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Tlemsani C, Heske CM, Elloumi F, Pongor L, Khandagale P, Varma S, Luna A, Meltzer PS, Khan J, Reinhold WC, Pommier Y. Sarcoma_CellminerCDB: A tool to interrogate the genomic and functional characteristics of a comprehensive collection of sarcoma cell lines. iScience 2024; 27:109781. [PMID: 38868205 PMCID: PMC11167437 DOI: 10.1016/j.isci.2024.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/28/2023] [Accepted: 04/15/2024] [Indexed: 06/14/2024] Open
Abstract
Sarcomas are a diverse group of rare malignancies composed of multiple different clinical and molecular subtypes. Due to their rarity and heterogeneity, basic, translational, and clinical research in sarcoma has trailed behind that of other cancers. Outcomes for patients remain generally poor due to an incomplete understanding of disease biology and a lack of novel therapies. To address some of the limitations impeding preclinical sarcoma research, we have developed Sarcoma_CellMinerCDB, a publicly available interactive tool that merges publicly available sarcoma cell line data and newly generated omics data to create a comprehensive database of genomic, transcriptomic, methylomic, proteomic, metabolic, and pharmacologic data on 133 annotated sarcoma cell lines. The reproducibility, functionality, biological relevance, and therapeutic applications of Sarcoma_CellMinerCDB described herein are powerful tools to address and generate biological questions and test hypotheses for translational research. Sarcoma_CellMinerCDB (https://discover.nci.nih.gov/SarcomaCellMinerCDB) aims to contribute to advancing the preclinical study of sarcoma.
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Affiliation(s)
- Camille Tlemsani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Department of Medical Oncology, Cochin Hospital, Paris Cancer Institute CARPEM, Université Paris Cité, APHP. Centre, Paris, France
- Institut Cochin, INSERM U1016, CNRS UMR8104, Paris Cancer Institute CARPEM, Université Paris Cité, Paris, France
| | - Christine M. Heske
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Lorinc Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Hungarian Centre of Excellence for Molecular Medicine, Cancer Genomics and Epigenetics Core Group, Szeged, Hungary
| | - Prashant Khandagale
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Augustin Luna
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Computational Biology Branch, National Library of Medicine, NIH, Bethesda, Maryland 20892, USA
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William C. Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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2
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Battistella ME, Freire NH, Toson B, Dalmolin M, Fernandes MAC, Tassinari ID, Jaeger M, Brunetto AT, Brunetto AL, Gregianin L, de Farias CB, Roesler R. Stemness and Cell Cycle Regulators and Their Modulation by Retinoic Acid in Ewing Sarcoma. Curr Issues Mol Biol 2024; 46:3990-4003. [PMID: 38785514 PMCID: PMC11119684 DOI: 10.3390/cimb46050246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/13/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
Retinoic acid (RA) regulates stemness and differentiation in human embryonic stem cells (ESCs). Ewing sarcoma (ES) is a pediatric tumor that may arise from the abnormal development of ESCs. Here we show that RA impairs the viability of SK-ES-1 ES cells and affects the cell cycle. Cells treated with RA showed increased levels of p21 and its encoding gene, CDKN1A. RA reduced mRNA and protein levels of SRY-box transcription factor 2 (SOX2) as well as mRNA levels of beta III Tubulin (TUBB3), whereas the levels of CD99 increased. Exposure to RA reduced the capability of SK-ES-1 to form tumorspheres with high expression of SOX2 and Nestin. Gene expression of CD99 and CDKN1A was reduced in ES tumors compared to non-tumoral tissue, whereas transcript levels of SOX2 were significantly higher in tumors. For NES and TUBB3, differences between tumors and control tissue did not reach statistical significance. Low expression of CD99 and NES, and high expression of SOX2, were significantly associated with a poorer patient prognosis indicated by shorter overall survival (OS). Our results indicate that RA may display rather complex modulatory effects on multiple target genes associated with the maintenance of stem cell's features versus their differentiation, cell cycle regulation, and patient prognosis in ES.
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Affiliation(s)
- Maria Eduarda Battistella
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
| | - Natália Hogetop Freire
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, Brazil
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
| | - Bruno Toson
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
| | - Matheus Dalmolin
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- InovAI Lab, nPITI/IMD, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
- Bioinformatics Multidisciplinary Environment (BioME), Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
| | - Marcelo A. C. Fernandes
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- InovAI Lab, nPITI/IMD, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
- Bioinformatics Multidisciplinary Environment (BioME), Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
- Department of Computer Engineering and Automation, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
| | - Isadora D. Tassinari
- Laboratory of Neurobiology and Metabolism (NeuroMet), Department of Physiology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- Graduate Program in Physiology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
| | - Mariane Jaeger
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, Brazil
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
| | - André T. Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, Brazil
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
| | - Algemir L. Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, Brazil
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
| | - Lauro Gregianin
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- Department of Pediatrics, School of Medicine, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- Pediatric Oncology Service, Clinical Hospital, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
| | - Caroline Brunetto de Farias
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, Brazil
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
| | - Rafael Roesler
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
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Xing YH, Dong R, Lee L, Rengarajan S, Riggi N, Boulay G, Rivera MN. DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins. Nat Biotechnol 2024; 42:52-64. [PMID: 37037903 PMCID: PMC10791585 DOI: 10.1038/s41587-023-01737-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023]
Abstract
Intrinsically disordered regions (IDRs) in DNA-associated proteins are known to influence gene regulation, but their distribution and cooperative functions in genome-wide regulatory programs remain poorly understood. Here we describe DisP-seq (disordered protein precipitation followed by DNA sequencing), an antibody-independent chemical precipitation assay that can simultaneously map endogenous DNA-associated disordered proteins genome-wide through a combination of biotinylated isoxazole precipitation and next-generation sequencing. DisP-seq profiles are composed of thousands of peaks that are associated with diverse chromatin states, are enriched for disordered transcription factors (TFs) and are often arranged in large lineage-specific clusters with high local concentrations of disordered proteins and different combinations of histone modifications linked to regulatory potential. We use DisP-seq to analyze cancer cells and reveal how disordered protein-associated islands enable IDR-dependent mechanisms that control the binding and function of disordered TFs, including oncogene-dependent sequestration of TFs through long-range interactions and the reactivation of differentiation pathways upon loss of oncogenic stimuli in Ewing sarcoma.
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Affiliation(s)
- Yu-Hang Xing
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Rui Dong
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Lukuo Lee
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Shruthi Rengarajan
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Nicolò Riggi
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Gaylor Boulay
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Miguel N Rivera
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
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Yasir M, Park J, Chun W. EWS/FLI1 Characterization, Activation, Repression, Target Genes and Therapeutic Opportunities in Ewing Sarcoma. Int J Mol Sci 2023; 24:15173. [PMID: 37894854 PMCID: PMC10607184 DOI: 10.3390/ijms242015173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Despite their clonal origins, tumors eventually develop into complex communities made up of phenotypically different cell subpopulations, according to mounting evidence. Tumor cell-intrinsic programming and signals from geographically and temporally changing microenvironments both contribute to this variability. Furthermore, the mutational load is typically lacking in childhood malignancies of adult cancers, and they still exhibit high cellular heterogeneity levels largely mediated by epigenetic mechanisms. Ewing sarcomas represent highly aggressive malignancies affecting both bone and soft tissue, primarily afflicting adolescents. Unfortunately, the outlook for patients facing relapsed or metastatic disease is grim. These tumors are primarily fueled by a distinctive fusion event involving an FET protein and an ETS family transcription factor, with the most prevalent fusion being EWS/FLI1. Despite originating from a common driver mutation, Ewing sarcoma cells display significant variations in transcriptional activity, both within and among tumors. Recent research has pinpointed distinct fusion protein activities as a principal source of this heterogeneity, resulting in markedly diverse cellular phenotypes. In this review, we aim to characterize the role of the EWS/FLI fusion protein in Ewing sarcoma by exploring its general mechanism of activation and elucidating its implications for tumor heterogeneity. Additionally, we delve into potential therapeutic opportunities to target this aberrant fusion protein in the context of Ewing sarcoma treatment.
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Affiliation(s)
| | | | - Wanjoo Chun
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea; (M.Y.); (J.P.)
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5
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Silveira DA, Gupta S, da Cunha Jaeger M, Brunetto de Farias C, Mombach JCM, Sinigaglia M. A logical model of Ewing sarcoma cell epithelial-to-mesenchymal transition supports the existence of hybrid cellular phenotypes. FEBS Lett 2023; 597:2446-2460. [PMID: 37597508 DOI: 10.1002/1873-3468.14724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/21/2023]
Abstract
Ewing sarcoma (ES) is a highly aggressive pediatric tumor driven by the RNA-binding protein EWS (EWS)/friend leukemia integration 1 transcription factor (FLI1) chimeric transcription factor, which is involved in epithelial-mesenchymal transition (EMT). EMT stabilizes a hybrid cell state, boosting metastatic potential and drug resistance. Nevertheless, the mechanisms underlying the maintenance of this hybrid phenotype in ES remain elusive. Our study proposes a logical EMT model for ES, highlighting zinc finger E-box-binding homeobox 2 (ZEB2), miR-145, and miR-200 circuits that maintain hybrid states. The model aligns with experimental findings and reveals a previously unknown circuit supporting the mesenchymal phenotype. These insights emphasize the role of ZEB2 in the maintenance of the hybrid state in ES.
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Affiliation(s)
- Daner A Silveira
- Children's Cancer Institute, Porto Alegre, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, Brazil
| | | | - Mariane da Cunha Jaeger
- Children's Cancer Institute, Porto Alegre, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, Brazil
| | - Caroline Brunetto de Farias
- Children's Cancer Institute, Porto Alegre, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, Brazil
| | | | - Marialva Sinigaglia
- Children's Cancer Institute, Porto Alegre, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, Brazil
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6
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Jassim A, Rahrmann EP, Simons BD, Gilbertson RJ. Cancers make their own luck: theories of cancer origins. Nat Rev Cancer 2023; 23:710-724. [PMID: 37488363 DOI: 10.1038/s41568-023-00602-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Cancer has been a leading cause of death for decades. This dismal statistic has increased efforts to prevent the disease or to detect it early, when treatment is less invasive, relatively inexpensive and more likely to cure. But precisely how tissues are transformed continues to provoke controversy and debate, hindering cancer prevention and early intervention strategies. Various theories of cancer origins have emerged, including the suggestion that it is 'bad luck': the inevitable consequence of random mutations in proliferating stem cells. In this Review, we discuss the principal theories of cancer origins and the relative importance of the factors that underpin them. The body of available evidence suggests that developing and ageing tissues 'walk a tightrope', retaining adequate levels of cell plasticity to generate and maintain tissues while avoiding overstepping into transformation. Rather than viewing cancer as 'bad luck', understanding the complex choreography of cell intrinsic and extrinsic factors that characterize transformation holds promise to discover effective new ways to prevent, detect and stop cancer before it becomes incurable.
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Affiliation(s)
- Amir Jassim
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Eric P Rahrmann
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ben D Simons
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Richard J Gilbertson
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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Dupuy M, Lamoureux F, Mullard M, Postec A, Regnier L, Baud’huin M, Georges S, Brounais-Le Royer B, Ory B, Rédini F, Verrecchia F. Ewing sarcoma from molecular biology to the clinic. Front Cell Dev Biol 2023; 11:1248753. [PMID: 37752913 PMCID: PMC10518617 DOI: 10.3389/fcell.2023.1248753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
In Europe, with an incidence of 7.5 cases per million, Ewing sarcoma (ES) is the second most common primary malignant bone tumor in children, adolescents and young adults, after osteosarcoma. Since the 1980s, conventional treatment has been based on the use of neoadjuvant and adjuvant chemotherapeutic agents combined with surgical resection of the tumor when possible. These treatments have increased the patient survival rate to 70% for localized forms, which drops drastically to less than 30% when patients are resistant to chemotherapy or when pulmonary metastases are present at diagnosis. However, the lack of improvement in these survival rates over the last decades points to the urgent need for new therapies. Genetically, ES is characterized by a chromosomal translocation between a member of the FET family and a member of the ETS family. In 85% of cases, the chromosomal translocation found is (11; 22) (q24; q12), between the EWS RNA-binding protein and the FLI1 transcription factor, leading to the EWS-FLI1 fusion protein. This chimeric protein acts as an oncogenic factor playing a crucial role in the development of ES. This review provides a non-exhaustive overview of ES from a clinical and biological point of view, describing its main clinical, cellular and molecular aspects.
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Affiliation(s)
- Maryne Dupuy
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, CRCI2NA, Université d'Angers, Nantes, France
| | | | | | | | | | | | | | | | | | | | - Franck Verrecchia
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, CRCI2NA, Université d'Angers, Nantes, France
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Vanoli F, Antonescu CR. Modeling sarcoma relevant translocations using CRISPR-Cas9 in human embryonic stem derived mesenchymal precursors. Genes Chromosomes Cancer 2023; 62:501-509. [PMID: 36965130 PMCID: PMC10725040 DOI: 10.1002/gcc.23141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/06/2023] [Accepted: 03/16/2023] [Indexed: 03/27/2023] Open
Abstract
The role of cancer relevant translocations in tumorigenesis has been historically hampered by the lack of faithful in vitro and in vivo models. The development of the latest genome editing tools (e.g., CRISPR-Cas9) allowed modeling of various chromosomal translocations with different effects on proliferation and transformation capacity depending on the cell line used and secondary genetic alterations. The cellular context is particularly relevant in the case of oncogenic fusions expressed in sarcomas whose histogenesis remain uncertain. Moreover, recent studies have emphasized the increased frequency of gene fusion promiscuity across different mesenchymal tumor entities, which are clinicopathologically unrelated. This review provides a summary of different strategies utilized to generate cancer models with a focus on fusion-driven mesenchymal neoplasia.
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Affiliation(s)
- Fabio Vanoli
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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9
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Tanaka M, Nakamura T. Targeting epigenetic aberrations of sarcoma in CRISPR era. Genes Chromosomes Cancer 2023; 62:510-525. [PMID: 36967299 DOI: 10.1002/gcc.23142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Sarcomas are rare malignancies that exhibit diverse biological, genetic, morphological, and clinical characteristics. Genetic alterations, such as gene fusions, mutations in transcriptional machinery components, histones, and DNA methylation regulatory molecules, play an essential role in sarcomagenesis. These mutations induce and/or cooperate with specific epigenetic aberrations required for the growth and maintenance of sarcomas. Appropriate mouse models have been developed to clarify the significance of genetic and epigenetic interactions in sarcomas. Studies using the mouse models for human sarcomas have demonstrated major advances in our understanding the developmental processes as well as tumor microenvironment of sarcomas. Recent technological progresses in epigenome editing will not only improve the studies using animal models but also provide a direct clue for epigenetic therapies. In this manuscript, we review important epigenetic aberrations in sarcomas and their representative mouse models, current methods of epigenetic editing using CRISPR/dCas9 systems, and potential applications in sarcoma studies and therapeutics.
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Affiliation(s)
- Miwa Tanaka
- Project for Cancer Epigenomics, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Takuro Nakamura
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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10
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Chatzopoulos K, Davila JI, Fadra N, Jackson RA, Minn KT, Sotiriou S, Oliveira AM, Erickson LA, Halling KC, Rumilla KM, Rivera M. Transcriptomic and immunophenotypic characterization of two cases of adamantinoma-like Ewing sarcoma of the thyroid gland. Histopathology 2023; 83:426-434. [PMID: 37195579 DOI: 10.1111/his.14961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/22/2023] [Accepted: 05/08/2023] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Adamantinoma-like Ewing sarcoma (ALES) is a rare aggressive malignancy occasionally diagnosed in the thyroid gland. ALES shows basaloid cytomorphology, expresses keratins, p63, p40, frequently CD99, and harbours the t(11;22) EWSR1::FLI1 translocation. There is debate on whether ALES resembles more sarcoma or carcinoma. METHODS We performed RNA sequencing from two ALES cases and compared findings with skeletal Ewing's sarcomas and nonneoplastic thyroid tissue. ALES was investigated by in situ hybridization (ISH) for high-risk human papillomavirus (HPV) DNA and immunohistochemistry for the following antigens: keratin 7, keratin 20, keratin 5, keratins (AE1/AE3 and CAM5.2), CD45, CD20, CD5, CD99, chromogranin, synaptophysin, calcitonin, thyroglobulin, PAX8, TTF1, S100, p40, p63, p16, NUT, desmin, ER, FLI1, INI1, and myogenin. RESULTS An uncommon EWSR1::FLI transcript with retained EWSR1 exon 8 was detected in both ALES cases. Regulators of EWSR1::FLI1 splicing (HNRNPH1, SUPT6H, SF3B1) necessary for production of a functional fusion oncoprotein, as well as 53 genes (including TNNT1, NKX2.2) activated downstream to the EWSR1::FLI1 cascade, were overexpressed. Eighty-six genes were uniquely overexpressed in ALES, most of which were related to squamous differentiation. Immunohistochemically, ALES strongly expressed keratins 5, AE1/AE3 and CAM5.2, p63, p40, p16, and focally CD99. INI1 was retained. The remaining immunostains and HPV DNA ISH were negative. CONCLUSION Comparative transcriptomic profiling reveals overlapping features of ALES with skeletal Ewing's sarcoma and an epithelial carcinoma, as evidenced by immunohistochemical expression of keratin 5, p63, p40, CD99, the transcriptome profile, and detection of EWSR1::FLI1 fusion transcript by RNA sequencing.
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Affiliation(s)
- Kyriakos Chatzopoulos
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Department of General and Anatomic Pathology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Jaime I Davila
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Numrah Fadra
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rory A Jackson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- NeoGenomics Laboratories, Aliso Viejo, CA, USA
| | - Kay T Minn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sotiris Sotiriou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Department of General and Anatomic Pathology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andre M Oliveira
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Lori A Erickson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kandelaria M Rumilla
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Michael Rivera
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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Koshevarova V, Kim A, Wilhelm AB, Eyzaguirre EJ, Bhargava P. Paratesticular Ewing's sarcoma. Radiol Case Rep 2023; 18:3260-3263. [PMID: 37456614 PMCID: PMC10339124 DOI: 10.1016/j.radcr.2023.06.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023] Open
Abstract
This case report follows a 23-year-old man who presented with a painful right scrotal mass which was found to be a paratesticular vascular solid mass on ultrasound, and after uncomplicated orchiectomy, was revealed to be a high-grade extraskeletal Ewing's sarcoma. Diagnosis leading up to the orchiectomy was primarily clinical with only ultrasound used in identification and characterization of the paratesticular mass. Paratesticular masses are more commonly benign, and ultrasound is the first modality, with computed tomography and magnetic resonance imaging providing more definitive findings. We discuss imaging findings and histopathology of this rare tumor with an uncommon presentation.
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12
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Sanalkumar R, Dong R, Lee L, Xing YH, Iyer S, Letovanec I, La Rosa S, Finzi G, Musolino E, Papait R, Chebib I, Nielsen GP, Renella R, Cote GM, Choy E, Aryee M, Stegmaier K, Stamenkovic I, Rivera MN, Riggi N. Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity. SCIENCE ADVANCES 2023; 9:eabo3789. [PMID: 37000878 DOI: 10.1126/sciadv.abo3789] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 01/18/2023] [Indexed: 06/19/2023]
Abstract
Cell fate transitions observed in embryonic development involve changes in three-dimensional genomic organization that provide proper lineage specification. Whether similar events occur within tumor cells and contribute to cancer evolution remains largely unexplored. We modeled this process in the pediatric cancer Ewing sarcoma and investigated high-resolution looping and large-scale nuclear conformation changes associated with the oncogenic fusion protein EWS-FLI1. We show that chromatin interactions in tumor cells are dominated by highly connected looping hubs centered on EWS-FLI1 binding sites, which directly control the activity of linked enhancers and promoters to establish oncogenic expression programs. Conversely, EWS-FLI1 depletion led to the disassembly of these looping networks and a widespread nuclear reorganization through the establishment of new looping patterns and large-scale compartment configuration matching those observed in mesenchymal stem cells, a candidate Ewing sarcoma progenitor. Our data demonstrate that major architectural features of nuclear organization in cancer cells can depend on single oncogenes and are readily reversed to reestablish latent differentiation programs.
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Affiliation(s)
- Rajendran Sanalkumar
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Rui Dong
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Lukuo Lee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Yu-Hang Xing
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sowmya Iyer
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Igor Letovanec
- Department of Histopathology, Central Institute, Valais Hospital, Sion, Switzerland
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stefano La Rosa
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Giovanna Finzi
- Department of Pathology, ASST Sette Laghi, Varese, Italy
| | - Elettra Musolino
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Roberto Papait
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- IRCSS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Ivan Chebib
- Department of Pathology and Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - G Petur Nielsen
- Department of Pathology and Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raffaele Renella
- Department Woman-Mother-Child, Division of Pediatrics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gregory M Cote
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Edwin Choy
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Martin Aryee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Kimberly Stegmaier
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Ivan Stamenkovic
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Miguel N Rivera
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Nicolò Riggi
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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13
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Regulation of EWSR1-FLI1 Function by Post-Transcriptional and Post-Translational Modifications. Cancers (Basel) 2023; 15:cancers15020382. [PMID: 36672331 PMCID: PMC9857208 DOI: 10.3390/cancers15020382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Ewing sarcoma is the second most common bone tumor in childhood and adolescence. Currently, first-line therapy includes multidrug chemotherapy with surgery and/or radiation. Although most patients initially respond to chemotherapy, recurrent tumors become treatment refractory. Pathologically, Ewing sarcoma consists of small round basophilic cells with prominent nuclei marked by expression of surface protein CD99. Genetically, Ewing sarcoma is driven by a fusion oncoprotein that results from one of a small number of chromosomal translocations composed of a FET gene and a gene encoding an ETS family transcription factor, with ~85% of tumors expressing the EWSR1::FLI1 fusion. EWSR1::FLI1 regulates transcription, splicing, genome instability and other cellular functions. Although a tumor-specific target, EWSR1::FLI1-targeted therapy has yet to be developed, largely due to insufficient understanding of EWSR1::FLI1 upstream and downstream signaling, and the challenges in targeting transcription factors with small molecules. In this review, we summarize the contemporary molecular understanding of Ewing sarcoma, and the post-transcriptional and post-translational regulatory mechanisms that control EWSR1::FLI1 function.
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14
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Yu F, Liu G, Zhang H, Wang X, Wu Z, Xu Q, Wu Y, Chen D. Cell Adhesion Molecule CD99 in Cancer Immunotherapy. Curr Mol Med 2023; 23:1028-1036. [PMID: 36214301 DOI: 10.2174/1566524023666221007143513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/22/2022]
Abstract
The CD99 antigen is a transmembrane protein expressed in a broad variety of tissues, particularly in hematopoietic cells, thymus, endothelial cells, etc. It participates in several crucial biological processes, including cell adhesion, migration, death, differentiation, and inflammation. CD99 has shown oncogenic or tumor suppressor roles in different types of cancer. Therefore, it has been used as a biomarker and therapeutic target for several types of cancer. Moreover, it has also been reported to be involved in several critical immune processes, such as T cell activation and differentiation, dendritic cell differentiation, and so on. Hence, CD99 may have potential values in cancer immunotherapy. Anti-CD99 antibodies have shown therapeutic effects on certain types of cancer, especially on Ewing sarcoma and T cell acute lymphoblastic leukemia (ALL). This review summarizes the recent progress of CD99 in cancer research and targeting therapies, especially in cancer immunotherapy, which may help researchers understand the crucial roles of CD99 in cancer development and design new therapeutic strategies.
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Affiliation(s)
- Feng Yu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Guodong Liu
- Department of Gastroenterology, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian 223812, China
| | - Hailing Zhang
- Department of Gastroenterology, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian 223812, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian 223812, China
| | - Zhi Wu
- Jiangsu Key Laboratory of High-Tech Research and Development of Veterinary Biopharmaceuticals, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 22530, China
| | - Qinggang Xu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Yan Wu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Dongfeng Chen
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
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15
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Wang S, Huo X, Yang Y, Mo Y, Kollipara RK, Kittler R. Ablation of EWS-FLI1 by USP9X inhibition suppresses cancer cell growth in Ewing sarcoma. Cancer Lett 2023; 552:215984. [PMID: 36330954 DOI: 10.1016/j.canlet.2022.215984] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/11/2022] [Accepted: 10/24/2022] [Indexed: 11/26/2022]
Abstract
The neomorphic transcription factor EWS-FLI1 is a key driver of Ewing sarcoma. Ablation of EWS-FLI1 may present a promising therapeutic strategy for this malignancy. Here we found that the deubiquitinase, ubiquitin specific peptidase 9 X-linked (USP9X) stabilizes EWS-FLI1 protein expression in Ewing sarcoma. We show that USP9X binds the ETS domain of EWS-FLI1 in Ewing sarcoma cells and deubiquitinates EWS-FLI1 and that USP9X and EWS-FLI1 protein expression is correlated in clinical Ewing sarcoma specimens. We found that treatment of Ewing sarcoma cells with the USP9X inhibitor WP1130 mediates rapid EWS-FLI1 degradation in vitro and in vivo which coincides with reduced growth of Ewing sarcoma cells and tumors. Our results suggest that USP9X might be a potential therapeutic target to mediate EWS-FLI1 depletion in Ewing sarcoma.
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Affiliation(s)
- Shan Wang
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, China; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofang Huo
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yiping Yang
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Yingxi Mo
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ralf Kittler
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA; Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA; Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA.
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16
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Suvarna K, Jayabal P, Ma X, Shiio Y. Slit2 signaling stimulates Ewing sarcoma growth. Genes Cancer 2022; 13:88-99. [PMID: 36533189 PMCID: PMC9753566 DOI: 10.18632/genesandcancer.227] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
Ewing sarcoma is a cancer of bone and soft tissue in children driven by EWS::ETS fusion, most commonly EWS::FLI1. Because current cytotoxic chemotherapies are not improving the survival of those with metastatic or recurrent Ewing sarcoma cases, there is a need for novel and more effective targeted therapies. While EWS::FLI1 is the major driver of Ewing sarcoma, EWS::FLI1 has been difficult to target. A promising alternative approach is to identify and target the molecular vulnerabilities created by EWS::FLI1. Here we report that EWS::FLI1 induces the expression of Slit2, the ligand of Roundabout (Robo) receptors implicated in axon guidance and multiple other developmental processes. EWS::FLI1 binds to the Slit2 gene promoter and stimulates the expression of Slit2. Slit2 inactivates cdc42 and stabilizes the BAF chromatin remodeling complexes, enhancing EWS::FLI1 transcriptional output. Silencing of Slit2 strongly inhibited anchorage-dependent and anchorage-independent growth of Ewing sarcoma cells. Silencing of Slit2 receptors, Robo1 and Robo2, inhibited Ewing sarcoma growth as well. These results uncover a new role for Slit2 signaling in stimulating Ewing sarcoma growth and suggest that this pathway can be targeted therapeutically.
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Affiliation(s)
- Kruthi Suvarna
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Panneerselvam Jayabal
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Xiuye Ma
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Yuzuru Shiio
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA,2Cancer Therapy and Research Center, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA,3Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA,Correspondence to:Yuzuru Shiio, email:
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17
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Orth MF, Surdez D, Faehling T, Ehlers AC, Marchetto A, Grossetête S, Volckmann R, Zwijnenburg DA, Gerke JS, Zaidi S, Alonso J, Sastre A, Baulande S, Sill M, Cidre-Aranaz F, Ohmura S, Kirchner T, Hauck SM, Reischl E, Gymrek M, Pfister SM, Strauch K, Koster J, Delattre O, Grünewald TGP. Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation. Cell Rep 2022; 41:111761. [PMID: 36476851 DOI: 10.1016/j.celrep.2022.111761] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/25/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Ewing sarcoma (EwS) is characterized by EWSR1-ETS fusion transcription factors converting polymorphic GGAA microsatellites (mSats) into potent neo-enhancers. Although the paucity of additional mutations makes EwS a genuine model to study principles of cooperation between dominant fusion oncogenes and neo-enhancers, this is impeded by the limited number of well-characterized models. Here we present the Ewing Sarcoma Cell Line Atlas (ESCLA), comprising whole-genome, DNA methylation, transcriptome, proteome, and chromatin immunoprecipitation sequencing (ChIP-seq) data of 18 cell lines with inducible EWSR1-ETS knockdown. The ESCLA shows hundreds of EWSR1-ETS-targets, the nature of EWSR1-ETS-preferred GGAA mSats, and putative indirect modes of EWSR1-ETS-mediated gene regulation, converging in the duality of a specific but plastic EwS signature. We identify heterogeneously regulated EWSR1-ETS-targets as potential prognostic EwS biomarkers. Our freely available ESCLA (http://r2platform.com/escla/) is a rich resource for EwS research and highlights the power of comprehensive datasets to unravel principles of heterogeneous gene regulation by chimeric transcription factors.
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Affiliation(s)
- Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Didier Surdez
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zürich, 8008 Zürich, Switzerland
| | - Tobias Faehling
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Anna C Ehlers
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Sandrine Grossetête
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Richard Volckmann
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Danny A Zwijnenburg
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Julia S Gerke
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Sakina Zaidi
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CB06/07/1009, CIBERER-ISCIII), 28029 Madrid, Spain
| | - Ana Sastre
- Unidad Hemato-oncología Pediátrica, Hospital Infantil Universitario La Paz, 28029 Madrid, Spain
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, 75005 Paris, France
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Florencia Cidre-Aranaz
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Shunya Ohmura
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, 80337 Munich, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Eva Reischl
- Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Melissa Gymrek
- Division of Genetics, Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Department of Pediatric Hematology & Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Konstantin Strauch
- Institute of Medical Biometry, Epidemiology, and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, LMU Munich, 81377 Munich, Germany
| | - Jan Koster
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Olivier Delattre
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany; Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
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18
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Apfelbaum AA, Wrenn ED, Lawlor ER. The importance of fusion protein activity in Ewing sarcoma and the cell intrinsic and extrinsic factors that regulate it: A review. Front Oncol 2022; 12:1044707. [PMID: 36505823 PMCID: PMC9727305 DOI: 10.3389/fonc.2022.1044707] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidence shows that despite clonal origins tumors eventually become complex communities comprised of phenotypically distinct cell subpopulations. This heterogeneity arises from both tumor cell intrinsic programs and signals from spatially and temporally dynamic microenvironments. While pediatric cancers usually lack the mutational burden of adult cancers, they still exhibit high levels of cellular heterogeneity that are largely mediated by epigenetic mechanisms. Ewing sarcomas are aggressive bone and soft tissue malignancies with peak incidence in adolescence and the prognosis for patients with relapsed and metastatic disease is dismal. Ewing sarcomas are driven by a single pathognomonic fusion between a FET protein and an ETS family transcription factor, the most common of which is EWS::FLI1. Despite sharing a single driver mutation, Ewing sarcoma cells demonstrate a high degree of transcriptional heterogeneity both between and within tumors. Recent studies have identified differential fusion protein activity as a key source of this heterogeneity which leads to profoundly different cellular phenotypes. Paradoxically, increased invasive and metastatic potential is associated with lower EWS::FLI1 activity. Here, we review what is currently understood about EWS::FLI1 activity, the cell autonomous and tumor microenvironmental factors that regulate it, and the downstream consequences of these activity states on tumor progression. We specifically highlight how transcription factor regulation, signaling pathway modulation, and the extracellular matrix intersect to create a complex network of tumor cell phenotypes. We propose that elucidation of the mechanisms by which these essential elements interact will enable the development of novel therapeutic approaches that are designed to target this complexity and ultimately improve patient outcomes.
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19
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Ewing Sarcoma Meets Epigenetics, Immunology and Nanomedicine: Moving Forward into Novel Therapeutic Strategies. Cancers (Basel) 2022; 14:cancers14215473. [PMID: 36358891 PMCID: PMC9658520 DOI: 10.3390/cancers14215473] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Simple Summary Ewing Sarcoma treatment is traditionally based on chemotherapy, surgery, and radiotherapy. Although these standard of care regimens are efficient at early disease stages, many patients fail to respond appropriately, which has prompted the search for more efficacious and specific treatments. A deeper understanding of the basic molecular mechanisms underlying the biology of both tumor cells and the tumor microenvironment, as well as advances in drug delivery, has led to the development of different approaches to improve the treatment in Ewing Sarcoma patients. Thus, epigenetic, and immunotherapy-based drugs, along with nanotechnology delivery strategies, represent novel preclinical and clinical studies in the treatment of Ewing Sarcoma. In this review, we provide a comprehensive overview of these emerging therapeutic strategies and summarize the potential of the latest preclinical and clinical trials in Ewing Sarcoma research. Finally, we underline the value and future directions of these new treatments. Abstract Ewing Sarcoma (EWS) is an aggressive bone and soft tissue tumor that mainly affects children, adolescents, and young adults. The standard therapy, including chemotherapy, surgery, and radiotherapy, has substantially improved the survival of EWS patients with localized disease. Unfortunately, this multimodal treatment remains elusive in clinics for those patients with recurrent or metastatic disease who have an unfavorable prognosis. Consistently, there is an urgent need to find new strategies for patients that fail to respond to standard therapies. In this regard, in the last decade, treatments targeting epigenetic dependencies in tumor cells and the immune system have emerged into the clinical scenario. Additionally, recent advances in nanomedicine provide novel delivery drug systems, which may address challenges such as side effects and toxicity. Therefore, therapeutic strategies stemming from epigenetics, immunology, and nanomedicine yield promising alternatives for treating these patients. In this review, we highlight the most relevant EWS preclinical and clinical studies in epigenetics, immunotherapy, and nanotherapy conducted in the last five years.
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20
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Kim MS, Lee WS, Lee H, Jin W. TrkC, a novel prognostic marker, induces and maintains cell survival and metastatic dissemination of Ewing sarcoma by inhibiting EWSR1-FLI1 degradation. Cell Death Dis 2022; 13:836. [PMID: 36171207 PMCID: PMC9519565 DOI: 10.1038/s41419-022-05275-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 01/23/2023]
Abstract
Upregulation of EWSR1-FLI1 expression has been associated with invasiveness, induced cell survival, metastatic dissemination, and acquisition of self-renewal traits in Ewing sarcoma (ES). Although existing evidence implies that TrkC expression is linked to the pathogenesis of other cancer types, its role and the mechanism behind its correlation with EWSR1-FLI1 in the pathogenesis of ES remain unclear. In this study, we uncovered a novel physiological role of TrkC as a key regulator of EWSR1-FLI1 involved in the survival and metastatic dissemination of ES. TrkC was observed to be frequently overexpressed in human metastatic ES cells in vitro and in vivo, facilitating enhanced survival, tumorigenicity, and metastasis of ES cells. TrkC-mediated metastasis of ES cells was induced by the inhibition of the proteasomal degradation of EWSR1-FLI1 via the TrkC/EWSR1-FLI1 complex, which subsequently enabled the induction of the target proteins, EGR2 and NKX2.2. Moreover, TrkC significantly inhibited tumor suppressor activity of TGF-β through reduction of the mRNA expression of one of its receptors, TGFBR2 via TrkC-induced stabilization of EWSR1-FLI1. Furthermore, loss of TrkC expression inhibited tumor growth and metastasis in experimental mouse models. This study is the first to report the involvement and functional role of TrkC in the pathogenesis of ES, suggesting important implications for understanding the alterations of TrkC in Ewing tumors.
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Affiliation(s)
- Min Soo Kim
- grid.256155.00000 0004 0647 2973Laboratory of Molecular Disease and Cell Regulation, Department of Biochemistry, School of Medicine, Gachon University, Incheon, 21999 Republic of Korea
| | - Won Sung Lee
- grid.256155.00000 0004 0647 2973Laboratory of Molecular Disease and Cell Regulation, Department of Biochemistry, School of Medicine, Gachon University, Incheon, 21999 Republic of Korea
| | - Hanki Lee
- grid.410898.c0000 0001 2339 0388Graduate School of Interdisciplinary Program of Biomodulation, Myongji University, Yongin, Gyeonggi-do 17058 Republic of Korea
| | - Wook Jin
- grid.256155.00000 0004 0647 2973Laboratory of Molecular Disease and Cell Regulation, Department of Biochemistry, School of Medicine, Gachon University, Incheon, 21999 Republic of Korea
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21
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Karlina I, Schroeder BA, Kirgizov K, Romantsova O, Istranov AL, Nedorubov A, Timashev P, Ulasov I. Latest developments in the pathobiology of Ewing sarcoma. J Bone Oncol 2022; 35:100440. [PMID: 35855933 PMCID: PMC9287185 DOI: 10.1016/j.jbo.2022.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Irina Karlina
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Brett A. Schroeder
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Kirill Kirgizov
- Research Institute of Pediatric Oncology and Hematology at N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia Moscow, 115478, Russia
| | - Olga Romantsova
- Research Institute of Pediatric Oncology and Hematology at N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia Moscow, 115478, Russia
| | - Andrey L. Istranov
- Department of Oncology, radiation therapy and plastic surgery, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Andrey Nedorubov
- Center for Preclinical Research, Institute of Translational Medicine and Biotechnology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Peter Timashev
- World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Ilya Ulasov
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Corresponding author at: Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia.
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22
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Xie Z, Janczyk PL, Shi X, Wang Q, Singh S, Cornelison R, Xu J, Mandell JW, Barr FG, Li H. Rhabdomyosarcomas are oncogene addicted to the activation of AVIL. Proc Natl Acad Sci U S A 2022; 119:e2118048119. [PMID: 37146302 PMCID: PMC9214494 DOI: 10.1073/pnas.2118048119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/11/2022] [Indexed: 11/23/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is one of the most common pediatric soft-tissue cancer. Previously, we discovered a gene fusion, MARS-AVIL formed by chromosomal inversion in RMS. Suspecting that forming a fusion with a housekeeping gene may be one of the mechanisms to dysregulate an oncogene, we investigated AVIL expression and its role in RMS. We first showed that MARS-AVIL translates into an in-frame fusion protein, which is critical for RMS cell tumorigenesis. Besides forming a gene fusion with the housekeeping gene, MARS, the AVIL locus is often amplified, and its RNA and protein expression are overexpressed in the majority of RMSs. Tumors with AVIL dysregulation exhibit evidence of oncogene addiction: Silencing MARS-AVIL in cells harboring the fusion, or silencing AVIL in cells with AVIL overexpression, nearly eradicated the cells in culture, as well as inhibited in vivo xenograft growth in mice. Conversely, gain-of-function manipulations of AVIL led to increased cell growth and migration, enhanced foci formation in mouse fibroblasts, and most importantly transformed mesenchymal stem cells in vitro and in vivo. Mechanistically, AVIL seems to serve as a converging node functioning upstream of two oncogenic pathways, PAX3-FOXO1 and RAS, thus connecting two types of RMS associated with these pathways. Interestingly, AVIL is overexpressed in other sarcoma cells as well, and its expression correlates with clinical outcomes, with higher levels of AVIL expression being associated with worse prognosis. AVIL is a bona fide oncogene in RMS, and RMS cells are addicted to its activity.
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Affiliation(s)
- Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Pawel L. Janczyk
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Xinrui Shi
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Qiong Wang
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Urology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Robert Cornelison
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Jingjing Xu
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - James W. Mandell
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Frederic G. Barr
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908
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23
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Pedot G, Marques JG, Ambühl PP, Wachtel M, Kasper S, Ngo QA, Niggli FK, Schäfer BW. Inhibition of HDACs reduces Ewing sarcoma tumor growth through EWS-FLI1 protein destabilization. Neoplasia 2022; 27:100784. [PMID: 35366465 PMCID: PMC8971315 DOI: 10.1016/j.neo.2022.100784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/26/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022]
Abstract
Oncogenic transcription factors lacking enzymatic activity or targetable binding pockets are typically considered "undruggable". An example is provided by the EWS-FLI1 oncoprotein, whose continuous expression and activity as transcription factor are critically required for Ewing sarcoma tumor formation, maintenance, and proliferation. Because neither upstream nor downstream targets have so far disabled its oncogenic potential, we performed a high-throughput drug screen (HTS), enriched for FDA-approved drugs, coupled to a Global Protein Stability (GPS) approach to identify novel compounds capable to destabilize EWS-FLI1 protein by enhancing its degradation through the ubiquitin-proteasome system. The protein stability screen revealed the dual histone deacetylase (HDAC) and phosphatidylinositol-3-kinase (PI3K) inhibitor called fimepinostat (CUDC-907) as top candidate to modulate EWS-FLI1 stability. Fimepinostat strongly reduced EWS-FLI1 protein abundance, reduced viability of several Ewing sarcoma cell lines and PDX-derived primary cells and delayed tumor growth in a xenograft mouse model, whereas it did not significantly affect healthy cells. Mechanistically, we demonstrated that EWS-FLI1 protein levels were mainly regulated by fimepinostat's HDAC activity. Our study demonstrates that HTS combined to GPS is a reliable approach to identify drug candidates able to modulate stability of EWS-FLI1 and lays new ground for the development of novel therapeutic strategies aimed to reduce Ewing sarcoma tumor progression.
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Affiliation(s)
- Gloria Pedot
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Joana Graça Marques
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Philip P Ambühl
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Stephanie Kasper
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Quy A Ngo
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Felix K Niggli
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland.
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24
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Inhibitor of DNA binding 2 (ID2) regulates the expression of developmental genes and tumorigenesis in ewing sarcoma. Oncogene 2022; 41:2873-2884. [PMID: 35422476 PMCID: PMC9107507 DOI: 10.1038/s41388-022-02310-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 11/24/2022]
Abstract
Sarcomas are difficult to treat and the therapy, even when effective, is associated with long-term and life-threatening side effects. In addition, the treatment regimens for many sarcomas, including Ewing sarcoma, rhabdomyosarcoma, and osteosarcoma, are relatively unchanged over the past two decades, indicating a critical lack of progress. Although differentiation-based therapies are used for the treatment of some cancers, the application of this approach to sarcomas has proven challenging. Here, using a CRISPR-mediated gene knockout approach, we show that Inhibitor of DNA Binding 2 (ID2) is a critical regulator of developmental-related genes and tumor growth in vitro and in vivo in Ewing sarcoma tumors. We also identified that homoharringtonine, which is an inhibitor of protein translation and FDA-approved for the treatment of leukemia, decreases the level of the ID2 protein and significantly reduces tumor growth and prolongs mouse survival in an Ewing sarcoma xenograft model. Furthermore, in addition to targeting ID2, homoharringtonine also reduces the protein levels of ID1 and ID3, which are additional members of the ID family of proteins with well-described roles in tumorigenesis, in multiple types of cancer. Overall, these results provide insight into developmental regulation in Ewing sarcoma tumors and identify a novel, therapeutic approach to target the ID family of proteins using an FDA-approved drug.
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25
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Carrabotta M, Laginestra MA, Durante G, Mancarella C, Landuzzi L, Parra A, Ruzzi F, Toracchio L, De Feo A, Giusti V, Pasello M, Righi A, Lollini PL, Palmerini E, Donati DM, Manara MC, Scotlandi K. Integrated Molecular Characterization of Patient-Derived Models Reveals Therapeutic Strategies for Treating CIC-DUX4 Sarcoma. Cancer Res 2022; 82:708-720. [PMID: 34903601 PMCID: PMC9359717 DOI: 10.1158/0008-5472.can-21-1222] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/18/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023]
Abstract
Capicua-double homeobox 4 (CIC-DUX4)-rearranged sarcomas (CDS) are extremely rare, highly aggressive primary sarcomas that represent a major therapeutic challenge. Patients are treated according to Ewing sarcoma protocols, but CDS-specific therapies are strongly needed. In this study, RNA sequencing was performed on patient samples to identify a selective signature that differentiates CDS from Ewing sarcoma and other fusion-driven sarcomas. This signature was used to validate the representativeness of newly generated CDS experimental models-patient-derived xenografts (PDX) and PDX-derived cell lines-and to identify specific therapeutic vulnerabilities. Annotation analysis of differentially expressed genes and molecular gene validation highlighted an HMGA2/IGF2BP/IGF2/IGF1R/AKT/mTOR axis that characterizes CDS and renders the tumors particularly sensitive to combined treatments with trabectedin and PI3K/mTOR inhibitors. Trabectedin inhibited IGF2BP/IGF2/IGF1R activity, but dual inhibition of the PI3K and mTOR pathways was required to completely dampen downstream signaling mediators. Proof-of-principle efficacy for the combination of the dual AKT/mTOR inhibitor NVP-BEZ235 (dactolisib) with trabectedin was obtained in vitro and in vivo using CDS PDX-derived cell lines, demonstrating a strong inhibition of local tumor growth and multiorgan metastasis. Overall, the development of representative experimental models (PDXs and PDX-derived cell lines) has helped to identify the unique sensitivity of the CDS to AKT/mTOR inhibitors and trabectedin, revealing a mechanism-based therapeutic strategy to fight this lethal cancer. SIGNIFICANCE This study identifies altered HMGA2/IGF2BP/IGF2 signaling in CIC-DUX4 sarcomas and provides proof of principle for combination therapy with trabectedin and AKT/mTOR dual inhibitors to specifically combat the disease.
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Affiliation(s)
- Marianna Carrabotta
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | | | - Giorgio Durante
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Caterina Mancarella
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Lorena Landuzzi
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alessandro Parra
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Francesca Ruzzi
- Laboratory of Immunology and Biology of Metastasis, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Lisa Toracchio
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alessandra De Feo
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Veronica Giusti
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Michela Pasello
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alberto Righi
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Pier-Luigi Lollini
- Laboratory of Immunology and Biology of Metastasis, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Emanuela Palmerini
- Osteoncology, Bone and Soft Tissue Sarcoma and Novel Therapy Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Davide Maria Donati
- Third Orthopaedic Clinic and Traumatology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Katia Scotlandi
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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26
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Korsching E, Matschke J, Hotfilder M. Splice variants denote differences between a cancer stem cell side population of EWSR1‑ERG‑based Ewing sarcoma cells, its main population and EWSR1‑FLI‑based cells. Int J Mol Med 2022; 49:39. [PMID: 35088879 PMCID: PMC8815407 DOI: 10.3892/ijmm.2022.5094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/17/2021] [Indexed: 11/06/2022] Open
Abstract
Ewing sarcoma is a challenging cancer entity, which, besides the characteristic presence of a fusion gene, is driven by multiple alternative splicing events. So far, splice variants in Ewing sarcoma cells were mainly analyzed for EWSR1‑FLI1. The present study provided a comprehensive alternative splicing study on CADO‑ES1, an Ewing model cell line for an EWSR1‑ERG fusion gene. Based on a well‑-characterized RNA‑sequencing dataset with extensive control mechanisms across all levels of analysis, the differential spliced genes in Ewing cancer stem cells were ATP13A3 and EPB41, while the main population was defined by ACADVL, NOP58 and TSPAN3. All alternatively spliced genes were further characterized by their Gene Ontology (GO) terms and by their membership in known protein complexes. These results confirm and extend previous studies towards a systematic whole‑transcriptome analysis. A highlight is the striking segregation of GO terms associated with five basic splice events. This mechanistic insight, together with a coherent integration of all observations with prior knowledge, indicates that EWSR1‑ERG is truly a close twin to EWSR1‑FLI1, but still exhibits certain individuality. Thus, the present study provided a measure of variability in Ewing sarcoma, whose understanding is essential both for clinical procedures and basic mechanistic insight.
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Affiliation(s)
- Eberhard Korsching
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, D‑48149 Münster, Germany
| | - Julian Matschke
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, D‑48149 Münster, Germany
| | - Marc Hotfilder
- Department of Pediatric Hematology and Oncology, University Hospital Münster, D‑48149 Münster, Germany
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27
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Noncanonical roles of p53 in cancer stemness and their implications in sarcomas. Cancer Lett 2022; 525:131-145. [PMID: 34742870 DOI: 10.1016/j.canlet.2021.10.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/24/2021] [Accepted: 10/25/2021] [Indexed: 12/25/2022]
Abstract
Impairment of the prominent tumor suppressor p53, well known for its canonical role as the "guardian of the genome", is found in almost half of human cancers. More recently, p53 has been suggested to be a crucial regulator of stemness, orchestrating the differentiation of embryonal and adult stem cells, suppressing reprogramming into induced pluripotent stem cells, or inhibiting cancer stemness (i.e., cancer stem cells, CSCs), which underlies the development of therapy-resistant tumors. This review addresses these noncanonical roles of p53 and their implications in sarcoma initiation and progression. Indeed, dysregulation of p53 family proteins is a common event in sarcomas and is associated with poor survival. Additionally, emerging studies have demonstrated that loss of wild-type p53 activity hinders the terminal differentiation of mesenchymal stem cells and leads to the development of aggressive sarcomas. This review summarizes recent findings on the roles of aberrant p53 in sarcoma development and stemness and further describes therapeutic approaches to restore normal p53 activity as a promising anti-CSC strategy to treat refractory sarcomas.
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28
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Graham GT, Selvanathan SP, Zöllner SK, Stahl E, Shlien A, Caplen N, Üren A, Toretsky JA. Comprehensive profiling of mRNA splicing indicates that GC content signals altered cassette exon inclusion in Ewing sarcoma. NAR Cancer 2022; 4:zcab052. [PMID: 35047826 PMCID: PMC8759570 DOI: 10.1093/narcan/zcab052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/30/2021] [Accepted: 01/06/2022] [Indexed: 11/29/2022] Open
Abstract
Ewing sarcoma (EwS) is a small round blue cell tumor and is the second most frequent pediatric bone cancer. 85% of EwS tumors express the fusion oncoprotein EWS-FLI1, the product of a t(11;22) reciprocal translocation. Prior work has indicated that transcription regulation alone does not fully describe the oncogenic capacity of EWS-FLI1, nor does it provide an effective means to stratify patient tumors. Research using EwS cell lines and patient samples has suggested that EWS-FLI1 also disrupts mRNA biogenesis. In this work we both describe the underlying characteristics of mRNA that are aberrantly spliced in EwS tumor samples as well as catalogue mRNA splicing events across other pediatric tumor types. Here, we also use short- and long-read sequencing to identify cis-factors that contribute to splicing profiles we observe in Ewing sarcoma. Our analysis suggests that GC content upstream of cassette exons is a defining factor of mRNA splicing in EwS. We also describe specific splicing events that discriminate EwS tumor samples from the assumed cell of origin, human mesenchymal stem cells derived from bone marrow (hMSC-BM). Finally, we identify specific splicing factors PCBP2, RBMX, and SRSF9 by motif enrichment and confirm findings from tumor samples in EwS cell lines.
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Affiliation(s)
| | | | | | | | | | | | | | - Jeffrey A Toretsky
- To whom correspondence should be addressed. Tel: +1 202 687 8909; Fax: +1 202 687 8909;
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29
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Jayabal P, Ma X, Shiio Y. EZH2 suppresses endogenous retroviruses and an interferon response in cancers. Genes Cancer 2021; 12:96-105. [PMID: 34966479 PMCID: PMC8711646 DOI: 10.18632/genesandcancer.218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
Ewing sarcoma is an aggressive cancer of bone and soft tissue in children. It is characterized by the chromosomal translocation between EWS and an Ets family transcription factor, most commonly FLI1. We recently reported that Ewing sarcoma depends on the autocrine signaling mediated by a cytokine, NELL2. NELL2 signaling stimulates the transcriptional output of EWS-FLI1 through the BAF chromatin remodeling complexes. While studying the impact of NELL2 silencing on Ewing sarcoma, we found that suppression of NELL2 signaling induces the expression of endogenous retroviruses (ERVs) and LINE-1 retrotransposons, an interferon response, and growth arrest. We determined that a histone methyltransferase, EZH2, is the critical downstream target of NELL2 signaling in suppressing ERVs, LINE-1, an interferon response, and growth arrest. We show that EZH2 inhibitors induce ERVs, LINE-1, and an interferon response in a variety of cancer types. These results uncover the role for NELL2–EZH2 signaling in suppressing endogenous virus-like agents and an antiviral response, and suggest the potential utility of EZH2 inhibitors in enhancing anti-tumor immunity.
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Affiliation(s)
- Panneerselvam Jayabal
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Xiuye Ma
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Yuzuru Shiio
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA.,Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA.,Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
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30
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Flores G, Grohar PJ. One oncogene, several vulnerabilities: EWS/FLI targeted therapies for Ewing sarcoma. J Bone Oncol 2021; 31:100404. [PMID: 34976713 PMCID: PMC8686064 DOI: 10.1016/j.jbo.2021.100404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 12/23/2022] Open
Abstract
EWS/FLI is the defining mutation of Ewing sarcoma. This oncogene drives malignant transformation and progression and occurs in a genetic background characterized by few other recurrent cooperating mutations. In addition, the tumor is absolutely dependent on the continued expression of EWS/FLI to maintain the malignant phenotype. However, EWS/FLI is a transcription factor and therefore a challenging drug target. The difficulty of directly targeting EWS/FLI stems from unique features of this fusion protein as well as the network of interacting proteins required to execute the transcriptional program. This network includes interacting proteins as well as upstream and downstream effectors that together reprogram the epigenome and transcriptome. While the vast number of proteins involved in this process challenge the development of a highly specific inhibitors, they also yield numerous therapeutic opportunities. In this report, we will review how this vast EWS-FLI transcriptional network has been exploited over the last two decades to identify compounds that directly target EWS/FLI and/or associated vulnerabilities.
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Affiliation(s)
- Guillermo Flores
- Van Andel Research Institute, Grand Rapids, MI, USA
- Michigan State University, College of Human Medicine, USA
| | - Patrick J Grohar
- Children's Hospital of Philadelphia, University of Pennsylvania, Perelman School of Medicine, 3501 Civic Center Blvd., Philadelphia, PA, USA
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31
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García-García L, Fernández-Tabanera E, Cervera ST, Melero-Fernández de Mera RM, Josa S, González-González L, Rodríguez-Martín C, Grünewald TGP, Alonso J. The Transcription Factor FEZF1, a Direct Target of EWSR1-FLI1 in Ewing Sarcoma Cells, Regulates the Expression of Neural-Specific Genes. Cancers (Basel) 2021; 13:5668. [PMID: 34830820 PMCID: PMC8616448 DOI: 10.3390/cancers13225668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Ewing sarcoma is a rare pediatric tumor characterized by chromosomal translocations that give rise to aberrant chimeric transcription factors (e.g., EWSR1-FLI1). EWSR1-FLI1 promotes a specific cellular transcriptional program. Therefore, the study of EWSR1-FLI1 target genes is important to identify critical pathways involved in Ewing sarcoma tumorigenesis. In this work, we focused on the transcription factors regulated by EWSR1-FLI1 in Ewing sarcoma. Transcriptomic analysis of the Ewing sarcoma cell line A673 indicated that one of the genes more strongly upregulated by EWSR1-FLI1 was FEZF1 (FEZ family zinc finger protein 1), a transcriptional repressor involved in neural cell identity. The functional characterization of FEZF1 was performed in three Ewing sarcoma cell lines (A673, SK-N-MC, SK-ES-1) through an shRNA-directed silencing approach. FEZF1 knockdown inhibited clonogenicity and cell proliferation. Finally, the analysis of the FEZF1-dependent expression profile in A673 cells showed several neural genes regulated by FEZF1 and concomitantly regulated by EWSR1-FLI1. In summary, FEZF1 is transcriptionally regulated by EWSR1-FLI1 in Ewing sarcoma cells and is involved in the regulation of neural-specific genes, which could explain the neural-like phenotype observed in several Ewing sarcoma tumors and cell lines.
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Affiliation(s)
- Laura García-García
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
| | - Enrique Fernández-Tabanera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Saint T. Cervera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Raquel M. Melero-Fernández de Mera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Santiago Josa
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
| | - Laura González-González
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
| | - Carlos Rodríguez-Martín
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Thomas G. P. Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany;
- Hopp-Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
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Morales E, Olson M, Iglesias F, Dahiya S, Luetkens T, Atanackovic D. Role of immunotherapy in Ewing sarcoma. J Immunother Cancer 2021; 8:jitc-2020-000653. [PMID: 33293354 PMCID: PMC7725096 DOI: 10.1136/jitc-2020-000653] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Ewing sarcoma (ES) is thought to arise from mesenchymal stem cells and is the second most common bone sarcoma in pediatric patients and young adults. Given the dismal overall outcomes and very intensive therapies used, there is an urgent need to explore and develop alternative treatment modalities including immunotherapies. In this article, we provide an overview of ES biology, features of ES tumor microenvironment (TME) and review various tumor-associated antigens that can be targeted with immune-based approaches including cancer vaccines, monoclonal antibodies, T cell receptor-transduced T cells, and chimeric antigen receptor T cells. We highlight key reasons for the limited efficacy of various immunotherapeutic approaches for the treatment of ES to date. These factors include absence of human leukocyte antigen class I molecules from the tumor tissue, lack of an ideal surface antigen, and immunosuppressive TME due to the presence of myeloid-derived suppressor cells, F2 fibrocytes, and M2-like macrophages. Lastly, we offer insights into strategies for novel therapeutics development in ES. These strategies include the development of gene-modified T cell receptor T cells against cancer–testis antigen such as XAGE-1, surface target discovery through detailed profiling of ES surface proteome, and combinatorial approaches. In summary, we provide state-of-the-art science in ES tumor immunology and immunotherapy, with rationale and recommendations for future therapeutics development.
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Affiliation(s)
- Erin Morales
- Pediatric Oncology and Hematology, University of Utah, Salt Lake City, Utah, USA
| | - Michael Olson
- Cancer Immunotherapy, Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Fiorella Iglesias
- Pediatric Oncology and Hematology, University of Utah, Salt Lake City, Utah, USA
| | - Saurabh Dahiya
- Department of Medicine, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Tim Luetkens
- Pediatric Oncology and Hematology, University of Utah, Salt Lake City, Utah, USA.,Cancer Immunotherapy, Huntsman Cancer Institute, Salt Lake City, Utah, USA.,Department of Medicine, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, Maryland, USA.,Hematology and Hematologic Malignancies, University of Utah/Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Djordje Atanackovic
- Cancer Immunotherapy, Huntsman Cancer Institute, Salt Lake City, Utah, USA .,Department of Medicine, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, Maryland, USA.,Hematology and Hematologic Malignancies, University of Utah/Huntsman Cancer Institute, Salt Lake City, Utah, USA
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Yang S, Liu L, Yan Y, Jiang L, Han S, Shen D, Zhang B. CIC-NUTM1 Sarcomas Affecting the Spine: A Subset of CIC-Rearranged Sarcomas Commonly Present in the Axial Skeleton. Arch Pathol Lab Med 2021; 146:735-741. [PMID: 34525172 DOI: 10.5858/arpa.2021-0153-oa] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Tumors harboring CIC-NUTM1 fusion are a newly recognized rare sarcoma, but the documented cases are still limited. It is unclear whether it is the same as classic CIC-DUX4 sarcoma in terms of its clinical, pathologic, and behavioral aspects. OBJECTIVE.— To further explore the clinicopathologic characteristics of CIC-NUTM1 sarcoma. DESIGN.— The cases were diagnosed based on immunophenotype, next-generation sequencing, and fluorescence in situ hybridization tests and compared with the reported CIC-NUTM1 sarcomas in the literature. RESULTS.— Three cases of CIC-NUTM1 sarcomas involving the spine in adults were described. They were 2 men and 1 woman, aged 38 to 61 years. Two tumors were located in thoracic vertebrae and 1 in a cervical vertebra. All were locally advanced lesions destroying the bone and soft tissues without spinal cord involvement or metastasis. The tumors were composed of monomorphic small to medium-sized cells with round to epithelioid appearance. The architecture was lobulated and solid with diffuse or multifocal myxoid stroma. Next-generation sequencing revealed an in-frame fusion between CIC (exon 16 or 17) and NUTM1 (exon 5 or 6) in 3 cases. Fluorescence in situ hybridization confirmed CIC and NUTM1 breaks, and immunohistochemistry showed NUT staining in the nucleus. The patients died of disease 8 to 15 months (mean, 10.7 months) after presentation. Of the CIC-NUTM1 sarcomas reported in the literature along with our cases (n = 11), 8 cases developed in axial bone (5 spine, 3 skull base). CONCLUSIONS.— CIC-NUTM1 sarcomas showed distinct anatomic tropism for the axial skeleton and unfavorable behavior compared with classic CIC sarcoma.
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Affiliation(s)
- Shaomin Yang
- From the Department of Pathology, School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, China (Yang, Zhang)
| | - LiLi Liu
- the Department of Pathology, Peking University People's Hospital, Beijing, China (Liu, Yan, Shen)
| | - Yu Yan
- the Department of Pathology, Peking University People's Hospital, Beijing, China (Liu, Yan, Shen)
| | - Liang Jiang
- and the Departments of Orthopedics (Jiang) and Radiology (Han), Peking University Third Hospital, Beijing, China
| | - Songbo Han
- and the Departments of Orthopedics (Jiang) and Radiology (Han), Peking University Third Hospital, Beijing, China
| | - Danhua Shen
- the Department of Pathology, Peking University People's Hospital, Beijing, China (Liu, Yan, Shen).,Zhang and Shen are co-lead authors of this paper
| | - Bo Zhang
- From the Department of Pathology, School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, China (Yang, Zhang).,Zhang and Shen are co-lead authors of this paper
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34
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Oncogenes, Proto-Oncogenes, and Lineage Restriction of Cancer Stem Cells. Int J Mol Sci 2021; 22:ijms22189667. [PMID: 34575830 PMCID: PMC8470404 DOI: 10.3390/ijms22189667] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 01/03/2023] Open
Abstract
In principle, an oncogene is a cellular gene (proto-oncogene) that is dysfunctional, due to mutation and fusion with another gene or overexpression. Generally, oncogenes are viewed as deregulating cell proliferation or suppressing apoptosis in driving cancer. The cancer stem cell theory states that most, if not all, cancers are a hierarchy of cells that arises from a transformed tissue-specific stem cell. These normal counterparts generate various cell types of a tissue, which adds a new dimension to how oncogenes might lead to the anarchic behavior of cancer cells. It is that stem cells, such as hematopoietic stem cells, replenish mature cell types to meet the demands of an organism. Some oncogenes appear to deregulate this homeostatic process by restricting leukemia stem cells to a single cell lineage. This review examines whether cancer is a legacy of stem cells that lose their inherent versatility, the extent that proto-oncogenes play a role in cell lineage determination, and the role that epigenetic events play in regulating cell fate and tumorigenesis.
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Heisey DAR, Jacob S, Lochmann TL, Kurupi R, Ghotra MS, Calbert ML, Shende M, Maves YK, Koblinski JE, Dozmorov MG, Boikos SA, Benes CH, Faber AC. Pharmaceutical Interference of the EWS-FLI1-driven Transcriptome By Cotargeting H3K27ac and RNA Polymerase Activity in Ewing Sarcoma. Mol Cancer Ther 2021; 20:1868-1879. [PMID: 34315769 DOI: 10.1158/1535-7163.mct-20-0489] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 12/23/2020] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
Abstract
The EWSR1-FLI1 t(11;22)(q24;q12) translocation is the hallmark genomic alteration of Ewing sarcoma, a malignancy of the bone and surrounding tissue, predominantly affecting children and adolescents. Although significant progress has been made for the treatment of localized disease, patients with metastasis or who relapse after chemotherapy have less than a 30% five-year survival rate. EWS-FLI1 is currently not clinically druggable, driving the need for more effective targeted therapies. Treatment with the H3K27 demethylase inhibitor, GSK-J4, leads to an increase in H3K27me and a decrease in H3K27ac, a significant event in Ewing sarcoma because H3K27ac associates strongly with EWS-FLI1 binding at enhancers and promoters and subsequent activity of EWS-FLI1 target genes. We were able to identify targets of EWS-FLI1 tumorigenesis directly inhibited by GSK-J4. GSK-J4 disruption of EWS-FLI1-driven transcription was toxic to Ewing sarcoma cells and slowed tumor growth in patient-derived xenografts (PDX) of Ewing sarcoma. Responses were markedly exacerbated by cotreatment with a disruptor of RNA polymerase II activity, the CDK7 inhibitor THZ1. This combination together suppressed EWS-FLI1 target genes and viability of ex vivo PDX Ewing sarcoma cells in a synergistic manner. In PDX models of Ewing Sarcoma, the combination shrank tumors. We present a new therapeutic strategy to treat Ewing sarcoma by decreasing H3K27ac at EWS-FLI1-driven transcripts, exacerbated by blocking phosphorylation of the C-terminal domain of RNA polymerase II to further hinder the EWS-FLI1-driven transcriptome.
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Affiliation(s)
- Daniel A R Heisey
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Sheeba Jacob
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Timothy L Lochmann
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Richard Kurupi
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Maninderjit S Ghotra
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Marissa L Calbert
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Mayuri Shende
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | | | | | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
| | - Sosipatros A Boikos
- Hematology, Oncology and Palliative Care, School of Medicine and Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia.
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Anthony C Faber
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia.
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Su S, Chen J, Jiang Y, Wang Y, Vital T, Zhang J, Laggner C, Nguyen KT, Zhu Z, Prevatte AW, Barker NK, Herring LE, Davis IJ, Liu P. SPOP and OTUD7A Control EWS-FLI1 Protein Stability to Govern Ewing Sarcoma Growth. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004846. [PMID: 34060252 PMCID: PMC8292909 DOI: 10.1002/advs.202004846] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/11/2021] [Indexed: 05/08/2023]
Abstract
Chromosomal translocation results in development of an Ewing sarcoma breakpoint region 1-Friend leukemia integration 1 (EWS-FLI1) fusion oncogene in the majority of Ewing sarcoma. The persistent dependence of the tumor for this oncoprotein points to EWS-FLI1 as an ideal drug target. Although EWS-FLI1 transcriptional targets and binding partners are evaluated, the mechanisms regulating EWS-FLI1 protein stability remain elusive. Speckle-type POZ protein (SPOP) and OTU domain-containing protein 7A (OTUD7A) are identified as the bona fide E3 ligase and deubiquitinase, respectively, that control EWS-FLI1 protein turnover in Ewing sarcoma. Casein kinase 1-mediated phosphorylation of the VTSSS degron in the FLI1 domain enhances SPOP activity to degrade EWS-FLI1. Opposing this process, OTUD7A deubiquitinates and stabilizes EWS-FLI1. Depletion of OTUD7A in Ewing sarcoma cell lines reduces EWS-FLI1 protein abundance and impedes Ewing sarcoma growth in vitro and in mice. Performing an artificial-intelligence-based virtual drug screen of a 4-million small molecule library, 7Ai is identified as a potential OTUD7A catalytic inhibitor. 7Ai reduces EWS-FLI1 protein levels and decreases Ewing sarcoma growth in vitro and in a xenograft mouse model. This study supports the therapeutic targeting of OTUD7A as a novel strategy for Ewing sarcoma bearing EWS-FLI1 and related fusions, and may also be applicable to other cancers dependent on aberrant FLI1 expression.
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Affiliation(s)
- Siyuan Su
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Jianfeng Chen
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Yao Jiang
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Present address:
Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Ying Wang
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Tamara Vital
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of GeneticsThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of PediatricsThe University of North Carolina at Chapel HillChapel HillNC 27599USA
| | - Jiaming Zhang
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Present address:
Department of Oral Medicine, Infection, and ImmunityHarvard School of Dental MedicineBostonMA02215USA
| | | | | | - Zhichuan Zhu
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Alex W. Prevatte
- UNC Proteomics Core FacilityDepartment of PharmacologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Natalie K. Barker
- UNC Proteomics Core FacilityDepartment of PharmacologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Laura E. Herring
- UNC Proteomics Core FacilityDepartment of PharmacologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Ian J. Davis
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of GeneticsThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of PediatricsThe University of North Carolina at Chapel HillChapel HillNC 27599USA
| | - Pengda Liu
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
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Damerell V, Pepper MS, Prince S. Molecular mechanisms underpinning sarcomas and implications for current and future therapy. Signal Transduct Target Ther 2021; 6:246. [PMID: 34188019 PMCID: PMC8241855 DOI: 10.1038/s41392-021-00647-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/18/2021] [Accepted: 05/18/2021] [Indexed: 02/06/2023] Open
Abstract
Sarcomas are complex mesenchymal neoplasms with a poor prognosis. Their clinical management is highly challenging due to their heterogeneity and insensitivity to current treatments. Although there have been advances in understanding specific genomic alterations and genetic mutations driving sarcomagenesis, the underlying molecular mechanisms, which are likely to be unique for each sarcoma subtype, are not fully understood. This is in part due to a lack of consensus on the cells of origin, but there is now mounting evidence that they originate from mesenchymal stromal/stem cells (MSCs). To identify novel treatment strategies for sarcomas, research in recent years has adopted a mechanism-based search for molecular markers for targeted therapy which has included recapitulating sarcomagenesis using in vitro and in vivo MSC models. This review provides a comprehensive up to date overview of the molecular mechanisms that underpin sarcomagenesis, the contribution of MSCs to modelling sarcomagenesis in vivo, as well as novel topics such as the role of epithelial-to-mesenchymal-transition (EMT)/mesenchymal-to-epithelial-transition (MET) plasticity, exosomes, and microRNAs in sarcomagenesis. It also reviews current therapeutic options including ongoing pre-clinical and clinical studies for targeted sarcoma therapy and discusses new therapeutic avenues such as targeting recently identified molecular pathways and key transcription factors.
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Affiliation(s)
- Victoria Damerell
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Michael S Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Sharon Prince
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa.
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38
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Surdez D, Zaidi S, Grossetête S, Laud-Duval K, Ferre AS, Mous L, Vourc'h T, Tirode F, Pierron G, Raynal V, Baulande S, Brunet E, Hill V, Delattre O. STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma. Cancer Cell 2021; 39:810-826.e9. [PMID: 33930311 DOI: 10.1016/j.ccell.2021.04.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 08/31/2020] [Accepted: 04/02/2021] [Indexed: 12/19/2022]
Abstract
STAG2, a cohesin family gene, is among the most recurrently mutated genes in cancer. STAG2 loss of function (LOF) is associated with aggressive behavior in Ewing sarcoma, a childhood cancer driven by aberrant transcription induced by the EWSR1-FLI1 fusion oncogene. Here, using isogenic Ewing cells, we show that, while STAG2 LOF profoundly changes the transcriptome, it does not significantly impact EWSR1-FLI1, CTCF/cohesin, or acetylated H3K27 DNA binding patterns. In contrast, it strongly alters the anchored dynamic loop extrusion process at boundary CTCF sites and dramatically decreases promoter-enhancer interactions, particularly affecting the expression of genes regulated by EWSR1-FLI1 at GGAA microsatellite neo-enhancers. Down-modulation of cis-mediated EWSR1-FLI1 activity, observed in STAG2-LOF conditions, is associated with enhanced migration and invasion properties of Ewing cells previously observed in EWSR1-FLI1low cells. Our study illuminates a process whereby STAG2-LOF fine-tunes the activity of an oncogenic transcription factor through altered CTCF-anchored loop extrusion and cis-mediated enhancer mechanisms.
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MESH Headings
- Bone Neoplasms/genetics
- Bone Neoplasms/mortality
- Bone Neoplasms/pathology
- CCCTC-Binding Factor/chemistry
- CCCTC-Binding Factor/genetics
- CCCTC-Binding Factor/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Cell Movement/genetics
- Chromatin Immunoprecipitation
- Chromosomal Proteins, Non-Histone/metabolism
- Enhancer Elements, Genetic
- Gene Expression Regulation, Neoplastic
- Histones/metabolism
- Humans
- Loss of Function Mutation
- Lysine/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic
- Sarcoma, Ewing/genetics
- Sarcoma, Ewing/mortality
- Sarcoma, Ewing/pathology
- Cohesins
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Affiliation(s)
- Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France.
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Karine Laud-Duval
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Anna Sole Ferre
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer and Université de Paris, Imagine Institute, 75005 Paris, France
| | - Lieke Mous
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Thomas Vourc'h
- UMR 168, Biology Inspired Physics at Mesoscales, PSL Research University, Institut Curie Research Centre, 75005 Paris, France
| | - Franck Tirode
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS 5286, INSERM U1052, Cancer Research Center of Lyon, 69008 Lyon, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, 75005 Paris, France
| | - Virginie Raynal
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France; Institut Curie Genomics of Excellence (ICGex) Platform, PSL Université, Institut Curie Research Centre, 75005 Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Université, Institut Curie Research Centre, 75005 Paris, France
| | - Erika Brunet
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer and Université de Paris, Imagine Institute, 75005 Paris, France
| | - Véronique Hill
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France; Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, 75005 Paris, France.
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39
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Panicker S, Venkatabalasubramanian S, Pathak S, Ramalingam S. The impact of fusion genes on cancer stem cells and drug resistance. Mol Cell Biochem 2021; 476:3771-3783. [PMID: 34095988 DOI: 10.1007/s11010-021-04203-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022]
Abstract
With ever increasing evidences on the role of fusion genes as the oncogenic protagonists in myriad cancers, it's time to explore if fusion genes can be the next generational drug targets in meeting the current demands of higher drug efficacy. Eliminating cancer stem cells (CSC) has become the current focus; however, we have reached a standstill in drug development owing to the lack of effective strategies to eradicate CSC. We believe that fusion genes could be the novel targets to overcome this limitation. The intriguing feature of fusion genes is that it dominantly impacts every aspect of CSC including self-renewal, differentiation, lineage commitment, tumorigenicity and stemness. Given the clinical success of fusion gene-based drugs in hematological cancers, our attempt to target fusion genes in eradicating CSC can be rewarding. As fusion genes are expressed explicitly in cancer cells, eradicating CSC by targeting fusion genes provides yet an another advantage of negligible patient side effects since normal cells remain unaffected by the drug. We hereby delineate the latest evidences on how fusion genes regulate CSC and drug resistance.
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Affiliation(s)
- Saurav Panicker
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kanchipuram, 603203, Tamil Nadu, India
| | | | - Surajit Pathak
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, Chennai, 603103, Tamil Nadu, India
| | - Satish Ramalingam
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kanchipuram, 603203, Tamil Nadu, India.
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40
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Fukushima K, Tsuji O, Suzuki S, Nori S, Nagoshi N, Okada E, Yagi M, Emoto K, Nakayama R, Watanabe K, Nakamura M, Matsumoto M. Cervical intramedullary recurrent Ewing sarcoma after 10-year disease-free survival in an adult: a case report and review of literature. Spinal Cord Ser Cases 2021; 7:45. [PMID: 34045432 DOI: 10.1038/s41394-021-00406-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Intramedullary metastasis of Ewing sarcoma is extremely rare. Here, we report an adult case of cervical intramedullary recurrent Ewing sarcoma after a 10-year disease-free survival after the initial surgery for a thoracic lesion. CASE PRESENTATION A 39-year-old man with a history of surgery and chemoradiotherapy for thoracic Ewing sarcoma ten years ago presented with neck pain and incomplete motor paralysis in the right upper extremity, which had suddenly appeared three months before. Cervical magnetic resonance imaging revealed a tear-drop-shaped intramedullary lesion at the C3 level accompanied by diffuse edematous change. Because of the rapid progression of his myelopathy, he underwent surgery for this intramedullary lesion. Intraoperatively, the tumor exhibited an orangish exophytic appearance. The unclearness of the tumor boundary compelled us to perform a partial resection. The histopathology showed the tumor comprised small round atypical cells with immunoreactivity for Nkx2.2 and CD99, diagnosing a metastatic Ewing sarcoma. Postoperatively, although his myelopathy improved transiently and adjuvant chemotherapy radiation was undergone, he died of cranial dissemination of the tumor two months and a half later. DISCUSSION To our knowledge, 31 cases of primary and only 4 cases of recurrent intramedullary spinal Ewing sarcoma have been reported to date; however, this is the first case of recurrent intramedullary Ewing sarcoma with a 10-year disease-free survival. Sadly, the prognosis of the current case was extremely poor. There is no clear treatment guideline for recurrent intramedullary Ewing sarcoma because of its rarity, and further collection of similar cases would be required.
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Affiliation(s)
- Keita Fukushima
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Osahiko Tsuji
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan.
| | - Satoshi Suzuki
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Satoshi Nori
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Narihito Nagoshi
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Eijiro Okada
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Mitsuru Yagi
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Katsura Emoto
- Division of Diagnostic Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Robert Nakayama
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kota Watanabe
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Masaya Nakamura
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Morio Matsumoto
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
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41
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Reverse Engineering of Ewing Sarcoma Regulatory Network Uncovers PAX7 and RUNX3 as Master Regulators Associated with Good Prognosis. Cancers (Basel) 2021; 13:cancers13081860. [PMID: 33924679 PMCID: PMC8070584 DOI: 10.3390/cancers13081860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/16/2021] [Accepted: 04/01/2021] [Indexed: 12/24/2022] Open
Abstract
Ewing Sarcoma (ES) is a rare malignant tumor occurring most frequently in adolescents and young adults. The ES hallmark is a chromosomal translocation between the chromosomes 11 and 22 that results in an aberrant transcription factor (TF) through the fusion of genes from the FET and ETS families, commonly EWSR1 and FLI1. The regulatory mechanisms behind the ES transcriptional alterations remain poorly understood. Here, we reconstruct the ES regulatory network using public available transcriptional data. Seven TFs were identified as potential MRs and clustered into two groups: one composed by PAX7 and RUNX3, and another composed by ARNT2, CREB3L1, GLI3, MEF2C, and PBX3. The MRs within each cluster act as reciprocal agonists regarding the regulation of shared genes, regulon activity, and implications in clinical outcome, while the clusters counteract each other. The regulons of all the seven MRs were differentially methylated. PAX7 and RUNX3 regulon activity were associated with good prognosis while ARNT2, CREB3L1, GLI3, and PBX3 were associated with bad prognosis. PAX7 and RUNX3 appear as highly expressed in ES biopsies and ES cell lines. This work contributes to the understanding of the ES regulome, identifying candidate MRs, analyzing their methilome and pointing to potential prognostic factors.
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Keskin T, Bakaric A, Waszyk P, Boulay G, Torsello M, Cornaz-Buros S, Chevalier N, Geiser T, Martin P, Volorio A, Iyer S, Kulkarni A, Letovanec I, Cherix S, Cote GM, Choy E, Digklia A, Montemurro M, Chebib I, Nielsen PG, Carcaboso AM, Mora J, Renella R, Suvà ML, Fusco C, Provero P, Rivera MN, Riggi N, Stamenkovic I. LIN28B Underlies the Pathogenesis of a Subclass of Ewing Sarcoma LIN28B Control of EWS-FLI1 Stability. Cell Rep 2021; 30:4567-4583.e5. [PMID: 32234488 DOI: 10.1016/j.celrep.2019.12.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 06/19/2019] [Accepted: 12/13/2019] [Indexed: 12/26/2022] Open
Abstract
Ewing sarcoma (EwS) is associated with poor prognosis despite current multimodal therapy. Targeting of EWS-FLI1, the fusion protein responsible for its pathogenesis, and its principal downstream targets has not yet produced satisfactory therapeutic options, fueling the search for alternative approaches. Here, we show that the oncofetal RNA-binding protein LIN28B regulates the stability of EWS-FLI1 mRNA in ~10% of EwSs. LIN28B depletion in these tumors leads to a decrease in the expression of EWS-FLI1 and its direct transcriptional network, abrogating EwS cell self-renewal and tumorigenicity. Moreover, pharmacological inhibition of LIN28B mimics the effect of LIN28B depletion, suggesting that LIN28B sustains the emergence of a subset of EwS in which it also serves as an effective therapeutic target.
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Affiliation(s)
- Tugba Keskin
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Arnaud Bakaric
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Patricia Waszyk
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Gaylor Boulay
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matteo Torsello
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Sandrine Cornaz-Buros
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland; Department of Pediatrics, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Nadja Chevalier
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland; Department Woman-Mother-Child, Division of Pediatrics, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Thibaud Geiser
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Patricia Martin
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Angela Volorio
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Sowmya Iyer
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Anupriya Kulkarni
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Igor Letovanec
- Department of Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Stéphane Cherix
- Department of Orthopaedics and Traumatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Gregory M Cote
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Edwin Choy
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Antonia Digklia
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Michael Montemurro
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Ivan Chebib
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Petur G Nielsen
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Angel M Carcaboso
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Jaume Mora
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Raffaele Renella
- Department Woman-Mother-Child, Division of Pediatrics, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Carlo Fusco
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Paolo Provero
- Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, 20132 Milan, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, 10124 Turin, Italy
| | - Miguel N Rivera
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nicolò Riggi
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Ivan Stamenkovic
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland.
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Su XA, Ma D, Parsons JV, Replogle JM, Amatruda JF, Whittaker CA, Stegmaier K, Amon A. RAD21 is a driver of chromosome 8 gain in Ewing sarcoma to mitigate replication stress. Genes Dev 2021; 35:556-572. [PMID: 33766983 PMCID: PMC8015718 DOI: 10.1101/gad.345454.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/25/2021] [Indexed: 01/08/2023]
Abstract
In this study, Su et al. investigate why ∼50% of Ewing sarcomas, driven by the EWS-FLI1 fusion oncogene, harbor chromosome 8 gains. Using an evolution approach, they show that trisomy 8 mitigates EWS-FLI1-induced replication stress through gain of a copy of RAD21, and deleting one copy of RAD21 in trisomy 8 cells largely neutralizes the fitness benefit of chromosome 8 gain and reduces tumorgenicity of a Ewing sarcoma cancer cell line in soft agar assays. Aneuploidy, defined as whole-chromosome gain or loss, causes cellular stress but, paradoxically, is a frequent occurrence in cancers. Here, we investigate why ∼50% of Ewing sarcomas, driven by the EWS-FLI1 fusion oncogene, harbor chromosome 8 gains. Expression of the EWS-FLI1 fusion in primary cells causes replication stress that can result in cellular senescence. Using an evolution approach, we show that trisomy 8 mitigates EWS-FLI1-induced replication stress through gain of a copy of RAD21. Low-level ectopic expression of RAD21 is sufficient to dampen replication stress and improve proliferation in EWS-FLI1-expressing cells. Conversely, deleting one copy in trisomy 8 cells largely neutralizes the fitness benefit of chromosome 8 gain and reduces tumorgenicity of a Ewing sarcoma cancer cell line in soft agar assays. We propose that RAD21 promotes tumorigenesis through single gene copy gain. Such genes may explain some recurrent aneuploidies in cancer.
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Affiliation(s)
- Xiaofeng A Su
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Duanduan Ma
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility, Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - James V Parsons
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - John M Replogle
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - James F Amatruda
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Charles A Whittaker
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility, Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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44
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Scopim-Ribeiro R, Lizardo MM, Zhang HF, Dhez AC, Hughes CS, Sorensen PH. NSG Mice Facilitate ex vivo Characterization of Ewing Sarcoma Lung Metastasis Using the PuMA Model. Front Oncol 2021; 11:645757. [PMID: 33828989 PMCID: PMC8019912 DOI: 10.3389/fonc.2021.645757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Ewing sarcoma (EwS) is a highly malignant bone and soft tissue tumor primarily affecting children and young adults. While most patients initially respond well to conventional front-line therapy, frequent metastasis results in poor 5-year overall survival rates for this disease. Accordingly, there is a critical need to develop better models to understand EwS metastasis. We and others previously used the ex vivo pulmonary metastasis assay (PuMA) to study lung metastasis in solid tumors including osteosarcoma (OS), but this technique has to date not been achievable for EwS. PuMA involves tail vein injection of fluorescent tumor cells into NOD-SCID mice, followed by their visualization in long-term cultures of tumor-bearing lung explants. Here we demonstrate successful implementation of PuMA for EwS cells using NOD-SCID-IL2 receptor gamma null (NSG) immunocompromised mice, which demonstrated high engraftment of EwS cell lines compared to NOD-SCID mice. This may be linked to immune permissiveness required by EwS cells, as increased basal cytotoxicity of EwS cells was observed in NOD-SCID compared to NSG lung sections, possibly due to the absence of natural killer (NK) cell activity in the latter. Together, our data demonstrate the utility of NSG mice for PuMA modeling of EwS lung metastasis.
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Affiliation(s)
| | | | - Hai-Feng Zhang
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Anne-Chloé Dhez
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Poul H Sorensen
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada.,Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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45
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Kannan S, Lock I, Ozenberger BB, Jones KB. Genetic drivers and cells of origin in sarcomagenesis. J Pathol 2021; 254:474-493. [DOI: 10.1002/path.5617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/01/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Sarmishta Kannan
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
| | - Ian Lock
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
| | - Benjamin B Ozenberger
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
| | - Kevin B Jones
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
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46
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Affiliation(s)
- Nicolò Riggi
- From the Institute of Pathology, Faculty of Biology and Medicine, University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland (N.R., I.S.); and the Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, and the Broad Institute of Harvard University and the Massachusetts Institute of Technology, Cambridge - both in Massachusetts (M.L.S.)
| | - Mario L Suvà
- From the Institute of Pathology, Faculty of Biology and Medicine, University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland (N.R., I.S.); and the Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, and the Broad Institute of Harvard University and the Massachusetts Institute of Technology, Cambridge - both in Massachusetts (M.L.S.)
| | - Ivan Stamenkovic
- From the Institute of Pathology, Faculty of Biology and Medicine, University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland (N.R., I.S.); and the Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, and the Broad Institute of Harvard University and the Massachusetts Institute of Technology, Cambridge - both in Massachusetts (M.L.S.)
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47
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Boulay G, Cironi L, Garcia SP, Rengarajan S, Xing YH, Lee L, Awad ME, Naigles B, Iyer S, Broye LC, Keskin T, Cauderay A, Fusco C, Letovanec I, Chebib I, Nielsen PG, Tercier S, Cherix S, Nguyen-Ngoc T, Cote G, Choy E, Provero P, Suvà ML, Rivera MN, Stamenkovic I, Riggi N. The chromatin landscape of primary synovial sarcoma organoids is linked to specific epigenetic mechanisms and dependencies. Life Sci Alliance 2020; 4:4/2/e202000808. [PMID: 33361335 PMCID: PMC7768195 DOI: 10.26508/lsa.202000808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/01/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022] Open
Abstract
We have addressed the mechanisms by which the fusion protein SS18-SSX modifies the epigenome toward the development of synovial sarcoma and the establishment of its potentially targetable vulnerabilities. Synovial sarcoma (SyS) is an aggressive mesenchymal malignancy invariably associated with the chromosomal translocation t(X:18; p11:q11), which results in the in-frame fusion of the BAF complex gene SS18 to one of three SSX genes. Fusion of SS18 to SSX generates an aberrant transcriptional regulator, which, in permissive cells, drives tumor development by initiating major chromatin remodeling events that disrupt the balance between BAF-mediated gene activation and polycomb-dependent repression. Here, we developed SyS organoids and performed genome-wide epigenomic profiling of these models and mesenchymal precursors to define SyS-specific chromatin remodeling mechanisms and dependencies. We show that SS18-SSX induces broad BAF domains at its binding sites, which oppose polycomb repressor complex (PRC) 2 activity, while facilitating recruitment of a non-canonical (nc)PRC1 variant. Along with the uncoupling of polycomb complexes, we observed H3K27me3 eviction, H2AK119ub deposition and the establishment of de novo active regulatory elements that drive SyS identity. These alterations are completely reversible upon SS18-SSX depletion and are associated with vulnerability to USP7 loss, a core member of ncPRC1.1. Using the power of primary tumor organoids, our work helps define the mechanisms of epigenetic dysregulation on which SyS cells are dependent.
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Affiliation(s)
- Gaylor Boulay
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Luisa Cironi
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sara P Garcia
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shruthi Rengarajan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yu-Hang Xing
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lukuo Lee
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mary E Awad
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Beverly Naigles
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sowmya Iyer
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Liliane C Broye
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tugba Keskin
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alexandra Cauderay
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Carlo Fusco
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Igor Letovanec
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Ivan Chebib
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Petur Gunnalugur Nielsen
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stéphane Tercier
- Department of Woman-Mother Child, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Stéphane Cherix
- Department of Orthopedics, Faculty of Biology and Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Tu Nguyen-Ngoc
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Gregory Cote
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Edwin Choy
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Paolo Provero
- Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Miguel N Rivera
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ivan Stamenkovic
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland .,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Nicolò Riggi
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland .,Swiss Cancer Center Leman, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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48
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Park H, Kim H, Hassebroek V, Azuma Y, Slawson C, Azuma M. Chromosomal localization of Ewing sarcoma EWSR1/FLI1 protein promotes the induction of aneuploidy. J Biol Chem 2020; 296:100164. [PMID: 33293370 PMCID: PMC7857440 DOI: 10.1074/jbc.ra120.014328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 11/06/2022] Open
Abstract
Ewing sarcoma is a pediatric bone cancer that expresses the chimeric protein EWSR1/FLI1. We previously demonstrated that EWSR1/FLI1 impairs the localization of Aurora B kinase to the midzone (the midline structure located between segregating chromosomes) during anaphase. While localization of Aurora B is essential for faithful cell division, it is unknown whether interference with midzone organization by EWSR1/FLI1 induces aneuploidy. To address this, we generated stable Tet-on inducible cell lines with EWSR1/FLI1, using CRISPR/Cas9 technology to integrate the transgene at the safe-harbor AAVS1 locus in DLD-1 cells. Induced cells expressing EWSR1/FLI1 displayed an increased incidence of aberrant localization of Aurora B, and greater levels of aneuploidy, compared with noninduced cells. Furthermore, the expression of EWSR1/FLI1-T79A, containing a threonine (Thr) to alanine (Ala) substitution at amino acid 79, failed to induce these phenotypes, indicating that Thr 79 is critical for EWSR1/FLI1 interference with mitosis. In contrast, the phosphomimetic mutant EWSR1/FLI1-T79D (Thr to aspartic acid (Asp)) retained the high activity as wild-type EWSR1/FLI1. Together, these findings suggest that phosphorylation of EWSR1/FLI1 at Thr 79 promotes the colocalization of EWSR1/FLI1 and Aurora B on the chromosomes during prophase and metaphase and, in addition, impairs the localization of Aurora B during anaphase, leading to induction of aneuploidy. This is the first demonstration of the mechanism for EWSR1/FLI1-dependent induction of aneuploidy associated with mitotic dysfunction and the identification of the phosphorylation of the Thr 79 of EWSR1/FLI1 as a critical residue required for this induction.
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Affiliation(s)
- Hyewon Park
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Haeyoung Kim
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Victoria Hassebroek
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Yoshiaki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Chad Slawson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City Kansas, USA
| | - Mizuki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA.
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Fahr L, Sunami Y, Maeritz N, Steiger K, Grünewald TGP, Gericke M, Kong B, Raulefs S, Mayerle J, Michalski CW, Regel I, Kleeff J. Expression of the EWSR1-FLI1 fusion oncogene in pancreas cells drives pancreatic atrophy and lipomatosis. Pancreatology 2020; 20:1673-1681. [PMID: 33051146 DOI: 10.1016/j.pan.2020.10.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/30/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) harbors mutant KRAS as the most common driver mutation. Studies on mouse models have uncovered the tumorigenic characteristics of the Kras oncogene driving pancreatic carcinogenesis. Similarly, Ewing sarcoma predominantly depends on the occurrence of the EWSR1-FLI1 fusion oncogene. The expression of EWSR1-FLI1 affects pro-tumorigenic pathways and induces cell transformation. In this study, we investigated whether mutant Kras could be exchanged by another potent oncogene, such as EWSR1-FLI1, to initiate pancreatic cancer development. METHODS We generated two conditional mouse models expressing mutant KrasG12D (KC) or the EWSR1-FLI1 oncogene (E/F) in pancreas cells. Pancreatic tissue was collected from the mice at 4-6 weeks and 11-13 weeks of age as well as from survival cohorts to determine the development of spontaneous acinar-to-ductal metaplasia (ADM) and neoplastic lesions. Immunohistochemistry and immunofluorescence staining were performed to characterize and quantify changes in tissue morphology. RESULTS The expression of the EWSR1-FLI1 fusion protein in pancreas cells was confirmed by positive FLI1 immunohistochemistry staining. Notably, the EWSR1-FLI1 expression in pancreas cells resulted in a strong depletion of the acinar cell mass and an extensive lipomatosis. Although the E/F mice exhibited spontaneous ADM formation and a shorter overall survival rate compared to KC mice, no development of neoplastic lesion was observed in aging E/F mice. CONCLUSIONS The expression of the EWSR1-FLI1 oncogene leads to a strong pancreatic atrophy and lipomatosis. ADM formation indicates that pancreatic acinar cells are susceptible for EWSR1-FLI1-mediated oncogenic transformation to a limited extent. However, the EWSR1-FLI1 oncogene is insufficient to induce pancreatic cancer development.
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Affiliation(s)
- Lisa Fahr
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Yoshiaki Sunami
- Department of Visceral, Vascular and Endocrine Surgery, Martin-Luther-University Halle-Wittenberg, University Medical Center Halle, Halle, Germany
| | - Nadja Maeritz
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, University Hospital, LMU Munich, Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Gericke
- Institute of Anatomy and Cell Biology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Bo Kong
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Susanne Raulefs
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Christoph W Michalski
- Department of Visceral, Vascular and Endocrine Surgery, Martin-Luther-University Halle-Wittenberg, University Medical Center Halle, Halle, Germany
| | - Ivonne Regel
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.
| | - Jörg Kleeff
- Department of Visceral, Vascular and Endocrine Surgery, Martin-Luther-University Halle-Wittenberg, University Medical Center Halle, Halle, Germany.
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Shi X, Zheng Y, Jiang L, Zhou B, Yang W, Li L, Ding L, Huang M, Gery S, Lin DC, Koeffler HP. EWS-FLI1 regulates and cooperates with core regulatory circuitry in Ewing sarcoma. Nucleic Acids Res 2020; 48:11434-11451. [PMID: 33080033 PMCID: PMC7672457 DOI: 10.1093/nar/gkaa901] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/22/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Core regulatory circuitry (CRC)-dependent transcriptional network is critical for developmental tumors in children and adolescents carrying few gene mutations. However, whether and how CRC contributes to transcription regulation in Ewing sarcoma is unknown. Here, we identify and functionally validate a CRC 'trio' constituted by three transcription factors (TFs): KLF15, TCF4 and NKX2-2, in Ewing sarcoma cells. Epigenomic analyses demonstrate that EWS-FLI1, the primary fusion driver for this cancer, directly establishes super-enhancers of each of these three TFs to activate their transcription. In turn, KLF15, TCF4 and NKX2-2 co-bind to their own and each other's super-enhancers and promoters, forming an inter-connected auto-regulatory loop. Functionally, CRC factors contribute significantly to cell proliferation of Ewing sarcoma both in vitro and in vivo. Mechanistically, CRC factors exhibit prominent capacity of co-regulating the epigenome in cooperation with EWS-FLI1, occupying 77.2% of promoters and 55.6% of enhancers genome-wide. Downstream, CRC TFs coordinately regulate gene expression networks in Ewing sarcoma, controlling important signaling pathways for cancer, such as lipid metabolism pathway, PI3K/AKT and MAPK signaling pathways. Together, molecular characterization of the oncogenic CRC model advances our understanding of the biology of Ewing sarcoma. Moreover, CRC-downstream genes and signaling pathways may contain potential therapeutic targets for this malignancy.
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Affiliation(s)
- Xianping Shi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation; State Key Laboratory of Respiratory Disease; Affiliated Cancer Hospital of Guangzhou Medical University; Sino-French Hoffmann institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 510120, P.R. China
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Liling Jiang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation; State Key Laboratory of Respiratory Disease; Affiliated Cancer Hospital of Guangzhou Medical University; Sino-French Hoffmann institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 510120, P.R. China
| | - Bo Zhou
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Liyan Li
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Lingwen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117600, Singapore
| | - Moli Huang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, P.R. China
| | - Sigal Gery
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117600, Singapore
- National University Cancer Institute, National University Hospital Singapore, Singapore 119074, Singapore
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