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Dang J, Nance S, Ma J, Cheng J, Walsh MP, Vogel P, Easton J, Song G, Rusch M, Gedman AL, Koss C, Downing JR, Gruber TA. AMKL chimeric transcription factors are potent inducers of leukemia. Leukemia 2017; 31:2228-2234. [PMID: 28174417 DOI: 10.1038/leu.2017.51] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 01/23/2017] [Indexed: 01/08/2023]
Abstract
Acute megakaryoblastic leukemia in patients without Down syndrome is a rare malignancy with a poor prognosis. RNA sequencing of fourteen pediatric cases previously identified novel fusion transcripts that are predicted to be pathological including CBFA2T3-GLIS2, GATA2-HOXA9, MN1-FLI and NIPBL-HOXB9. In contrast to CBFA2T3-GLIS2, which is insufficient to induce leukemia, we demonstrate that the introduction of GATA2-HOXA9, MN1-FLI1 or NIPBL-HOXB9 into murine bone marrow induces overt disease in syngeneic transplant models. With the exception of MN1, full penetrance was not achieved through the introduction of fusion partner genes alone, suggesting that the chimeric transcripts possess a unique gain-of-function phenotype. Leukemias were found to exhibit elements of the megakaryocyte erythroid progenitor gene expression program, as well as unique leukemia-specific signatures that contribute to transformation. Comprehensive genomic analyses of resultant murine tumors revealed few cooperating mutations confirming the strength of the fusion genes and their role as pathological drivers. These models are critical for both the understanding of the biology of disease as well as providing a tool for the identification of effective therapeutic agents in preclinical studies.
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Affiliation(s)
- J Dang
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - S Nance
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J Ma
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J Cheng
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - M P Walsh
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - P Vogel
- Department of Veterinary Pathology Core, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J Easton
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - G Song
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - M Rusch
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - A L Gedman
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - C Koss
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J R Downing
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - T A Gruber
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
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2
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Levine JH, Simonds EF, Bendall SC, Davis KL, Amir EAD, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER, Finck R, Gedman AL, Radtke I, Downing JR, Pe'er D, Nolan GP. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell 2015; 162:184-97. [PMID: 26095251 DOI: 10.1016/j.cell.2015.05.047] [Citation(s) in RCA: 1269] [Impact Index Per Article: 141.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/16/2015] [Accepted: 05/04/2015] [Indexed: 12/20/2022]
Abstract
Acute myeloid leukemia (AML) manifests as phenotypically and functionally diverse cells, often within the same patient. Intratumor phenotypic and functional heterogeneity have been linked primarily by physical sorting experiments, which assume that functionally distinct subpopulations can be prospectively isolated by surface phenotypes. This assumption has proven problematic, and we therefore developed a data-driven approach. Using mass cytometry, we profiled surface and intracellular signaling proteins simultaneously in millions of healthy and leukemic cells. We developed PhenoGraph, which algorithmically defines phenotypes in high-dimensional single-cell data. PhenoGraph revealed that the surface phenotypes of leukemic blasts do not necessarily reflect their intracellular state. Using hematopoietic progenitors, we defined a signaling-based measure of cellular phenotype, which led to isolation of a gene expression signature that was predictive of survival in independent cohorts. This study presents new methods for large-scale analysis of single-cell heterogeneity and demonstrates their utility, yielding insights into AML pathophysiology.
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Affiliation(s)
- Jacob H Levine
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY 10027, USA
| | - Erin F Simonds
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kara L Davis
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - El-ad D Amir
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY 10027, USA
| | - Michelle D Tadmor
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY 10027, USA
| | - Oren Litvin
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY 10027, USA
| | - Harris G Fienberg
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Astraea Jager
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Eli R Zunder
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Rachel Finck
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Amanda L Gedman
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ina Radtke
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Dana Pe'er
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY 10027, USA.
| | - Garry P Nolan
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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Huether R, Dong L, Chen X, Wu G, Parker M, Wei L, Ma J, Edmonson MN, Hedlund EK, Rusch MC, Shurtleff SA, Mulder HL, Boggs K, Vadordaria B, Cheng J, Yergeau D, Song G, Becksfort J, Lemmon G, Weber C, Cai Z, Dang J, Walsh M, Gedman AL, Faber Z, Easton J, Gruber T, Kriwacki RW, Partridge JF, Ding L, Wilson RK, Mardis ER, Mullighan CG, Gilbertson RJ, Baker SJ, Zambetti G, Ellison DW, Zhang J, Downing JR. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun 2014; 5:3630. [PMID: 24710217 DOI: 10.1038/ncomms4630] [Citation(s) in RCA: 288] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 03/12/2014] [Indexed: 02/07/2023] Open
Abstract
Studies of paediatric cancers have shown a high frequency of mutation across epigenetic regulators. Here we sequence 633 genes, encoding the majority of known epigenetic regulatory proteins, in over 1,000 paediatric tumours to define the landscape of somatic mutations in epigenetic regulators in paediatric cancer. Our results demonstrate a marked variation in the frequency of gene mutations across 21 different paediatric cancer subtypes, with the highest frequency of mutations detected in high-grade gliomas, T-lineage acute lymphoblastic leukaemia and medulloblastoma, and a paucity of mutations in low-grade glioma and retinoblastoma. The most frequently mutated genes are H3F3A, PHF6, ATRX, KDM6A, SMARCA4, ASXL2, CREBBP, EZH2, MLL2, USP7, ASXL1, NSD2, SETD2, SMC1A and ZMYM3. We identify novel loss-of-function mutations in the ubiquitin-specific processing protease 7 (USP7) in paediatric leukaemia, which result in decreased deubiquitination activity. Collectively, our results help to define the landscape of mutations in epigenetic regulatory genes in paediatric cancer and yield a valuable new database for investigating the role of epigenetic dysregulations in cancer.
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Affiliation(s)
- Robert Huether
- 1] Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2]
| | - Li Dong
- 1] Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2]
| | - Xiang Chen
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gang Wu
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Matthew Parker
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Lei Wei
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jing Ma
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael N Edmonson
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Erin K Hedlund
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael C Rusch
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Sheila A Shurtleff
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Heather L Mulder
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Kristy Boggs
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Bhavin Vadordaria
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinjun Cheng
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Donald Yergeau
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Guangchun Song
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jared Becksfort
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gordon Lemmon
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Catherine Weber
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Zhongling Cai
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinjun Dang
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael Walsh
- Department of Oncology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Amanda L Gedman
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Zachary Faber
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - John Easton
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Tanja Gruber
- 1] Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2] Department of Oncology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Janet F Partridge
- Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Li Ding
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Richard K Wilson
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Elaine R Mardis
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Richard J Gilbertson
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gerard Zambetti
- Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - James R Downing
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
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4
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Gruber TA, Gedman AL, Ta H, Zhang J, Koss C, Marada S, Chen SC, Su X, Ogden S, Gupta V, Andersson A, Pounds S, Shi L, Easton J, Wang J, Rusch M, Ding L, Cazzaniga G, Biondi A, Kornblau S, Ravandi-Kashani F, Kantarjian H, Nimer SD, Doehner K, Doehner H, Ley TJ, Ballerini P, Mercher T, Shurtleff S, Shih LY, Liang DC, Rubnitz J, Pui CH, Mardis E, Wilson RK, Downing JR. Abstract 4867: Identification of an inv(16)-encoded CBFA2T3-GLIS2 fusion protein in 34% of non-infant acute megkaryoblastic leukemias: A report from the Pediatric Cancer Genome Project. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4867] [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
Acute Megakaryoblastic Leukemia (AMKL) accounts for ∼10% of childhood acute myeloid leukemia (AML). Although AMKL patients with Down syndrome (DS-AMKL) have an excellent 5 year event-free survival (EFS), non-DS-AMKL patients have an extremely poor outcome with a 3 year EFS < 40%. To define the landscape of mutations that occur in non-DS-AMKL, we performed transcriptome sequencing on diagnostic blasts from 14 cases. Our results identified chromosomal rearrangements resulting in the expression of novel fusion transcripts in 12/14 cases. Remarkably, in 7/14 cases, we detected an inversion on chromosome 16 [inv(16)(p13.3;q24.3)] that resulted in the juxtaposition of CBFA2T3, a member of the ETO family of transcription factors, next to GLIS2 resulting in a CBFA2T3-GLIS2 chimeric gene encoding an in frame fusion protein. GLIS2 is a member of the GLI family of transcription factors that mediate sonic hedgehog (SHH) signaling and has been demonstrated to play a role in regulating expression of GLI target genes. Evaluation of a recurrency cohort of 52 samples including 24 additional pediatric cases and 28 adult cases revealed 6 additional pediatric samples carrying the fusion for an overall frequency of 34% in pediatric AMKL. To gain insight into the mechanism whereby CBFA2T3-GLIS2 promotes leukemogenesis, we introduced the fusion into murine hematopoietic cells and assessed its effect on in vitro colony replating as a surrogate measure of self-renewal. Cells transduced with a mCherry expressing retrovirus failed to form colonies after the 2nd replating. By contrast, expression of either wild-type GLIS2 or CBFA2T3-GLIS2 resulted in a marked increase in the self-renewal capacity, with colony formation persisting through 12 replatings. Immunophenotypic analysis of the CBFA2T3-GLIS2 expressing colonies revealed evidence of megakaryocytic differentiation. GLI transcription factors modulate expression of multiple downstream targets including components of BMP, WNT, and SHH pathways. To interrogate these pathways as potential contributors to the enhanced self-renewal capacity, we conducted luciferase reporter assays and found that CBFA2T3-GLIS2 functioned as a strong activator of the BMP responsive element. Furthermore, expression of CBFA2T3-GLIS2 in Drosophila resulted in ectopic expression of endogenous dpp, the fly homolog of BMP4, and conferred a dpp gain of function phenotype. Taken together these data identify a novel inv(16)-encoded CBFA2T3-GLIS2 fusion protein as a recurrent driver mutation in ∼35% of non-infant pediatric non-DS-AMKLs. The alteration of a key transcriptional regulator within the SHH signaling pathways in a substantial percentage of pediatric AMKL raises the possibility that inhibition of this pathway or downstream activated pathways may have a therapeutic benefit in this aggressive form of AML.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4867. doi:1538-7445.AM2012-4867
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Affiliation(s)
| | | | - Huy Ta
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | - Cary Koss
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | | | | | - Stacey Ogden
- 1St. Jude Children's Research Hospital, Memphis, TN
| | - Vedant Gupta
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | | | - Lei Shi
- 1St. Jude Children's Research Hospital, Memphis, TN
| | - John Easton
- 1St. Jude Children's Research Hospital, Memphis, TN
| | - Jianmin Wang
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | - Li Ding
- 3Washington University, St. Louis, MO
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