLife 2021; 10:65905. [PMID: 33527899 PMCID: PMC7886351 DOI: 10.7554/elife.65905] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 12/18/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
Dysregulated gene expression contributes to most prevalent features in human cancers. Here, we show that most subtypes of acute myeloid leukemia (AML) depend on the aberrant assembly of MYB transcriptional co-activator complex. By rapid and selective peptidomimetic interference with the binding of CBP/P300 to MYB, but not CREB or MLL1, we find that the leukemic functions of MYB are mediated by CBP/P300 co-activation of a distinct set of transcription factor complexes. These MYB complexes assemble aberrantly with LYL1, E2A, C/EBP family members, LMO2, and SATB1. They are organized convergently in genetically diverse subtypes of AML and are at least in part associated with inappropriate transcription factor co-expression. Peptidomimetic remodeling of oncogenic MYB complexes is accompanied by specific proteolysis and dynamic redistribution of CBP/P300 with alternative transcription factors such as RUNX1 to induce myeloid differentiation and apoptosis. Thus, aberrant assembly and sequestration of MYB:CBP/P300 complexes provide a unifying mechanism of oncogenic gene expression in AML. This work establishes a compelling strategy for their pharmacologic reprogramming and therapeutic targeting for diverse leukemias and possibly other human cancers caused by dysregulated gene control.
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Affiliation(s)
- Sumiko Takao
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Lauren Forbes
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Masahiro Uni
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Shuyuan Cheng
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Medical Scientist Training Program, University of Washington, Seattle, United States.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
| | - Yusuke Tarumoto
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States
| | - Gerard Minuesa
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States
| | - Celine Chen
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States
| | - Michael G Kharas
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
| | | | - Richard P Koche
- Center for Epigenetics Research, Sloan Kettering Institute, New York, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
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15
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Saqcena M, Leandro-Garcia LJ, Maag JLV, Tchekmedyian V, Krishnamoorthy GP, Tamarapu PP, Tiedje V, Reuter V, Knauf JA, de Stanchina E, Xu B, Liao XH, Refetoff S, Ghossein R, Chi P, Ho AL, Koche RP, Fagin JA. SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies. Cancer Discov 2020; 11:1158-1175. [PMID: 33318036 DOI: 10.1158/2159-8290.cd-20-0735] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [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: 05/22/2020] [Revised: 10/16/2020] [Accepted: 12/09/2020] [Indexed: 12/21/2022]
Abstract
Mutations of subunits of the SWI/SNF chromatin remodeling complexes occur commonly in cancers of different lineages, including advanced thyroid cancers. Here we show that thyroid-specific loss of Arid1a, Arid2, or Smarcb1 in mouse BRAFV600E-mutant tumors promotes disease progression and decreased survival, associated with lesion-specific effects on chromatin accessibility and differentiation. As compared with normal thyrocytes, BRAFV600E-mutant mouse papillary thyroid cancers have decreased lineage transcription factor expression and accessibility to their target DNA binding sites, leading to impairment of thyroid-differentiated gene expression and radioiodine incorporation, which is rescued by MAPK inhibition. Loss of individual SWI/SNF subunits in BRAF tumors leads to a repressive chromatin state that cannot be reversed by MAPK pathway blockade, rendering them insensitive to its redifferentiation effects. Our results show that SWI/SNF complexes are central to the maintenance of differentiated function in thyroid cancers, and their loss confers radioiodine refractoriness and resistance to MAPK inhibitor-based redifferentiation therapies. SIGNIFICANCE: Reprogramming cancer differentiation confers therapeutic benefit in various disease contexts. Oncogenic BRAF silences genes required for radioiodine responsiveness in thyroid cancer. Mutations in SWI/SNF genes result in loss of chromatin accessibility at thyroid lineage specification genes in BRAF-mutant thyroid tumors, rendering them insensitive to the redifferentiation effects of MAPK blockade.This article is highlighted in the In This Issue feature, p. 995.
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Affiliation(s)
- Mahesh Saqcena
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jesper L V Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vatche Tchekmedyian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gnana P Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prasanna P Tamarapu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vera Tiedje
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vincent Reuter
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeffrey A Knauf
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xiao-Hui Liao
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Samuel Refetoff
- Departments of Medicine and Pediatrics and the Committee on Genetics, The University of Chicago, Chicago, Illinois
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alan L Ho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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16
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Pastore F, Bhagwat N, Pastore A, Radzisheuskaya A, Karzai A, Krishnan A, Li B, Bowman RL, Xiao W, Viny AD, Zouak A, Park YC, Cordner KB, Braunstein S, Maag JL, Grego A, Mehta J, Wang M, Lin H, Durham BH, Koche RP, Rampal RK, Helin K, Scherle P, Vaddi K, Levine RL. PRMT5 Inhibition Modulates E2F1 Methylation and Gene-Regulatory Networks Leading to Therapeutic Efficacy in JAK2 V617F-Mutant MPN. Cancer Discov 2020; 10:1742-1757. [PMID: 32669286 PMCID: PMC7642059 DOI: 10.1158/2159-8290.cd-20-0026] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 01/08/2020] [Revised: 05/26/2020] [Accepted: 07/10/2020] [Indexed: 11/16/2022]
Abstract
We investigated the role of PRMT5 in myeloproliferative neoplasm (MPN) pathogenesis and aimed to elucidate key PRMT5 targets contributing to MPN maintenance. PRMT5 is overexpressed in primary MPN cells, and PRMT5 inhibition potently reduced MPN cell proliferation ex vivo. PRMT5 inhibition was efficacious at reversing elevated hematocrit, leukocytosis, and splenomegaly in a model of JAK2V617F+ polycythemia vera and leukocyte and platelet counts, hepatosplenomegaly, and fibrosis in the MPLW515L model of myelofibrosis. Dual targeting of JAK and PRMT5 was superior to JAK or PRMT5 inhibitor monotherapy, further decreasing elevated counts and extramedullary hematopoiesis in vivo. PRMT5 inhibition reduced expression of E2F targets and altered the methylation status of E2F1 leading to attenuated DNA damage repair, cell-cycle arrest, and increased apoptosis. Our data link PRMT5 to E2F1 regulatory function and MPN cell survival and provide a strong mechanistic rationale for clinical trials of PRMT5 inhibitors in MPN. SIGNIFICANCE: Expression of PRMT5 and E2F targets is increased in JAK2V617F+ MPN. Pharmacologic inhibition of PRMT5 alters the methylation status of E2F1 and shows efficacy in JAK2V617F/MPLW515L MPN models and primary samples. PRMT5 represents a potential novel therapeutic target for MPN, which is now being clinically evaluated.This article is highlighted in the In This Issue feature, p. 1611.
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Affiliation(s)
- Friederike Pastore
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Alessandro Pastore
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aliaksandra Radzisheuskaya
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Cell Biology Program, Memorial Sloan Kettering CancerCenter, New York, New York
| | - Abdul Karzai
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aishwarya Krishnan
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bing Li
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert L Bowman
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wenbin Xiao
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aaron D Viny
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anouar Zouak
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Young C Park
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Keith B Cordner
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephanie Braunstein
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jesper L Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Min Wang
- Prelude Therapeutics Inc., Wilmington, Delaware
| | - Hong Lin
- Prelude Therapeutics Inc., Wilmington, Delaware
| | - Benjamin H Durham
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Raajit K Rampal
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kristian Helin
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Cell Biology Program, Memorial Sloan Kettering CancerCenter, New York, New York
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation of Stem Cell Research (Danstem), University of Copenhagen, Copenhagen, Denmark
| | | | - Kris Vaddi
- Prelude Therapeutics Inc., Wilmington, Delaware
| | - Ross L Levine
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
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17
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Weis-Banke SE, Lerdrup M, Kleine-Kohlbrecher D, Mohammad F, Sidoli S, Jensen ON, Yanase T, Nakamura T, Iwase A, Stylianou A, Abu-Rustum NR, Aghajanian C, Soslow R, Da Cruz Paula A, Koche RP, Weigelt B, Christensen J, Helin K, Cloos PAC. Mutant FOXL2 C134W Hijacks SMAD4 and SMAD2/3 to Drive Adult Granulosa Cell Tumors. Cancer Res 2020; 80:3466-3479. [PMID: 32641411 DOI: 10.1158/0008-5472.can-20-0259] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/26/2020] [Accepted: 06/30/2020] [Indexed: 12/11/2022]
Abstract
The mutant protein FOXL2C134W is expressed in at least 95% of adult-type ovarian granulosa cell tumors (AGCT) and is considered to be a driver of oncogenesis in this disease. However, the molecular mechanism by which FOXL2C134W contributes to tumorigenesis is not known. Here, we show that mutant FOXL2C134W acquires the ability to bind SMAD4, forming a FOXL2C134W/SMAD4/SMAD2/3 complex that binds a novel hybrid DNA motif AGHCAHAA, unique to the FOXL2C134W mutant. This binding induced an enhancer-like chromatin state, leading to transcription of nearby genes, many of which are characteristic of epithelial-to-mesenchymal transition. FOXL2C134W also bound hybrid loci in primary AGCT. Ablation of SMAD4 or SMAD2/3 resulted in strong reduction of FOXL2C134W binding at hybrid sites and decreased expression of associated genes. Accordingly, inhibition of TGFβ mitigated the transcriptional effect of FOXL2C134W. Our results provide mechanistic insight into AGCT pathogenesis, identifying FOXL2C134W and its interaction with SMAD4 as potential therapeutic targets to this condition. SIGNIFICANCE: FOXL2C134W hijacks SMAD4 and leads to the expression of genes involved in EMT, stemness, and oncogenesis in AGCT, making FOXL2C134W and the TGFβ pathway therapeutic targets in this condition. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/17/3466/F1.large.jpg.
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Affiliation(s)
- Stine E Weis-Banke
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark
| | - Mads Lerdrup
- Center for Chromosome Stability, University of Copenhagen, Copenhagen N, Denmark
| | - Daniela Kleine-Kohlbrecher
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark
| | - Faizaan Mohammad
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark
| | - Simone Sidoli
- Department of Biochemistry and Molecular Biology, VILLUM Centre for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Centre for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Toshihiko Yanase
- Seiwakai Muta Hospital, 3-9-1 Hoshikuma, Sawara-ku, Fukuoka, Japan
| | - Tomoko Nakamura
- Departments of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Akira Iwase
- Department of Obstetrics and Gynecology, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Anthe Stylianou
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jesper Christensen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark. .,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark.,Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul A C Cloos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark. .,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark
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18
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Cai SF, Chu SH, Goldberg AD, Parvin S, Koche RP, Glass JL, Stein EM, Tallman MS, Sen F, Famulare CA, Cusan M, Huang CH, Chen CW, Zou L, Cordner KB, DelGaudio NL, Durani V, Kini M, Rex M, Tian HS, Zuber J, Baslan T, Lowe SW, Rienhoff HY, Letai A, Levine RL, Armstrong SA. Leukemia Cell of Origin Influences Apoptotic Priming and Sensitivity to LSD1 Inhibition. Cancer Discov 2020; 10:1500-1513. [PMID: 32606137 DOI: 10.1158/2159-8290.cd-19-1469] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/09/2020] [Accepted: 06/25/2020] [Indexed: 11/16/2022]
Abstract
The cell of origin of oncogenic transformation is a determinant of therapeutic sensitivity, but the mechanisms governing cell-of-origin-driven differences in therapeutic response have not been delineated. Leukemias initiating in hematopoietic stem cells (HSC) are less sensitive to chemotherapy and highly express the transcription factor MECOM (EVI1) compared with leukemias derived from myeloid progenitors. Here, we compared leukemias initiated in either HSCs or myeloid progenitors to reveal a novel function for EVI1 in modulating p53 protein abundance and activity. HSC-derived leukemias exhibit decreased apoptotic priming, attenuated p53 transcriptional output, and resistance to lysine-specific demethylase 1 (LSD1) inhibitors in addition to classical genotoxic stresses. p53 loss of function in Evi1 lo progenitor-derived leukemias induces resistance to LSD1 inhibition, and EVI1hi leukemias are sensitized to LSD1 inhibition by venetoclax. Our findings demonstrate a role for EVI1 in p53 wild-type cancers in reducing p53 function and provide a strategy to circumvent drug resistance in chemoresistant EVI1 hi acute myeloid leukemia. SIGNIFICANCE: We demonstrate that the cell of origin of leukemia initiation influences p53 activity and dictates therapeutic sensitivity to pharmacologic LSD1 inhibitors via the transcription factor EVI1. We show that drug resistance could be overcome in HSC-derived leukemias by combining LSD1 inhibition with venetoclax.See related commentary by Gu et al., p. 1445.This article is highlighted in the In This Issue feature, p. 1426.
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Affiliation(s)
- Sheng F Cai
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Leukemia Service, Department of Medicine, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - S Haihua Chu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aaron D Goldberg
- Leukemia Service, Department of Medicine, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Salma Parvin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacob L Glass
- Leukemia Service, Department of Medicine, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eytan M Stein
- Leukemia Service, Department of Medicine, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Martin S Tallman
- Leukemia Service, Department of Medicine, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Filiz Sen
- Hematopathology Diagnostic Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher A Famulare
- Leukemia Service, Department of Medicine, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Monica Cusan
- University Hospital, Ludwig Maximilian University Munich, Munich, Germany
| | - Chun-Hao Huang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California
| | - Lihua Zou
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Keith B Cordner
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicole L DelGaudio
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vidushi Durani
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mitali Kini
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Madison Rex
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Helen S Tian
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Howard Hughes Medical Institute, New York, New York
| | | | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ross L Levine
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Leukemia Service, Department of Medicine, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.
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19
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Chu SH, Chabon JR, Matovina CN, Minehart JC, Chen BR, Zhang J, Kumar V, Xiong Y, Callen E, Hung PJ, Feng Z, Koche RP, Liu XS, Chaudhuri J, Nussenzweig A, Sleckman BP, Armstrong SA. Loss of H3K36 Methyltransferase SETD2 Impairs V(D)J Recombination during Lymphoid Development. iScience 2020; 23:100941. [PMID: 32169821 PMCID: PMC7066224 DOI: 10.1016/j.isci.2020.100941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/25/2020] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
Repair of DNA double-stranded breaks (DSBs) during lymphocyte development is essential for V(D)J recombination and forms the basis of immunoglobulin variable region diversity. Understanding of this process in lymphogenesis has historically been centered on the study of RAG1/2 recombinases and a set of classical non-homologous end-joining factors. Much less has been reported regarding the role of chromatin modifications on this process. Here, we show a role for the non-redundant histone H3 lysine methyltransferase, Setd2, and its modification of lysine-36 trimethylation (H3K36me3), in the processing and joining of DNA ends during V(D)J recombination. Loss leads to mis-repair of Rag-induced DNA DSBs, especially when combined with loss of Atm kinase activity. Furthermore, loss reduces immune repertoire and a severe block in lymphogenesis as well as causes post-mitotic neuronal apoptosis. Together, these studies are suggestive of an important role of Setd2/H3K36me3 in these two mammalian developmental processes that are influenced by double-stranded break repair.
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Affiliation(s)
- S Haihua Chu
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA
| | - Jonathan R Chabon
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA
| | - Chloe N Matovina
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA
| | | | - Bo-Ruei Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jian Zhang
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vipul Kumar
- Howard Hughes Medical Institute, Department of Pediatrics, Department of Genetics, Harvard Medical School, Boston, MA, USA; Harvard-MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
| | - Yijun Xiong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute National Institutes of Health, Bethesda, MD, USA
| | - Putzer J Hung
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhaohui Feng
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA
| | - Richard P Koche
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute National Institutes of Health, Bethesda, MD, USA
| | - Barry P Sleckman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA.
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20
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Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Garcia HD, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Publisher Correction: Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet 2020; 52:464. [PMID: 32107479 DOI: 10.1038/s41588-020-0598-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Elias Rodriguez-Fos
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Konstantin Helmsauer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Burkert
- Department of Biology, Humboldt University, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ian C MacArthur
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jesper Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rocio Chamorro
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalia Munoz-Perez
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Röefzaad
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Bardinet
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Theresa Thole
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Timme
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Katharina Kasack
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Fuchs
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Filippos Klironomos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Eric Blanc
- Berlin Institute of Health, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Theissen
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hedwig Deubzer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Joern Toedling
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland F Schwarz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany. .,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.
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21
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Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet 2019; 52:29-34. [PMID: 31844324 DOI: 10.1038/s41588-019-0547-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 01/25/2023]
Abstract
Extrachromosomal circularization of DNA is an important genomic feature in cancer. However, the structure, composition and genome-wide frequency of extrachromosomal circular DNA have not yet been profiled extensively. Here, we combine genomic and transcriptomic approaches to describe the landscape of extrachromosomal circular DNA in neuroblastoma, a tumor arising in childhood from primitive cells of the sympathetic nervous system. Our analysis identifies and characterizes a wide catalog of somatically acquired and undescribed extrachromosomal circular DNAs. Moreover, we find that extrachromosomal circular DNAs are an unanticipated major source of somatic rearrangements, contributing to oncogenic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. Cancer-causing lesions can emerge out of circle-derived rearrangements and are associated with adverse clinical outcome. It is highly probable that circle-derived rearrangements represent an ongoing mutagenic process. Thus, extrachromosomal circular DNAs represent a multihit mutagenic process, with important functional and clinical implications for the origins of genomic remodeling in cancer.
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Affiliation(s)
- Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Elias Rodriguez-Fos
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Konstantin Helmsauer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Burkert
- Department of Biology, Humboldt University, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ian C MacArthur
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jesper Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rocio Chamorro
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalia Munoz-Perez
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Röefzaad
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Bardinet
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Theresa Thole
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Timme
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Katharina Kasack
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Fuchs
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Filippos Klironomos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Eric Blanc
- Berlin Institute of Health, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Theissen
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hedwig Deubzer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Joern Toedling
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland F Schwarz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany. .,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.
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22
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Loizou E, Banito A, Livshits G, Ho YJ, Koche RP, Sánchez-Rivera FJ, Mayle A, Chen CC, Kinalis S, Bagger FO, Kastenhuber ER, Durham BH, Lowe SW. A Gain-of-Function p53-Mutant Oncogene Promotes Cell Fate Plasticity and Myeloid Leukemia through the Pluripotency Factor FOXH1. Cancer Discov 2019; 9:962-979. [PMID: 31068365 DOI: 10.1158/2159-8290.cd-18-1391] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/20/2019] [Accepted: 05/02/2019] [Indexed: 12/17/2022]
Abstract
Mutations in the TP53 tumor suppressor gene are common in many cancer types, including the acute myeloid leukemia (AML) subtype known as complex karyotype AML (CK-AML). Here, we identify a gain-of-function (GOF) Trp53 mutation that accelerates CK-AML initiation beyond p53 loss and, surprisingly, is required for disease maintenance. The Trp53R172H mutation (TP53R175H in humans) exhibits a neomorphic function by promoting aberrant self-renewal in leukemic cells, a phenotype that is present in hematopoietic stem and progenitor cells (HSPC) even prior to their transformation. We identify FOXH1 as a critical mediator of mutant p53 function that binds to and regulates stem cell-associated genes and transcriptional programs. Our results identify a context where mutant p53 acts as a bona fide oncogene that contributes to the pathogenesis of CK-AML and suggests a common biological theme for TP53 GOF in cancer. SIGNIFICANCE: Our study demonstrates how a GOF p53 mutant can hijack an embryonic transcription factor to promote aberrant self-renewal. In this context, mutant Trp53 functions as an oncogene to both initiate and sustain myeloid leukemia and suggests a potential convergent activity of mutant Trp53 across cancer types.This article is highlighted in the In This Issue feature, p. 813.
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Affiliation(s)
- Evangelia Loizou
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Graduate School of Medical Sciences, New York, New York
| | - Ana Banito
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geulah Livshits
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yu-Jui Ho
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Francisco J Sánchez-Rivera
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Allison Mayle
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chi-Chao Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Savvas Kinalis
- Center for Genomic Medicine, Rigshopitalet, University of Copenhagen, Copenhagen, Denmark
| | - Frederik O Bagger
- Center for Genomic Medicine, Rigshopitalet, University of Copenhagen, Copenhagen, Denmark.,Department of Biomedicine and Swiss Institute of Bioinformatics, UKBB Universitats-Kinderspital, Basel, Switzerland
| | - Edward R Kastenhuber
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin H Durham
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York. .,Howard Hughes Medical Institute, New York, New York
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23
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Brown FC, Still E, Koche RP, Yim CY, Takao S, Cifani P, Reed C, Gunasekera S, Ficarro SB, Romanienko P, Mark W, McCarthy C, de Stanchina E, Gonen M, Seshan V, Bhola P, O'Donnell C, Spitzer B, Stutzke C, Lavallée VP, Hébert J, Krivtsov AV, Melnick A, Paietta EM, Tallman MS, Letai A, Sauvageau G, Pouliot G, Levine R, Marto JA, Armstrong SA, Kentsis A. MEF2C Phosphorylation Is Required for Chemotherapy Resistance in Acute Myeloid Leukemia. Cancer Discov 2018; 8:478-497. [PMID: 29431698 PMCID: PMC5882571 DOI: 10.1158/2159-8290.cd-17-1271] [Citation(s) in RCA: 49] [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] [Received: 11/13/2017] [Revised: 01/22/2018] [Accepted: 01/30/2018] [Indexed: 11/16/2022]
Abstract
In acute myeloid leukemia (AML), chemotherapy resistance remains prevalent and poorly understood. Using functional proteomics of patient AML specimens, we identified MEF2C S222 phosphorylation as a specific marker of primary chemoresistance. We found that Mef2cS222A/S222A knock-in mutant mice engineered to block MEF2C phosphorylation exhibited normal hematopoiesis, but were resistant to leukemogenesis induced by MLL-AF9 MEF2C phosphorylation was required for leukemia stem cell maintenance and induced by MARK kinases in cells. Treatment with the selective MARK/SIK inhibitor MRT199665 caused apoptosis and conferred chemosensitivity in MEF2C-activated human AML cell lines and primary patient specimens, but not those lacking MEF2C phosphorylation. These findings identify kinase-dependent dysregulation of transcription factor control as a determinant of therapy response in AML, with immediate potential for improved diagnosis and therapy for this disease.Significance: Functional proteomics identifies phosphorylation of MEF2C in the majority of primary chemotherapy-resistant AML. Kinase-dependent dysregulation of this transcription factor confers susceptibility to MARK/SIK kinase inhibition in preclinical models, substantiating its clinical investigation for improved diagnosis and therapy of AML. Cancer Discov; 8(4); 478-97. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 371.
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MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- Cell Line
- Drug Resistance, Neoplasm
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- MEF2 Transcription Factors/chemistry
- MEF2 Transcription Factors/metabolism
- Mice
- Mice, Transgenic
- Phosphorylation
- Protein Processing, Post-Translational
- Proteomics
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Affiliation(s)
- Fiona C Brown
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eric Still
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard P Koche
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christina Y Yim
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumiko Takao
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Casie Reed
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shehana Gunasekera
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Scott B Ficarro
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Peter Romanienko
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Willie Mark
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Craig McCarthy
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Patrick Bhola
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Conor O'Donnell
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Vincent-Philippe Lavallée
- The Leucegene Project at Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Josée Hébert
- The Leucegene Project at Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Andrei V Krivtsov
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ari Melnick
- Departments of Pediatrics, Pharmacology, and Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, New York
| | - Elisabeth M Paietta
- Montefiore Medical Center-North Division, Albert Einstein College of Medicine, Bronx, New York, New York
| | - Martin S Tallman
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Guy Sauvageau
- The Leucegene Project at Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Gayle Pouliot
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ross Levine
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Medical College of Cornell University, New York, New York
| | - Jarrod A Marto
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott A Armstrong
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York.
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Departments of Pediatrics, Pharmacology, and Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, New York
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24
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Shukla S, Cyrta J, Murphy DA, Walczak EG, Ran L, Agrawal P, Xie Y, Chen Y, Wang S, Zhan Y, Li D, Wong EWP, Sboner A, Beltran H, Mosquera JM, Sher J, Cao Z, Wongvipat J, Koche RP, Gopalan A, Zheng D, Rubin MA, Scher HI, Chi P, Chen Y. Aberrant Activation of a Gastrointestinal Transcriptional Circuit in Prostate Cancer Mediates Castration Resistance. Cancer Cell 2017; 32:792-806.e7. [PMID: 29153843 PMCID: PMC5728174 DOI: 10.1016/j.ccell.2017.10.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 07/13/2017] [Accepted: 10/17/2017] [Indexed: 12/24/2022]
Abstract
Prostate cancer exhibits a lineage-specific dependence on androgen signaling. Castration resistance involves reactivation of androgen signaling or activation of alternative lineage programs to bypass androgen requirement. We describe an aberrant gastrointestinal-lineage transcriptome expressed in ∼5% of primary prostate cancer that is characterized by abbreviated response to androgen-deprivation therapy and in ∼30% of castration-resistant prostate cancer. This program is governed by a transcriptional circuit consisting of HNF4G and HNF1A. Cistrome and chromatin analyses revealed that HNF4G is a pioneer factor that generates and maintains enhancer landscape at gastrointestinal-lineage genes, independent of androgen-receptor signaling. In HNF4G/HNF1A-double-negative prostate cancer, exogenous expression of HNF4G at physiologic levels recapitulates the gastrointestinal transcriptome, chromatin landscape, and leads to relative castration resistance.
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Affiliation(s)
- Shipra Shukla
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joanna Cyrta
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Englander Institute for Precision Medicine of Weill Cornell Medicine and New York-Presbyterian, New York, NY 10065, USA
| | - Devan A Murphy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edward G Walczak
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Leili Ran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Praveen Agrawal
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Yuanyuan Xie
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuedan Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shangqian Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yu Zhan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dan Li
- Yale School of Medicine, New Haven, CT 06511, USA
| | - Elissa W P Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Englander Institute for Precision Medicine of Weill Cornell Medicine and New York-Presbyterian, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Medical College, New York, NY 10065, USA
| | - Himisha Beltran
- Englander Institute for Precision Medicine of Weill Cornell Medicine and New York-Presbyterian, New York, NY 10065, USA; Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Englander Institute for Precision Medicine of Weill Cornell Medicine and New York-Presbyterian, New York, NY 10065, USA
| | - Jessica Sher
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zhen Cao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - John Wongvipat
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Richard P Koche
- Center of Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Deyou Zheng
- Departments of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Englander Institute for Precision Medicine of Weill Cornell Medicine and New York-Presbyterian, New York, NY 10065, USA
| | - Howard I Scher
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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25
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Ran L, Chen Y, Sher J, Wong EWP, Murphy D, Zhang JQ, Li D, Deniz K, Sirota I, Cao Z, Wang S, Guan Y, Shukla S, Li KY, Chramiec A, Xie Y, Zheng D, Koche RP, Antonescu CR, Chen Y, Chi P. FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor. Cancer Discov 2017; 8:234-251. [PMID: 29162563 DOI: 10.1158/2159-8290.cd-17-0468] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/26/2017] [Accepted: 11/14/2017] [Indexed: 01/04/2023]
Abstract
The cellular context that integrates upstream signaling and downstream nuclear response dictates the oncogenic behavior and shapes treatment responses in distinct cancer types. Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specification and GIST tumorigenesis. Further, FOXF1 colocalizes with ETV1 at enhancers and functions as a pioneer factor that regulates the ETV1-dependent GIST lineage-specific transcriptome through modulation of the local chromatin context, including chromatin accessibility, enhancer maintenance, and ETV1 binding. Functionally, FOXF1 is required for human GIST cell growth in vitro and murine GIST tumor growth and maintenance in vivo The simultaneous control of the upstream signaling and nuclear response sets up a unique regulatory paradigm and highlights the critical role of FOXF1 in enforcing the GIST cellular context for highly lineage-restricted clinical behavior and treatment response.Significance: We uncover that FOXF1 defines the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function. The unique and simultaneous control of signaling and transcriptional circuitry by FOXF1 sets up an enforced transcriptional addiction to FOXF1 in GIST, which can be exploited diagnostically and therapeutically. Cancer Discov; 8(2); 234-51. ©2017 AACR.See related commentary by Lee and Duensing, p. 146This article is highlighted in the In This Issue feature, p. 127.
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Affiliation(s)
- Leili Ran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuedan Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York
| | - Jessica Sher
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elissa W P Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Devan Murphy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jenny Q Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dan Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kemal Deniz
- Department of Pathology, Erciyes University, Kayseri, Turkey
| | - Inna Sirota
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Zhen Cao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York
| | - Shangqian Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Youxin Guan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shipra Shukla
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katie Yang Li
- Center of Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alan Chramiec
- Center of Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Biomedical Engineering, Columbia University, New York, New York
| | - Yuanyuan Xie
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York.,Department of Neurology, Albert Einstein College of Medicine, Bronx, New York.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
| | - Richard P Koche
- Center of Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
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26
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Wang SP, Tang Z, Chen CW, Shimada M, Koche RP, Wang LH, Nakadai T, Chramiec A, Krivtsov AV, Armstrong SA, Roeder RG. A UTX-MLL4-p300 Transcriptional Regulatory Network Coordinately Shapes Active Enhancer Landscapes for Eliciting Transcription. Mol Cell 2017; 67:308-321.e6. [PMID: 28732206 DOI: 10.1016/j.molcel.2017.06.028] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [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: 10/20/2016] [Revised: 04/29/2017] [Accepted: 06/22/2017] [Indexed: 02/03/2023]
Abstract
Enhancer activation is a critical step for gene activation. Here we report an epigenetic crosstalk at enhancers between the UTX (H3K27 demethylase)-MLL4 (H3K4 methyltransferase) complex and the histone acetyltransferase p300. We demonstrate that UTX, in a demethylase activity-independent manner, facilitates conversion of inactive enhancers in embryonic stem cells to an active (H3K4me1+/H3K27ac+) state by recruiting and coupling the enzymatic functions of MLL4 and p300. Loss of UTX leads to attenuated enhancer activity, characterized by reduced levels of H3K4me1 and H3K27ac as well as impaired transcription. The UTX-MLL4 complex enhances p300-dependent H3K27 acetylation through UTX-dependent stimulation of p300 recruitment, while MLL4-mediated H3K4 monomethylation, reciprocally, requires p300 function. Importantly, MLL4-generated H3K4me1 further enhances p300-dependent transcription. This work reveals a previously unrecognized cooperativity among enhancer-associated chromatin modulators, including a unique function for UTX, in establishing an "active enhancer landscape" and defines a detailed mechanism for the joint deposition of H3K4me1 and H3K27ac.
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Affiliation(s)
- Shu-Ping Wang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Chun-Wei Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Richard P Koche
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lan-Hsin Wang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Taiwan
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Alan Chramiec
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrei V Krivtsov
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
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Xu H, Valerio DG, Eisold ME, Sinha A, Koche RP, Hu W, Chen CW, Chu SH, Brien GL, Park CY, Hsieh JJ, Ernst P, Armstrong SA. NUP98 Fusion Proteins Interact with the NSL and MLL1 Complexes to Drive Leukemogenesis. Cancer Cell 2016; 30:863-878. [PMID: 27889185 PMCID: PMC5501282 DOI: 10.1016/j.ccell.2016.10.019] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 07/29/2016] [Accepted: 10/27/2016] [Indexed: 01/09/2023]
Abstract
The nucleoporin 98 gene (NUP98) is fused to a variety of partner genes in multiple hematopoietic malignancies. Here, we demonstrate that NUP98 fusion proteins, including NUP98-HOXA9 (NHA9), NUP98-HOXD13 (NHD13), NUP98-NSD1, NUP98-PHF23, and NUP98-TOP1 physically interact with mixed lineage leukemia 1 (MLL1) and the non-specific lethal (NSL) histone-modifying complexes. Chromatin immunoprecipitation sequencing illustrates that NHA9 and MLL1 co-localize on chromatin and are found associated with Hox gene promoter regions. Furthermore, MLL1 is required for the proliferation of NHA9 cells in vitro and in vivo. Inactivation of MLL1 leads to decreased expression of genes bound by NHA9 and MLL1 and reverses a gene expression signature found in NUP98-rearranged human leukemias. Our data reveal a molecular dependency on MLL1 function in NUP98-fusion-driven leukemogenesis.
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Affiliation(s)
- Haiming Xu
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.
| | - Daria G Valerio
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Meghan E Eisold
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Amit Sinha
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Richard P Koche
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chun-Wei Chen
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - S Haihua Chu
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Gerard L Brien
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Christopher Y Park
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James J Hsieh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Patricia Ernst
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Scott A Armstrong
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.
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Xu H, Valerio DG, Eisold ME, Sinha A, Koche RP, Hu W, Chen CW, Chu SH, Brien GL, Armstrong SA. Abstract 883: NUP98-fusion proteins interact with the NSL/MLL1 complexes to drive leukemogenesis. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-883] [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 Nucleoporin 98 gene (NUP98) is fused to a variety of partner genes in an array of hematopoietic malignancies via chromosomal translocations involving 11p15. NUP98-rearranged leukemias show elevated HOXA and HOXB cluster genes and mouse model systems have recapitulated this high-level expression independent of whether the leukemias are derived from mouse or human bone marrow. However, the molecular mechanisms of NUP98-fusion mediated leukemogenesis and elevated HOX gene expression in this leukemia are unclear. Recent studies in Drosophila show that nucleoplasmic Nup98 functions as a potential transcriptional activator, and physically interacts with the non-specific lethal (NSL) and trithorax (Trx)/mixed lineage leukemia (MLL) complex (Kalverda et al., 2010; Pascual-Garcia et al., 2014). To test whether the intranuclear localized NUP98-fusion proteins interact with NSL/MLL1 complexes, coimmunoprecipitation (co-IP) experiments using 293T cells with overexpression of NUP98 fusions and wild type (WT) NUP98 were performed. NUP98-fusion proteins NUP98-HOXA9, NUP98-HOXD13, NUP98-NSD1 and NUP98-PHF23, but not the full-length WT NUP98, show physical interaction with MLL1 and the NSL histone acetyltransferase (HAT) complexes. Genome-wide chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) illustrated that NUP98-HOXA9 and MLL1 co-localize at Hoxa and Hoxb gene promoters, which correlates with the presence of activating chromatin modifications such as H4K16ac and H3K4me3. In vitro and in vivo functional assays further showed that Mll1 is crucial for the growth of NUP98-HOXA9-transformed cells, and for the initiation and maintenance of NUP98-HOXA9 driven AML. These findings were further supported by transcriptome analyses performed in mouse NUP98-HOXA9 transformed cells lacking Mll1. We found a significant enrichment of co-bound targets of MLL1 and NUP98-HOXA9 and genes downregulated in the absence of Mll1. Gene set enrichment analysis (GSEA) demonstrated strong similarity between Mll1-dependent gene expression signature in our murine NUP98-HOXA9 AML model and the expression profile of human NUP98-fusion AML, indicating that our findings in murine AML models can be extended to human AML. Finally, the overexpression of Hoxa9 and Meis1, direct binding targets of NUP98-HOXA9 and MLL1 that are downregulated upon Mll1 loss, rescues the in vitro transformation defects in NUP98-HOXA9 Mll1-/- cells. In conclusion, our findings support a model where NUP98-fusion proteins recruit the NSL/MLL1 complex as an important step during leukemogenesis. The deregulated HOX gene expression in NUP98 fusion transformed cells remains dependent on MLL1. The discovery of this common leukemogenic pathway for NUP98-fusion proteins opens up new avenues for potential therapeutic opportunities to treat patients with leukemia that harbor various NUP98 rearrangements.
Citation Format: Haiming Xu, Daria G. Valerio, Meghan E. Eisold, Amit Sinha, Richard. P. Koche, Wenhuo Hu, Chun-Wei Chen, Scott H. Chu, Gerard L. Brien, Scott A. Armstrong. NUP98-fusion proteins interact with the NSL/MLL1 complexes to drive leukemogenesis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 883.
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Affiliation(s)
- Haiming Xu
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Amit Sinha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Wenhuo Hu
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chun-Wei Chen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Scott H. Chu
- Memorial Sloan Kettering Cancer Center, New York, NY
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Chen CW, Koche RP, Sinha AU, Deshpande AJ, Zhu N, Eng R, Doench JG, Xu H, Chu SH, Qi J, Wang X, Delaney C, Bernt KM, Root DE, Hahn WC, Bradner JE, Armstrong SA. DOT1L inhibits SIRT1-mediated epigenetic silencing to maintain leukemic gene expression in MLL-rearranged leukemia. Nat Med 2015; 21:335-43. [PMID: 25822366 PMCID: PMC4390532 DOI: 10.1038/nm.3832] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/02/2015] [Indexed: 12/14/2022]
Abstract
MLL -rearrangements generate MLL-fusion proteins that bind DNA and drive leukemogenic gene expression. This gene expression program is dependent on the histone 3 lysine 79 (H3K79) methyltransferase DOT1L, and small molecule DOT1L inhibitors show promise as therapeutics for these leukemias. However, the mechanisms underlying this dependency are unclear. We conducted a genome-scale RNAi screen and found that the histone deacetylase SIRT1 is required for the establishment of a heterochromatin-like state around MLL-fusion target genes after DOT1L inhibition. DOT1L inhibits chromatin localization of a repressive complex composed of SIRT1 and SUV39H1, thereby maintaining an open chromatin state with elevated H3K9 acetylation and minimal H3K9 methylation at MLL-fusion target genes. Furthermore, the combination of SIRT1 activators and DOT1L inhibitors shows enhanced activity against MLL-rearranged leukemia cells. These results indicate that the dynamic interplay between chromatin regulators controlling activation and repression of gene expression could provide novel opportunities for combination therapy.
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Affiliation(s)
- Chun-Wei Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Richard P Koche
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Amit U Sinha
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Aniruddha J Deshpande
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nan Zhu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rowena Eng
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - John G Doench
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Haiming Xu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Scott H Chu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Xi Wang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christopher Delaney
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kathrin M Bernt
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - William C Hahn
- 1] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - James E Bradner
- 1] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Kühn MWM, Hadler MJ, Daigle SR, Koche RP, Krivtsov AV, Olhava EJ, Caligiuri MA, Huang G, Bradner JE, Pollock RM, Armstrong SA. MLL partial tandem duplication leukemia cells are sensitive to small molecule DOT1L inhibition. Haematologica 2015; 100:e190-3. [PMID: 25596271 DOI: 10.3324/haematol.2014.115337] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Michael W M Kühn
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael J Hadler
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Richard P Koche
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrei V Krivtsov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Michael A Caligiuri
- The Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Gang Huang
- Divisions of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Scott A Armstrong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Abstract
The orchestration of transcriptional programs depends on proper gene-enhancer pairing. While much remains to be learned about this process in normal development, two recent studies in Cell (Gröschel and colleagues) and this issue of Cancer Cell (Yamazaki and colleagues) highlight how the genomic rearrangement of an enhancer plays a causal role in the onset of a leukemogenic program.
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Affiliation(s)
- Richard P Koche
- Human Oncology and Pathogenesis Program and Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Scott A Armstrong
- Human Oncology and Pathogenesis Program and Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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Ku M, Jaffe JD, Koche RP, Rheinbay E, Endoh M, Koseki H, Carr SA, Bernstein BE. H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biol 2012; 13:R85. [PMID: 23034477 PMCID: PMC3491413 DOI: 10.1186/gb-2012-13-10-r85] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 10/03/2012] [Indexed: 12/20/2022] Open
Abstract
Background The histone variant H2A.Z has been implicated in nucleosome exchange, transcriptional activation and Polycomb repression. However, the relationships among these seemingly disparate functions remain obscure. Results We mapped H2A.Z genome-wide in mammalian ES cells and neural progenitors. H2A.Z is deposited promiscuously at promoters and enhancers, and correlates strongly with H3K4 methylation. Accordingly, H2A.Z is present at poised promoters with bivalent chromatin and at active promoters with H3K4 methylation, but is absent from stably repressed promoters that are specifically enriched for H3K27 trimethylation. We also characterized post-translational modification states of H2A.Z, including a novel species dually-modified by ubiquitination and acetylation that is enriched at bivalent chromatin. Conclusions Our findings associate H2A.Z with functionally distinct genomic elements, and suggest that post-translational modifications may reconcile its contrasting locations and roles.
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Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A. Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell 2011; 8:96-105. [PMID: 21211784 DOI: 10.1016/j.stem.2010.12.001] [Citation(s) in RCA: 285] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 10/22/2010] [Accepted: 11/24/2010] [Indexed: 12/15/2022]
Abstract
Despite rapid progress in characterizing transcription factor-driven reprogramming of somatic cells to an induced pluripotent stem cell (iPSC) state, many mechanistic questions still remain. To gain insight into the earliest events in the reprogramming process, we systematically analyzed the transcriptional and epigenetic changes that occur during early factor induction after discrete numbers of divisions. We observed rapid, genome-wide changes in the euchromatic histone modification, H3K4me2, at more than a thousand loci including large subsets of pluripotency-related or developmentally regulated gene promoters and enhancers. In contrast, patterns of the repressive H3K27me3 modification remained largely unchanged except for focused depletion specifically at positions where H3K4 methylation is gained. These chromatin regulatory events precede transcriptional changes within the corresponding loci. Our data provide evidence for an early, organized, and population-wide epigenetic response to ectopic reprogramming factors that clarify the temporal order through which somatic identity is reset during reprogramming.
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Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007; 448:553-60. [PMID: 17603471 PMCID: PMC2921165 DOI: 10.1038/nature06008] [Citation(s) in RCA: 3097] [Impact Index Per Article: 182.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 06/13/2007] [Indexed: 12/11/2022]
Abstract
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
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Abstract
At present, hundreds of microbial genomes have been sequenced, and hundreds more are currently in the pipeline. The Virtual Institute for Microbial Stress and Survival has developed a publicly available suite of Web-based comparative genomic tools (http://www.microbesonline.org) designed to facilitate multispecies comparison among prokaryotes. Highlights of the MicrobesOnline Web site include operon and regulon predictions, a multispecies genome browser, a multispecies Gene Ontology browser, a comparative KEGG metabolic pathway viewer, a Bioinformatics Workbench for in-depth sequence analysis, and Gene Carts that allow users to save genes of interest for further study while they browse. In addition, we provide an interface for genome annotation, which like all of the tools reported here, is freely available to the scientific community.
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Affiliation(s)
- Eric J Alm
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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