1
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Wei E, Mitanoska A, O'Brien Q, Porter K, Molina M, Ahsan H, Jung U, Mills L, Kyba M, Bosnakovski D. Pharmacological targeting of P300/CBP reveals EWS::FLI1-mediated senescence evasion in Ewing sarcoma. Mol Cancer 2024; 23:222. [PMID: 39367409 PMCID: PMC11453018 DOI: 10.1186/s12943-024-02115-7] [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: 06/03/2024] [Accepted: 09/05/2024] [Indexed: 10/06/2024] Open
Abstract
Ewing sarcoma (ES) poses a significant therapeutic challenge due to the difficulty in targeting its main oncodriver, EWS::FLI1. We show that pharmacological targeting of the EWS::FLI1 transcriptional complex via inhibition of P300/CBP drives a global transcriptional outcome similar to direct knockdown of EWS::FLI1, and furthermore yields prognostic risk factors for ES patient outcome. We find that EWS::FLI1 upregulates LMNB1 via repetitive GGAA motif recognition and acetylation codes in ES cells and EWS::FLI1-permissive mesenchymal stem cells, which when reversed by P300 inhibition leads to senescence of ES cells. P300-inhibited senescent ES cells can then be eliminated by senolytics targeting the PI3K signaling pathway. The vulnerability of ES cells to this combination therapy suggests an appealing synergistic strategy for future therapeutic exploration.
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Affiliation(s)
- Erdong Wei
- Department of Pediatrics, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
- , Minneapolis, USA
| | - Ana Mitanoska
- Department of Pediatrics, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
- , Minneapolis, USA
| | - Quinn O'Brien
- Department of Pediatrics, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
- , Minneapolis, USA
| | - Kendall Porter
- Department of Pediatrics, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
- , Minneapolis, USA
| | - MacKenzie Molina
- Department of Pediatrics, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
- , Minneapolis, USA
| | - Haseeb Ahsan
- Department of Pediatrics, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
- , Minneapolis, USA
| | - Usuk Jung
- Department of Pediatrics, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
- , Minneapolis, USA
| | - Lauren Mills
- Department of Pediatrics, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
- , Minneapolis, USA
| | - Michael Kyba
- Department of Pediatrics, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
- , Minneapolis, USA
| | - Darko Bosnakovski
- Department of Pediatrics, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA.
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA.
- , Minneapolis, USA.
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2
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Sohn EJ, Libich DS. Hijacking the BAF complex: the mechanistic interplay of ARID1A and EWS::FLI1 in Ewing sarcoma. Mol Oncol 2024. [PMID: 39344201 DOI: 10.1002/1878-0261.13742] [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: 09/04/2024] [Accepted: 09/13/2024] [Indexed: 10/01/2024] Open
Abstract
Ewing sarcoma, an aggressive pediatric cancer, is driven by the EWS::FLI1 fusion protein, which disrupts gene expression by hijacking the BAF chromatin remodeling complex. Central to this mechanism is the formation of biomolecular condensates, mediated by the prion-like domains (PrLDs) of EWS and ARID1A, a core BAF subunit. ARID1A serves as a critical interface between EWS::FLI1 and the BAF complex, with its condensate-forming ability essential for the aberrant gene expression that drives tumor growth. The loss of condensate-competent ARID1A significantly impairs tumor progression, identifying it as a potential therapeutic target. However, targeting condensate formation is challenging due to the transient nature of the interactions involved, complicating the development of effective inhibitors. This work underscores the importance of further investigation into therapeutic strategies aimed at disrupting condensate formation in Ewing sarcoma and other related malignancies.
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Affiliation(s)
- Erich J Sohn
- Greehey Children's Cancer Research Institute and Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - David S Libich
- Greehey Children's Cancer Research Institute and Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
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3
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Wang L, Wang Y, Ke Z, Wang Z, Guo Y, Zhang Y, Zhang X, Guo Z, Wan B. Liquid-liquid phase separation: a new perspective on respiratory diseases. Front Immunol 2024; 15:1444253. [PMID: 39391315 PMCID: PMC11464301 DOI: 10.3389/fimmu.2024.1444253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 09/09/2024] [Indexed: 10/12/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) is integral to various biological processes, facilitating signal transduction by creating a condensed, membrane-less environment that plays crucial roles in diverse physiological and pathological processes. Recent evidence has underscored the significance of LLPS in human health and disease. However, its implications in respiratory diseases remain poorly understood. This review explores current insights into the mechanisms and biological roles of LLPS, focusing particularly on its relevance to respiratory diseases, aiming to deepen our understanding and propose a new paradigm for studying phase separation in this context.
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Affiliation(s)
- Li Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Shanghai East Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Yongjun Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Zhangmin Ke
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Zexu Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Yufang Guo
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Yunlei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Xiuwei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Zhongliang Guo
- Shanghai East Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Bing Wan
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
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4
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Mancarella C, Scotlandi K. Targeting EWS::FLI1 to Advance Ewing Sarcoma Therapy. J Clin Oncol 2024:JCO2401323. [PMID: 39259926 DOI: 10.1200/jco-24-01323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/26/2024] [Accepted: 07/31/2024] [Indexed: 09/13/2024] Open
Affiliation(s)
- Caterina Mancarella
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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5
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Boulay G, Broye LC, Dong R, Iyer S, Sanalkumar R, Xing YH, Buisson R, Rengarajan S, Naigles B, Duc B, Volorio A, Awad ME, Renella R, Chebib I, Nielsen GP, Choy E, Cote GM, Zou L, Letovanec I, Stamenkovic I, Rivera MN, Riggi N. EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in desmoplastic small round cell tumors. Nat Commun 2024; 15:7460. [PMID: 39198430 PMCID: PMC11358472 DOI: 10.1038/s41467-024-51851-3] [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: 12/11/2022] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
EWS fusion oncoproteins underlie several human malignancies including Desmoplastic Small Round Cell Tumor (DSRCT), an aggressive cancer driven by EWS-WT1 fusion proteins. Here we combine chromatin occupancy and 3D profiles to identify EWS-WT1-dependent gene regulation networks and target genes. We show that EWS-WT1 is a powerful chromatin activator controlling an oncogenic gene expression program that characterizes primary tumors. Similar to wild type WT1, EWS-WT1 has two isoforms that differ in their DNA binding domain and we find that they have distinct DNA binding profiles and are both required to generate viable tumors that resemble primary DSRCT. Finally, we identify candidate EWS-WT1 target genes with potential therapeutic implications, including CCND1, whose inhibition by the clinically-approved drug Palbociclib leads to marked tumor burden decrease in DSRCT PDXs in vivo. Taken together, our studies identify gene regulation programs and therapeutic vulnerabilities in DSRCT and provide a mechanistic understanding of the complex oncogenic activity of EWS-WT1.
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Affiliation(s)
- Gaylor Boulay
- Department of Pathology & Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Liliane C Broye
- Experimental Pathology Service, Lausanne University Hospital & University of Lausanne, Lausanne, Switzerland
| | - Rui Dong
- Department of Pathology & Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sowmya Iyer
- Department of Pathology & Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Rajendran Sanalkumar
- Experimental Pathology Service, Lausanne University Hospital & University of Lausanne, Lausanne, Switzerland
| | - Yu-Hang Xing
- Department of Pathology & Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Rémi Buisson
- Department of Pathology & Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shruthi Rengarajan
- Department of Pathology & Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Beverly Naigles
- Department of Pathology & Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Benoît Duc
- Experimental Pathology Service, Lausanne University Hospital & University of Lausanne, Lausanne, Switzerland
| | - Angela Volorio
- Department of Pathology & Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mary E Awad
- Department of Pathology & 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
| | - Ivan Chebib
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - G Petur Nielsen
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin Choy
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Gregory M Cote
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Lee Zou
- Department of Pathology & Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, 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
| | - Ivan Stamenkovic
- Experimental Pathology Service, Lausanne University Hospital & University of Lausanne, Lausanne, Switzerland
| | - Miguel N Rivera
- Department of Pathology & Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Nicolò Riggi
- Experimental Pathology Service, Lausanne University Hospital & University of Lausanne, Lausanne, Switzerland.
- Genentech Inc, Department of Cell and Tissue Genomics (CTG), South San Francisco, CA, USA.
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6
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Suvarna K, Jayabal P, Ma X, Wang H, Chen Y, Weintraub ST, Han X, Houghton PJ, Shiio Y. Ceramide-induced cleavage of GPR64 intracellular domain drives Ewing sarcoma. Cell Rep 2024; 43:114497. [PMID: 39024100 PMCID: PMC11416865 DOI: 10.1016/j.celrep.2024.114497] [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: 12/17/2023] [Revised: 05/07/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024] Open
Abstract
Ewing sarcoma is a cancer of bone and soft tissue in children and young adults primarily driven by the EWS-FLI1 fusion oncoprotein, which has been undruggable. Here, we report that Ewing sarcoma depends on secreted sphingomyelin phosphodiesterase 1 (SMPD1), a ceramide-generating enzyme, and ceramide. We find that G-protein-coupled receptor 64 (GPR64)/adhesion G-protein-coupled receptor G2 (ADGRG2) responds to ceramide and mediates critical growth signaling in Ewing sarcoma. We show that ceramide induces the cleavage of the C-terminal intracellular domain of GPR64, which translocates to the nucleus and restrains the protein levels of RIF1 in a manner dependent on SPOP, a substrate adaptor of the Cullin3-RING E3 ubiquitin ligase. We demonstrate that both SMPD1 and GPR64 are transcriptional targets of EWS-FLI1, indicating that SMPD1 and GPR64 are EWS-FLI1-induced cytokine-receptor dependencies. These results reveal the SMPD1-ceramide-GPR64 pathway, which drives Ewing sarcoma growth and is amenable to therapeutic intervention.
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Affiliation(s)
- Kruthi Suvarna
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Panneerselvam Jayabal
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xiuye Ma
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Hu Wang
- Barshop Institute for Longevity and Aging Studies, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Population Health Sciences, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Susan T Weintraub
- Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Medicine, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Molecular Medicine, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yuzuru Shiio
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA.
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7
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Li J, Huang K, McBride F, Sadagopan A, Gallant DS, Thakur M, Khanna P, Li B, Ge M, Weiss CN, Achom M, Xu Q, Huang K, Ryback BA, Gui M, Bar-Peled L, Viswanathan SR. TFE3 fusions direct an oncogenic transcriptional program that drives OXPHOS and unveils vulnerabilities in translocation renal cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607311. [PMID: 39149323 PMCID: PMC11326252 DOI: 10.1101/2024.08.09.607311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Translocation renal cell carcinoma (tRCC) is an aggressive subtype of kidney cancer driven by TFE3 gene fusions, which act via poorly characterized downstream mechanisms. Here we report that TFE3 fusions transcriptionally rewire tRCCs toward oxidative phosphorylation (OXPHOS), contrasting with the highly glycolytic metabolism of most other renal cancers. This TFE3 fusion-driven OXPHOS program, together with heightened glutathione levels found in renal cancers, renders tRCCs sensitive to reductive stress - a metabolic stress state induced by an imbalance of reducing equivalents. Genome-scale CRISPR screening identifies tRCC-selective vulnerabilities linked to this metabolic state, including EGLN1, which hydroxylates HIF-1α and targets it for proteolysis. Inhibition of EGLN1 compromises tRCC cell growth by stabilizing HIF-1a and promoting metabolic reprogramming away from OXPHOS, thus representing a vulnerability to OXPHOS-dependent tRCC cells. Our study defines a distinctive tRCC-essential metabolic program driven by TFE3 fusions and nominates EGLN1 inhibition as a therapeutic strategy to counteract fusion-induced metabolic rewiring.
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Affiliation(s)
- Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Kaimeng Huang
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fiona McBride
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Ananthan Sadagopan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Daniel. S Gallant
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Meha Thakur
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Prateek Khanna
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Bingchen Li
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Maolin Ge
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Cary N. Weiss
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mingkee Achom
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Qingru Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Kun Huang
- Molecular Imaging Core and Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Birgitta A. Ryback
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Miao Gui
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, Zhejiang, China; Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Liron Bar-Peled
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Srinivas R. Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
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8
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Frenkel M, Corban JE, Hujoel MLA, Morris Z, Raman S. Large-scale discovery of chromatin dysregulation induced by oncofusions and other protein-coding variants. Nat Biotechnol 2024:10.1038/s41587-024-02347-4. [PMID: 39048711 DOI: 10.1038/s41587-024-02347-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
Population-scale databases have expanded to millions of protein-coding variants, yet insight into their mechanistic consequences has lagged. Here we present PROD-ATAC, a high-throughput method for discovering the effects of protein-coding variants on chromatin regulation. A pooled variant library is expressed in a disease-agnostic cell line, and single-cell assay for transposase-accessible chromatin resolves each variant's effect on the chromatin landscape. Using PROD-ATAC, we characterized the effects of more than 100 oncofusions (cancer-causing chimeric proteins) and controls and revealed that chromatin remodeling is common to fusions spanning an enormous range of fusion frequencies. Furthermore, fusion-induced dysregulation can be context agnostic, as observed mechanisms often overlapped with cancer and cell-type-specific prior knowledge. We also showed that gain-of-function activity is common among oncofusions. This work begins to outline a global map of fusion-induced chromatin alterations. We suggest that there might be convergent mechanisms among disparate oncofusions and shared modes of dysregulation among fusions present in tumors at different frequencies. PROD-ATAC is generalizable to any set of protein-coding variants.
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Affiliation(s)
- Max Frenkel
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - James E Corban
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Margaux L A Hujoel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zachary Morris
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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9
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Petrescu DI, Yustein JT, Dasgupta A. Preclinical models for the study of pediatric solid tumors: focus on bone sarcomas. Front Oncol 2024; 14:1388484. [PMID: 39091911 PMCID: PMC11291195 DOI: 10.3389/fonc.2024.1388484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
Sarcomas comprise between 10-15% of all pediatric malignancies. Osteosarcoma and Ewing sarcoma are the two most common pediatric bone tumors diagnosed in children and young adults. These tumors are commonly treated with surgery and/or radiation therapy and combination chemotherapy. However, there is a strong need for the development and utilization of targeted therapeutic methods to improve patient outcomes. Towards accomplishing this goal, pre-clinical models for these unique malignancies are of particular importance to design and test experimental therapeutic strategies prior to being introduced to patients due to their origination site and propensity to metastasize. Pre-clinical models offer several advantages for the study of pediatric sarcomas with unique benefits and shortcomings dependent on the type of model. This review addresses the types of pre-clinical models available for the study of pediatric solid tumors, with special attention to the bone sarcomas osteosarcoma and Ewing sarcoma.
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Affiliation(s)
- D. Isabel Petrescu
- Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, GA, United States
| | - Jason T. Yustein
- Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, GA, United States
| | - Atreyi Dasgupta
- The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Texas Children’s Cancer and Hematology Centers, Houston, TX, United States
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10
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Cristalli C, Scotlandi K. Targeting DNA Methylation Machinery in Pediatric Solid Tumors. Cells 2024; 13:1209. [PMID: 39056791 PMCID: PMC11275080 DOI: 10.3390/cells13141209] [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: 05/20/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA methylation is a key epigenetic regulatory mechanism that plays a critical role in a variety of cellular processes, including the regulation of cell fate during development, maintenance of cell identity, and genome stability. DNA methylation is tightly regulated by enzymatic reactions and its deregulation plays an important role in the development of cancer. Specific DNA methylation alterations have been found in pediatric solid tumors, providing new insights into the development of these tumors. In addition, DNA methylation profiles have greatly contributed to tune the diagnosis of pediatric solid tumors and to define subgroups of patients with different risks of progression, leading to the reduction in unwanted toxicity and the improvement of treatment efficacy. This review highlights the dysregulated DNA methylome in pediatric solid tumors and how this information provides promising targets for epigenetic therapies, particularly inhibitors of DNMT enzymes (DNMTis). Opportunities and limitations are considered, including the ability of DNMTis to induce viral mimicry and immune signaling by tumors. Besides intrinsic action against cancer cells, DNMTis have the potential to sensitize immune-cold tumors to immunotherapies and may represent a remarkable option to improve the treatment of challenging pediatric solid tumors.
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Affiliation(s)
- Camilla Cristalli
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
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11
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Ebegboni VJ, Jones TL, Brownmiller T, Zhao PX, Pehrsson EC, Rajan SS, Caplen NJ. ETS1, a Target Gene of the EWSR1::FLI1 Fusion Oncoprotein, Regulates the Expression of the Focal Adhesion Protein TENSIN3. Mol Cancer Res 2024; 22:625-641. [PMID: 38588446 PMCID: PMC11219265 DOI: 10.1158/1541-7786.mcr-23-1090] [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: 12/29/2023] [Revised: 03/25/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
The mechanistic basis for the metastasis of Ewing sarcomas remains poorly understood, as these tumors harbor few mutations beyond the chromosomal translocation that initiates the disease. Instead, the epigenome of Ewing sarcoma cells reflects the regulatory state of genes associated with the DNA-binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the EWSR1::FLI1/ERG's repression of transcription factor genes, concentrating on those that exhibit a broader range of expression in tumors than in Ewing sarcoma cell lines. Focusing on one of these target genes, ETS1, we detected EWSR1::FLI1 binding and an H3K27me3-repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1's binding of promoter regions, substantially altering the transcriptome of Ewing sarcoma cells, including the upregulation of the gene encoding TENSIN3 (TNS3), a focal adhesion protein. Ewing sarcoma cell lines expressing ETS1 (CRISPRa) exhibited increased TNS3 expression and enhanced movement compared with control cells. Visualization of control Ewing sarcoma cells showed a distributed vinculin signal and a network-like organization of F-actin; in contrast, ETS1-activated Ewing sarcoma cells showed an accumulation of vinculin and F-actin toward the plasma membrane. Interestingly, the phenotype of ETS1-activated Ewing sarcoma cell lines depleted of TNS3 resembled the phenotype of the control cells. Critically, these findings have clinical relevance as TNS3 expression in Ewing sarcoma tumors positively correlates with that of ETS1. Implications: ETS1's transcriptional regulation of the gene encoding the focal adhesion protein TENSIN3 in Ewing sarcoma cells promotes cell movement, a critical step in the evolution of metastasis.
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Affiliation(s)
- Vernon Justice Ebegboni
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tayvia Brownmiller
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Patrick X. Zhao
- Omics Bioinformatics Facility, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Erica C. Pehrsson
- Omics Bioinformatics Facility, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Mahnoor S, Molnar C, Velázquez D, Reina J, Llamazares S, Heinen JP, Mora J, Gonzalez C. Human EWS-FLI protein levels and neomorphic functions show a complex, function-specific dose-response relationship in Drosophila. Open Biol 2024; 14:240043. [PMID: 39013417 PMCID: PMC11251760 DOI: 10.1098/rsob.240043] [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: 02/20/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 07/18/2024] Open
Abstract
Ewing sarcoma (EwS) is a cancer that arises in the bones and soft tissues, typically driven by the Ewing's sarcoma breakpoint region 1-Friend leukemia virus integration 1 (EWS-FLI) oncogene. Implementation of genetically modified animal models of EwS has proved difficult largely owing to EWS-FLI's high toxicity. The EWS-FLI1FS frameshift variant that circumvents toxicity but is still able to perform key oncogenic functions provided the first study model in Drosophila. However, the quest for Drosophila lines expressing full-length, unmodified EWS-FLI remained open. Here, we show that EWS-FLI1FS's lower toxicity is owed to reduced protein levels caused by its frameshifted C-terminal peptide, and report new strategies through which we have generated Drosophila lines that express full-length, unmodified EWS-FLI. Using these lines, we have found that the upregulation of transcription from GGAA-microsatellites (GGAAμSats) presents a positive linear correlation within a wide range of EWS-FLI protein concentrations. In contrast, rather counterintuitively, GGAAμSats-independent transcriptomic dysregulation presents relatively minor differences across the same range, suggesting that GGAAμSat-dependent and -independent transcriptional upregulation present different kinetics of response with regards to changing EWS-FLI protein concentration. Our results underpin the functional relevance of varying EWS-FLI expression levels and provide experimental tools to investigate, in Drosophila, the effect of the EWS-FLI 'high' and 'low' states that have been reported and are suspected to be important for EwS in humans.
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Affiliation(s)
- Serena Mahnoor
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cristina Molnar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Diego Velázquez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Jose Reina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Salud Llamazares
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jan Peter Heinen
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Cayetano Gonzalez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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13
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Freund MM, Harrison MM, Torres-Zelada EF. Exploring the reciprocity between pioneer factors and development. Development 2024; 151:dev201921. [PMID: 38958075 PMCID: PMC11266817 DOI: 10.1242/dev.201921] [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] [Indexed: 07/04/2024]
Abstract
Development is regulated by coordinated changes in gene expression. Control of these changes in expression is largely governed by the binding of transcription factors to specific regulatory elements. However, the packaging of DNA into chromatin prevents the binding of many transcription factors. Pioneer factors overcome this barrier owing to unique properties that enable them to bind closed chromatin, promote accessibility and, in so doing, mediate binding of additional factors that activate gene expression. Because of these properties, pioneer factors act at the top of gene-regulatory networks and drive developmental transitions. Despite the ability to bind target motifs in closed chromatin, pioneer factors have cell type-specific chromatin occupancy and activity. Thus, developmental context clearly shapes pioneer-factor function. Here, we discuss this reciprocal interplay between pioneer factors and development: how pioneer factors control changes in cell fate and how cellular environment influences pioneer-factor binding and activity.
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Affiliation(s)
- Meghan M. Freund
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Eliana F. Torres-Zelada
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
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14
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Buteyn NJ, Burke CG, Sartori VJ, Deering-Gardner E, DeBruine ZJ, Kamarudin D, Chandler DP, Monovich AC, Perez MW, Yi JS, Ries RE, Alonzo TA, Ryan RJ, Meshinchi S, Triche TJ. EZH2-driven immune evasion defines high-risk pediatric AML with t(16;21) FUS::ERG gene fusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594150. [PMID: 38798454 PMCID: PMC11118270 DOI: 10.1101/2024.05.14.594150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Despite decades of research, acute myeloid leukemia (AML) remains a remarkably lethal malignancy. While pediatric AML (pAML) carries a more favorable prognosis than adult AML, the past 25 years of large clinical trials have produced few improvements in pAML survival. Nowhere is this more evident than in patients carrying a t(16;21)(p11;q22) translocation, which yields the FUS::ERG fusion transcript. Patients with FUS::ERG-positive AML are often primary refractory, and most responders quickly relapse. In COG clinical trials, allogeneic stem cell transplantation was of no benefit to FUS::ERG pAML patients; 100% of transplanted patients succumbed to their disease. Expression of major histocompatibility complex (MHC) class I & II and costimulatory molecules is absent at diagnosis in FUS::ERG AML, mirroring the epigenetic mechanism of post-transplant relapse seen in adult AML and its associated dismal outcomes. Here we show that this class-defining immune-repressive phenotype is driven by overexpression of the EZH2 histone lysine methyltransferase in vitro and in multiple clinical cohorts. We show that treatment with the FDA-approved EZH2 inhibitor tazemetostat along with IFN-γ reverses this phenotype, re-establishes MHC presentation, and severely impairs the viability of FUS::ERG AML cells. EZH2 inhibitors may thus provide the first targeted therapeutic option for patients with this high-risk subtype of pAML, with particular benefit as a bridge to successful allogeneic stem cell transplantation.
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Affiliation(s)
- Nathaniel J Buteyn
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI
| | - Connor G Burke
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI
| | - Vincent J Sartori
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI
| | | | - Zachary J DeBruine
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI
| | - Dahlya Kamarudin
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI
| | - Darrell P Chandler
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI
| | | | - Monika W Perez
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Joanna S Yi
- Department of Pediatrics, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Todd A Alonzo
- Children's Oncology Group, Monrovia, CA
- Department of Translational Genomics, University of Southern California, Los Angeles, CA
| | - Russell Jh Ryan
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Children's Oncology Group, Monrovia, CA
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Timothy J Triche
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI
- Department of Translational Genomics, University of Southern California, Los Angeles, CA
- Department of Pediatrics, College of Human Medicine, Michigan State University, East Lansing, MI
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15
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Goodspeed A, Bodlak A, Duffy AB, Nelson-Taylor S, Oike N, Porfilio T, Shirai R, Walker D, Treece A, Black J, Donaldson N, Cost C, Garrington T, Greffe B, Luna-Fineman S, Demedis J, Lake J, Danis E, Verneris M, Adams DL, Hayashi M. Characterization of transcriptional heterogeneity and novel therapeutic targets using single cell RNA-sequencing of primary and circulating Ewing sarcoma cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576251. [PMID: 38293103 PMCID: PMC10827204 DOI: 10.1101/2024.01.18.576251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Ewing sarcoma is the second most common bone cancer in children, accounting for 2% of pediatric cancer diagnoses. Patients who present with metastatic disease at the time of diagnosis have a dismal prognosis, compared to the >70% 5-year survival of those with localized disease. Here, we utilized single cell RNA-sequencing to characterize the transcriptional landscape of primary Ewing sarcoma tumors and surrounding tumor microenvironment (TME). Copy-number analysis identified subclonal evolution within patients prior to treatment. Primary tumor samples demonstrate a heterogenous transcriptional landscape with several conserved gene expression programs, including those composed of genes related to proliferation and EWS targets. Single cell RNA-sequencing and immunofluorescence of circulating tumor cells at the time of diagnosis identified TSPAN8 as a novel therapeutic target.
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16
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Shirai R, Biebighauser T, Walker D, Oviedo J, Nelson-Taylor S, Bodlak A, Porfilio T, Oike N, Goodspeed A, Hayashi M. Cadherin-11 contributes to the heterogenous and dynamic Wnt-Wnt-β-catenin pathway activation in Ewing sarcoma. PLoS One 2024; 19:e0305490. [PMID: 38875295 PMCID: PMC11178195 DOI: 10.1371/journal.pone.0305490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 05/30/2024] [Indexed: 06/16/2024] Open
Abstract
Ewing sarcoma is the second most common bone cancer in children, and while patients who present with metastatic disease at the time of diagnosis have a dismal prognosis. Ewing sarcoma tumors are driven by the fusion gene EWS/Fli1, and while these tumors are genetically homogenous, the transcriptional heterogeneity can lead to a variety of cellular processes including metastasis. In this study, we demonstrate that in Ewing sarcoma cells, the canonical Wnt/β-Catenin signaling pathway is heterogeneously activated in vitro and in vivo, correlating with hypoxia and EWS/Fli1 activity. Ewing sarcoma cells predominantly express β-Catenin on the cell membrane bound to CDH11, which can respond to exogenous Wnt ligands leading to the immediate activation of Wnt/β-Catenin signaling within a tumor. Knockdown of CDH11 leads to delayed and decreased response to exogenous Wnt ligand stimulation, and ultimately decreased metastatic propensity. Our findings strongly indicate that CDH11 is a key component of regulating Wnt//β-Catenin signaling heterogeneity within Ewing sarcoma tumors, and is a promising molecular target to alter Wnt//β-Catenin signaling in Ewing sarcoma patients.
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Affiliation(s)
- Ryota Shirai
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Tyler Biebighauser
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Deandra Walker
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Jillian Oviedo
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Sarah Nelson-Taylor
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Avery Bodlak
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Timothy Porfilio
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Naoki Oike
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Division of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Andrew Goodspeed
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Masanori Hayashi
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
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17
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de Souza Gama FH, Dutra LA, Hawgood M, Dos Reis CV, Serafim RAM, Ferreira MA, Teodoro BVM, Takarada JE, Santiago AS, Balourdas DI, Nilsson AS, Urien B, Almeida VM, Gileadi C, Ramos PZ, Salmazo A, Vasconcelos SNS, Cunha MR, Mueller S, Knapp S, Massirer KB, Elkins JM, Gileadi O, Mascarello A, Lemmens BBLG, Guimarães CRW, Azevedo H, Couñago RM. Novel Dihydropteridinone Derivatives As Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε. J Med Chem 2024; 67:8609-8629. [PMID: 38780468 DOI: 10.1021/acs.jmedchem.3c02250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division.
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Affiliation(s)
| | - Luiz A Dutra
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Michael Hawgood
- Science for Life Laboratory, Sweden, Tomtebodavägen 23A, 17165 Solna, Sweden
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Caio Vinícius Dos Reis
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Ricardo A M Serafim
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Marcos A Ferreira
- Aché Laboratórios Farmacêuticos S.A., Guarulhos, São Paulo 07034-904, Brazil
| | - Bruno V M Teodoro
- Aché Laboratórios Farmacêuticos S.A., Guarulhos, São Paulo 07034-904, Brazil
| | - Jéssica Emi Takarada
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - André S Santiago
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Ann-Sofie Nilsson
- Science for Life Laboratory, Sweden, Tomtebodavägen 23A, 17165 Solna, Sweden
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Bruno Urien
- Science for Life Laboratory, Sweden, Tomtebodavägen 23A, 17165 Solna, Sweden
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Vitor M Almeida
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Carina Gileadi
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Priscila Z Ramos
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Anita Salmazo
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Stanley N S Vasconcelos
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Micael R Cunha
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Susanne Mueller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Katlin B Massirer
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Jonathan M Elkins
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Opher Gileadi
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | | | - Bennie B L G Lemmens
- Science for Life Laboratory, Sweden, Tomtebodavägen 23A, 17165 Solna, Sweden
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | | | - Hatylas Azevedo
- Aché Laboratórios Farmacêuticos S.A., Guarulhos, São Paulo 07034-904, Brazil
| | - Rafael M Couñago
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
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18
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Luck C, Jacobs KA, Okimoto RA. The Capicua C1 Domain is Required for Full Activity of the CIC::DUX4 Fusion Oncoprotein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597815. [PMID: 38895482 PMCID: PMC11185703 DOI: 10.1101/2024.06.06.597815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Rearrangements between genes can yield neomorphic fusions that drive oncogenesis. Fusion oncogenes are made up of fractional segments of the partner genes that comprise them, with each partner potentially contributing some of its own function to the nascent fusion oncoprotein. Clinically, fusion oncoproteins driving one diagnostic entity are typically clustered into a single molecular subset and are often treated a similar fashion. However, knowledge of where specific fusion breakpoints occur in partner genes, and the resulting retention of functional domains in the fusion, is an important determinant of fusion oncoprotein activity and may differ between patients. This study investigates this phenomena through the example of CIC::DUX4, a fusion between the transcriptional repressor capicua (CIC) and the double homeobox 4 gene (DUX4), which drives an aggressive subset of undifferentiated round cell sarcoma. Using a harmonized dataset of over 100 patient fusion breakpoints from the literature, we show that most bona fide CIC::DUX4 fusions retain the C1 domain, which is known to contribute to DNA binding by wild type CIC. Mechanistically, deletion or mutation of the C1 domain reduces, but does not eliminate, activation of CIC target genes by CIC::DUX4. We also find that expression of C1-deleted CIC::DUX4 is capable of exerting intermediate transformation-related phenotypes compared with those imparted by full-length CIC::DUX4, but was not sufficient for tumorigenesis in a subcutaneous mouse model. In summary, our results suggest a supercharging role for the C1 domain in the activity of CIC::DUX4.
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Affiliation(s)
- Cuyler Luck
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Kyle A. Jacobs
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Ross A. Okimoto
- Department of Medicine, University of California, San Francisco, CA, USA
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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19
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Bayanjargal A, Taslim C, Showpnil IA, Selich-Anderson J, Crow JC, Lessnick SL, Theisen ER. DBD-α4 helix of EWSR1::FLI1 is required for GGAA microsatellite binding that underlies genome regulation in Ewing sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578127. [PMID: 38352344 PMCID: PMC10862889 DOI: 10.1101/2024.01.31.578127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ewing sarcoma is the second most common bone cancer in children and young adults. In 85% of patients, a translocation between chromosomes 11 and 22 results in a potent fusion oncoprotein, EWSR1::FLI1. EWSR1::FLI1 is the only genetic alteration in an otherwise unaltered genome of Ewing sarcoma tumors. The EWSR1 portion of the protein is an intrinsically disordered domain involved in transcriptional regulation by EWSR1::FLI1. The FLI portion of the fusion contains a DNA binding domain shown to bind core GGAA motifs and GGAA repeats. A small alpha-helix in the DNA binding domain of FLI1, DBD-𝛼4 helix, is critical for the transcription function of EWSR1::FLI1. In this study, we aimed to understand the mechanism by which the DBD-𝛼4 helix promotes transcription, and therefore oncogenic transformation. We utilized a multi-omics approach to assess chromatin organization, active chromatinmarks, genome binding, and gene expression in cells expressing EWSR1::FLI1 constructs with and without the DBD-𝛼4 helix. Our studies revealed DBD-𝛼4 helix is crucial for cooperative binding of EWSR1::FLI1 at GGAA microsatellites. This binding underlies many aspects of genome regulation by EWSR1::FLI1 such as formation of TADs, chromatin loops, enhancers and productive transcription hubs.
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20
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Rask GC, Taslim C, Bayanjargal A, Cannon MV, Selich-Anderson J, Crow JC, Duncan A, Theisen ER. Seclidemstat blocks the transcriptional function of multiple FET-fusion oncoproteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.19.594897. [PMID: 38826330 PMCID: PMC11142045 DOI: 10.1101/2024.05.19.594897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Genes encoding the RNA-binding proteins FUS, EWSR1, and TAF15 (FET proteins) are involved in chromosomal translocations in rare sarcomas. FET-rearranged sarcomas are often aggressive malignancies affecting patients of all ages. New therapies are needed. These translocations fuse the 5' portion of the FET gene with a 3' partner gene encoding a transcription factor (TF). The resulting fusion proteins are oncogenic TFs with a FET protein low complexity domain (LCD) and a DNA binding domain. FET fusion proteins have proven stubbornly difficult to target directly and promising strategies target critical co-regulators. One candidate is lysine specific demethylase 1 (LSD1). LSD1 is recruited by multiple FET fusions, including EWSR1::FLI1. LSD1 promotes EWSR1::FLI1 activity and treatment with the noncompetitive inhibitor SP-2509 blocks EWSR1::FLI1 transcriptional function. A similar molecule, seclidemstat (SP-2577), is currently in clinical trials for FET-rearranged sarcomas (NCT03600649). However, whether seclidemstat has pharmacological activity against FET fusions has not been demonstrated. Here, we evaluate the in vitro potency of seclidemstat against multiple FET-rearranged sarcoma cell lines, including Ewing sarcoma, desmoplastic small round cell tumor, clear cell sarcoma, and myxoid liposarcoma. We also define the transcriptomic effects of seclidemstat treatment and evaluated the activity of seclidemstat against FET fusion transcriptional regulation. Seclidemstat showed potent activity in cell viability assays across FET-rearranged sarcomas and disrupted the transcriptional function of all tested fusions. Though epigenetic and targeted inhibitors are unlikely to be effective as a single agents in the clinic, these data suggest seclidemstat remains a promising new treatment strategy for patients with FET-rearranged sarcomas.
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Affiliation(s)
- Galen C. Rask
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Cenny Taslim
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Ariunaa Bayanjargal
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
- Medical Scientist Training Program, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew V. Cannon
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Jesse C. Crow
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | | | - Emily R. Theisen
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
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21
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Xiao Y, Zhi Y, Cao G, Ma H, Gao J, Li F. Primary Ewing's sarcoma of the uterine cervix: a case report and review of the literature. J Cancer Res Clin Oncol 2024; 150:267. [PMID: 38769118 PMCID: PMC11106175 DOI: 10.1007/s00432-024-05698-2] [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: 02/19/2024] [Accepted: 03/12/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Ewing's sarcoma (ES) is an aggressive cancer of bone and soft tissue, most of which tend to occur in the bone. Extraosseous Ewing's sarcoma (EES) of the cervix is extremely rare. CASE PRESENTATION In the present work, we reported a 39-year-old cervical EES patient with a 2.5*2.1*1.8 cm tumor mass. According to previous literatures, our case is the smallest tumor found in primary cervical ES ever. The patient initially came to our hospital due to vaginal bleeding, and then the gynecological examination found a neoplasm between the cervical canal and partially in the external cervical orifice. The diagnosis of EES was confirmed below: Hematoxylin & Eosin staining (H&E) revealed small round blue malignant cells in biopsy specimens. Immunohistochemistry (IHC) showed the positive staining for CD99, NKX2.2, and FLI1. Disruption of EWSR1 gene was found by fluorescence in situ hybridization (FISH), and the EWSR1-FLI1 gene fusion was determined by next-generation sequencing (NGS). The patient received laparoscopic wide hysterectomy, bilateral adnexectomy, pelvic lymphadenectomy, and postoperative adjuvant chemotherapy and remained disease free with regular follow-up for 1 year. CONCLUSIONS Through a systematic review of previously reported cervical ES and this case, we highlighted the importance of FISH and NGS for the accuracy of ESS diagnosis, which could assist on the optimal treatment strategy. However, due to the rarity of the disease, there is no standard treatment schemes. Investigation on molecular pathological diagnosis and standardization of treatment regimens for cervical ES are critical to patients' prognosis.
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Affiliation(s)
- Yuhang Xiao
- Department of Gynecology, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Yong Zhi
- Department of Gynecology, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Guangxu Cao
- Department of Gynecology, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Heling Ma
- Department of Gynecology, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Jinli Gao
- Department of Pathology, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China.
| | - Fang Li
- Department of Gynecology, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China.
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22
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Magrath JW, Sampath SS, Flinchum DA, Hartono AB, Goldberg IN, Boehling JR, Savkovic SD, Lee SB. Comprehensive Transcriptomic Analysis of EWSR1::WT1 Targets Identifies CDK4/6 Inhibitors as an Effective Therapy for Desmoplastic Small Round Cell Tumors. Cancer Res 2024; 84:1426-1442. [PMID: 38588409 PMCID: PMC11063761 DOI: 10.1158/0008-5472.can-23-3334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/28/2023] [Accepted: 02/07/2024] [Indexed: 04/10/2024]
Abstract
Desmoplastic small round cell tumors (DSRCT) are a type of aggressive, pediatric sarcoma characterized by the EWSR1::WT1 fusion oncogene. Targeted therapies for DSRCT have not been developed, and standard multimodal therapy is insufficient, leading to a 5-year survival rate of only 15% to 25%. Here, we depleted EWSR1::WT1 in DSRCT and established its essentiality in vivo. Transcriptomic analysis revealed that EWSR1::WT1 induces unique transcriptional alterations compared with WT1 and other fusion oncoproteins and that EWSR1::WT1 binding directly mediates gene upregulation. The E-KTS isoform of EWSR1::WT1 played a dominant role in transcription, and it bound to the CCND1 promoter and stimulated DSRCT growth through the cyclin D-CDK4/6-RB axis. Treatment with the CDK4/6 inhibitor palbociclib successfully reduced growth in two DSRCT xenograft models. As palbociclib has been approved by the FDA for the treatment of breast cancer, these findings demonstrate the sensitivity of DSRCT to palbociclib and support immediate clinical investigation of palbociclib for treating this aggressive pediatric cancer. SIGNIFICANCE EWSR1::WT1 is essential for desmoplastic small round cell tumors and upregulates the cyclin D-CDK4/6-RB axis that can be targeted with palbociclib, providing a targeted therapeutic strategy for treating this deadly tumor type.
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Affiliation(s)
- Justin W. Magrath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Shruthi Sanjitha Sampath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Dane A. Flinchum
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Alifiani B. Hartono
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Ilon N. Goldberg
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Julia R. Boehling
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Suzana D. Savkovic
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Sean B. Lee
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
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23
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Wachtel M, Surdez D, Grünewald TGP, Schäfer BW. Functional Classification of Fusion Proteins in Sarcoma. Cancers (Basel) 2024; 16:1355. [PMID: 38611033 PMCID: PMC11010897 DOI: 10.3390/cancers16071355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Sarcomas comprise a heterogeneous group of malignant tumors of mesenchymal origin. More than 80 entities are associated with different mesenchymal lineages. Sarcomas with fibroblastic, muscle, bone, vascular, adipocytic, and other characteristics are distinguished. Nearly half of all entities contain specific chromosomal translocations that give rise to fusion proteins. These are mostly pathognomonic, and their detection by various molecular techniques supports histopathologic classification. Moreover, the fusion proteins act as oncogenic drivers, and their blockade represents a promising therapeutic approach. This review summarizes the current knowledge on fusion proteins in sarcoma. We categorize the different fusion proteins into functional classes, including kinases, epigenetic regulators, and transcription factors, and describe their mechanisms of action. Interestingly, while fusion proteins acting as transcription factors are found in all mesenchymal lineages, the others have a more restricted pattern. Most kinase-driven sarcomas belong to the fibroblastic/myofibroblastic lineage. Fusion proteins with an epigenetic function are mainly associated with sarcomas of unclear differentiation, suggesting that epigenetic dysregulation leads to a major change in cell identity. Comparison of mechanisms of action reveals recurrent functional modes, including antagonism of Polycomb activity by fusion proteins with epigenetic activity and recruitment of histone acetyltransferases by fusion transcription factors of the myogenic lineage. Finally, based on their biology, we describe potential approaches to block the activity of fusion proteins for therapeutic intervention. Overall, our work highlights differences as well as similarities in the biology of fusion proteins from different sarcomas and provides the basis for a functional classification.
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Affiliation(s)
- Marco Wachtel
- Department of Oncology and Children’s Research Center, University Children’s Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Didier Surdez
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), CH-8008 Zurich, Switzerland
| | - 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
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership between DKFZ and Heidelberg University Hospital, 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Beat W. Schäfer
- Department of Oncology and Children’s Research Center, University Children’s Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
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24
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Mooney B, Negri GL, Shyp T, Delaidelli A, Zhang HF, Spencer Miko SE, Weiner AK, Radaoui AB, Shraim R, Lizardo MM, Hughes CS, Li A, El-Naggar AM, Rouleau M, Li W, Dimitrov DS, Kurmasheva RT, Houghton PJ, Diskin SJ, Maris JM, Morin GB, Sorensen PH. Surface and Global Proteome Analyses Identify ENPP1 and Other Surface Proteins as Actionable Immunotherapeutic Targets in Ewing Sarcoma. Clin Cancer Res 2024; 30:1022-1037. [PMID: 37812652 PMCID: PMC10905525 DOI: 10.1158/1078-0432.ccr-23-2187] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
PURPOSE Ewing sarcoma is the second most common bone sarcoma in children, with 1 case per 1.5 million in the United States. Although the survival rate of patients diagnosed with localized disease is approximately 70%, this decreases to approximately 30% for patients with metastatic disease and only approximately 10% for treatment-refractory disease, which have not changed for decades. Therefore, new therapeutic strategies are urgently needed for metastatic and refractory Ewing sarcoma. EXPERIMENTAL DESIGN This study analyzed 19 unique Ewing sarcoma patient- or cell line-derived xenografts (from 14 primary and 5 metastatic specimens) using proteomics to identify surface proteins for potential immunotherapeutic targeting. Plasma membranes were enriched using density gradient ultracentrifugation and compared with a reference standard of 12 immortalized non-Ewing sarcoma cell lines prepared in a similar manner. In parallel, global proteome analysis was carried out on each model to complement the surfaceome data. All models were analyzed by Tandem Mass Tags-based mass spectrometry to quantify identified proteins. RESULTS The surfaceome and global proteome analyses identified 1,131 and 1,030 annotated surface proteins, respectively. Among surface proteins identified, both approaches identified known Ewing sarcoma-associated proteins, including IL1RAP, CD99, STEAP1, and ADGRG2, and many new cell surface targets, including ENPP1 and CDH11. Robust staining of ENPP1 was demonstrated in Ewing sarcoma tumors compared with other childhood sarcomas and normal tissues. CONCLUSIONS Our comprehensive proteomic characterization of the Ewing sarcoma surfaceome provides a rich resource of surface-expressed proteins in Ewing sarcoma. This dataset provides the preclinical justification for exploration of targets such as ENPP1 for potential immunotherapeutic application in Ewing sarcoma. See related commentary by Bailey, p. 934.
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Affiliation(s)
- Brian Mooney
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Taras Shyp
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alberto Delaidelli
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hai-Feng Zhang
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sandra E. Spencer Miko
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Amber K. Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alexander B. Radaoui
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rawan Shraim
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael M. Lizardo
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Christopher S. Hughes
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy Li
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amal M. El-Naggar
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Rouleau
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wei Li
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Dimiter S. Dimitrov
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Raushan T. Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Peter J. Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregg B. Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Poul H. Sorensen
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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25
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Pozner A, Li L, Verma SP, Wang S, Barrott JJ, Nelson ML, Yu JSE, Negri GL, Colborne S, Hughes CS, Zhu JF, Lambert SL, Carroll LS, Smith-Fry K, Stewart MG, Kannan S, Jensen B, John CM, Sikdar S, Liu H, Dang NH, Bourdage J, Li J, Vahrenkamp JM, Mortenson KL, Groundland JS, Wustrack R, Senger DL, Zemp FJ, Mahoney DJ, Gertz J, Zhang X, Lazar AJ, Hirst M, Morin GB, Nielsen TO, Shen PS, Jones KB. ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97. Nat Commun 2024; 15:1165. [PMID: 38326311 PMCID: PMC10850509 DOI: 10.1038/s41467-024-45280-5] [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] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
The t(X,17) chromosomal translocation, generating the ASPSCR1::TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCCs), frustrating efforts to identify therapeutic targets for these rare cancers. Here, proteomic analysis identifies VCP/p97, an AAA+ ATPase with known segregase function, as strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1::TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1::TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributes with ASPSCR1::TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrate the oncogenic transcriptional signature of ASPSCR1::TFE3, by facilitating assembly of higher-order chromatin conformation structures demonstrated by HiChIP. Finally, ASPSCR1::TFE3 and VCP demonstrate co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCP's potential as a novel therapeutic target.
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Affiliation(s)
- Amir Pozner
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Li Li
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Shiv Prakash Verma
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Shuxin Wang
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jared J Barrott
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Mary L Nelson
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jamie S E Yu
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Shane Colborne
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Ju-Fen Zhu
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sydney L Lambert
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Lara S Carroll
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Kyllie Smith-Fry
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael G Stewart
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sarmishta Kannan
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Bodrie Jensen
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Cini M John
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Saif Sikdar
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Hongrui Liu
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Ngoc Ha Dang
- Department of Oncology, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer Bourdage
- Department of Oncology, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jinxiu Li
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Katelyn L Mortenson
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - John S Groundland
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Rosanna Wustrack
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Donna L Senger
- Department of Oncology, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Oncology, McGill University and Lady Davis Institute for Medical Research, Montreal, QC, Canada
| | - Franz J Zemp
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Douglas J Mahoney
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Xiaoyang Zhang
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Alexander J Lazar
- Departments of Anatomic Pathology, Translational Molecular Pathology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Torsten O Nielsen
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Peter S Shen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Kevin B Jones
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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26
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Jayabal P, Ma X, Shiio Y. Roles of USP1 in Ewing sarcoma. Genes Cancer 2024; 15:15-27. [PMID: 38323120 PMCID: PMC10843185 DOI: 10.18632/genesandcancer.235] [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: 08/28/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024] Open
Abstract
Ewing sarcoma is a cancer of bone and soft tissue in children and young adults that is driven by the EWS-ETS fusion transcription factor, most commonly EWS-FLI1. We previously reported that Ewing sarcoma harbors two populations of cells, the CD133high population displaying higher growth rate and the CD133low population displaying chemotherapy resistance. We now find that the ubiquitin-specific protease 1 (USP1) is a transcriptional target of the EWS-FLI1 fusion oncoprotein, expressed at high and low levels in the CD133high and the CD133low populations, respectively, and determines chemo-sensitivity. We also find that USP1 inhibits cdc42, increases EWS-FLI1 transcriptional output, and simulates Ewing sarcoma growth. We show that chemo-sensitization by USP1 is independent of cdc42. A pharmacological inhibitor of USP1 was able to activate cdc42 and inhibit Ewing sarcoma growth. These results uncover critical roles for USP1 in Ewing sarcoma, which regulates growth and chemo-sensitivity via distinct mechanisms.
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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, USA
| | - Xiuye Ma
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yuzuru Shiio
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
- Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA
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27
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Salguero-Aranda C, Di Blasi E, Galán L, Zaldumbide L, Civantos G, Marcilla D, de Álava E, Díaz-Martín J. Identification of Novel/Rare EWSR1 Fusion Partners in Undifferentiated Mesenchymal Neoplasms. Int J Mol Sci 2024; 25:1735. [PMID: 38339014 PMCID: PMC10855420 DOI: 10.3390/ijms25031735] [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: 12/11/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Recurrent gene fusions (GFs) in translocated sarcomas are recognized as major oncogenic drivers of the disease, as well as diagnostic markers whose identification is necessary for differential diagnosis. EWSR1 is a 'promiscuous' gene that can fuse with many different partner genes, defining different entities among a broad range of mesenchymal neoplasms. Molecular testing of EWSR1 translocation traditionally relies on FISH assays with break-apart probes, which are unable to identify the fusion partner. Therefore, other ancillary molecular diagnostic modalities are being increasingly adopted for accurate classification of these neoplasms. Herein, we report three cases with rare GFs involving EWSR1 in undifferentiated mesenchymal neoplasms with uncertain differential diagnoses, using targeted RNA-seq and confirming with RT-PCR and Sanger sequencing. Two GFs involved hormone nuclear receptors as 3' partners, NR4A2 and RORB, which have not been previously reported. NR4A2 may functionally replace NR4A3, the usual 3' partner in extraskeletal myxoid chondrosarcoma. The third GF, EWSR1::BEND2, has previously been reported in a subtype of astroblastoma and other rare entities, including a single case of a soft-tissue tumor that we discuss in this work. In conclusion, our findings indicate that the catalogue of mesenchymal neoplasm-bearing EWSR1 fusions continues to grow, underscoring the value of using molecular ancillary techniques with higher diagnostic abilities in the routine clinical setting.
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Affiliation(s)
- Carmen Salguero-Aranda
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
- Centro de Investigación Biomédica en Red de Cáncer, Instituto de Salud Carlos III (CB16/12/00361; CIBERONC-ISCIII), 28029 Madrid, Spain
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, 41004 Seville, Spain
| | - Elena Di Blasi
- Istituto Nazionale dei Tumori, Università degli Studi di Milano, 20133 Milan, Italy
| | - Lourdes Galán
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
| | - Laura Zaldumbide
- Department of Pathology, Hospital Universitario Cruces, 48903 Barakaldo, Spain
| | - Gema Civantos
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
| | - David Marcilla
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
| | - Enrique de Álava
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
- Centro de Investigación Biomédica en Red de Cáncer, Instituto de Salud Carlos III (CB16/12/00361; CIBERONC-ISCIII), 28029 Madrid, Spain
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, 41004 Seville, Spain
| | - Juan Díaz-Martín
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
- Centro de Investigación Biomédica en Red de Cáncer, Instituto de Salud Carlos III (CB16/12/00361; CIBERONC-ISCIII), 28029 Madrid, Spain
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, 41004 Seville, Spain
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Bakaric A, Cironi L, Praz V, Sanalkumar R, Broye LC, Favre-Bulle K, Letovanec I, Digklia A, Renella R, Stamenkovic I, Ott CJ, Nakamura T, Antonescu CR, Rivera MN, Riggi N. CIC-DUX4 Chromatin Profiling Reveals New Epigenetic Dependencies and Actionable Therapeutic Targets in CIC-Rearranged Sarcomas. Cancers (Basel) 2024; 16:457. [PMID: 38275898 PMCID: PMC10814785 DOI: 10.3390/cancers16020457] [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: 12/04/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
CIC-DUX4-rearranged sarcoma (CDS) is a rare and aggressive soft tissue tumor that occurs most frequently in young adults. The key oncogenic driver of this disease is the expression of the CIC-DUX4 fusion protein as a result of chromosomal rearrangements. CIC-DUX4 displays chromatin binding properties, and is therefore believed to function as an aberrant transcription factor. However, the chromatin remodeling events induced by CIC-DUX4 are not well understood, limiting our ability to identify new mechanism-based therapeutic strategies for these patients. Here, we generated a genome-wide profile of CIC-DUX4 DNA occupancy and associated chromatin states in human CDS cell models and primary tumors. Combining chromatin profiling, proximity ligation assays, as well as genetic and pharmacological perturbations, we show that CIC-DUX4 operates as a potent transcriptional activator at its binding sites. This property is in contrast with the repressive function of the wild-type CIC protein, and is mainly mediated through the direct interaction of CIC-DUX4 with the acetyltransferase p300. In keeping with this, we show p300 to be essential for CDS tumor cell proliferation; additionally, we find its pharmacological inhibition to significantly impact tumor growth in vitro and in vivo. Taken together, our study elucidates the mechanisms underpinning CIC-DUX4-mediated transcriptional regulation.
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Affiliation(s)
- Arnaud Bakaric
- Clinical Pathology Service, Department of Diagnostics, Geneva University Hospital, 1205 Geneva, Switzerland
| | - Luisa Cironi
- Pediatric Hematology-Oncology Research Laboratory, Woman-Mother-Child Department, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Viviane Praz
- Platform Genomics Technologies, Center for Integrative Genomics, Faculty of Biology and Medicine, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Rajendran Sanalkumar
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
- Department of Cell and Tissue Genomics, Genentech. Inc., South San Francisco, CA 94103, USA
| | - Liliane C. Broye
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
| | - Kerria Favre-Bulle
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
| | - Igor Letovanec
- Department of Histopathology, Central Institute, Valais Hospital, 1951 Sion, Switzerland
| | - Antonia Digklia
- Department of Oncology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Raffaele Renella
- Pediatric Hematology-Oncology Research Laboratory, Woman-Mother-Child Department, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Ivan Stamenkovic
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
| | - Christopher J. Ott
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; (C.J.O.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Takuro Nakamura
- Institute of Medical Science, Tokyo Medical University, Tokyo 160-0023, Japan
| | - Cristina R. Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Miguel N. Rivera
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; (C.J.O.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicolò Riggi
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
- Department of Cell and Tissue Genomics, Genentech. Inc., South San Francisco, CA 94103, USA
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29
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Graca Marques J, Pavlovic B, Ngo QA, Pedot G, Roemmele M, Volken L, Kisele S, Perbet R, Wachtel M, Schäfer BW. The Chromatin Remodeler CHD4 Sustains Ewing Sarcoma Cell Survival by Controlling Global Chromatin Architecture. Cancer Res 2024; 84:241-257. [PMID: 37963210 DOI: 10.1158/0008-5472.can-22-3950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 08/30/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Ewing sarcoma is an aggressive cancer with a defective response to DNA damage leading to an enhanced sensitivity to genotoxic agents. Mechanistically, Ewing sarcoma is driven by the fusion transcription factor EWS-FLI1, which reprograms the tumor cell epigenome. The nucleosome remodeling and deacetylase (NuRD) complex is an important regulator of chromatin function, controlling both gene expression and DNA damage repair, and has been associated with EWS-FLI1 activity. Here, a NuRD-focused CRISPR/Cas9 inactivation screen identified the helicase CHD4 as essential for Ewing sarcoma cell proliferation. CHD4 silencing induced tumor cell death by apoptosis and abolished colony formation. Although CHD4 and NuRD colocalized with EWS-FLI1 at enhancers and super-enhancers, CHD4 promoted Ewing sarcoma cell survival not by modulating EWS-FLI1 activity and its oncogenic gene expression program but by regulating chromatin structure. CHD4 depletion led to a global increase in DNA accessibility and induction of spontaneous DNA damage, resulting in an increased susceptibility to DNA-damaging agents. CHD4 loss delayed tumor growth in vivo, increased overall survival, and combination with PARP inhibition by olaparib treatment further suppressed tumor growth. Collectively, these findings highlight the NuRD subunit CHD4 as a therapeutic target in Ewing sarcoma that can potentiate the antitumor activity of genotoxic agents. SIGNIFICANCE CRISPR/Cas9 screening in Ewing sarcoma identifies a dependency on CHD4, which is crucial for the maintenance of chromatin architecture to suppress DNA damage and a promising therapeutic target for DNA damage repair-deficient malignancies.
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Affiliation(s)
- Joana Graca Marques
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Blaz Pavlovic
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Quy A Ngo
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Gloria Pedot
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Michaela Roemmele
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Larissa Volken
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Samanta Kisele
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Romain Perbet
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
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30
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Xu Y, Shi F, Zhang Y, Yin M, Han X, Feng J, Wang G. Twenty-year outcome of prevalence, incidence, mortality and survival rate in patients with malignant bone tumors. Int J Cancer 2024; 154:226-240. [PMID: 37596989 DOI: 10.1002/ijc.34694] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/05/2023] [Accepted: 07/31/2023] [Indexed: 08/21/2023]
Abstract
Malignant bone tumors are a group of rare malignant tumors and our study aimed to update the recent epidemiologic estimates based on the Surveillance, Epidemiology and End Results database. Patients diagnosed with malignant bone tumors from 2000 to 2019 were included and their characteristics were retrospectively described. The limited-duration prevalence, annual age-adjusted incidence and mortality were calculated, and the annual percentage changes were analyzed to quantify the rate change. Finally, observed survival and relative survival rate were illustrated. Subgroup analysis across tumor type, age, gender, tumor Grade, primary tumor site and stage was also performed. As for results, a total of 11 655 eligible patients with malignant bone tumor were selected. Osteosarcoma was the most common tumor type, followed by chondrosarcoma, Ewing sarcoma and chordoma. The estimated limited-duration prevalence of malignant bone tumors increased from 2000 (0.00069%) to 2018 (0.00749%). Steady age-adjusted incidence was observed in all patients during the study period while the highest rate occurred in osteosarcoma. Mortality rates differed in subgroups while elder patients (older than 64 years) presented the highest mortality rate compared to other age groups. In all bone tumors, the 10-year observed survival and relative survival rates were 58.0% and 61.9%, respectively. Chondrosarcoma patients had the best survival outcome, followed by osteosarcoma, Ewing sarcoma, chordoma and other bone tumors. In conclusion, different epidemiologic performance in incidence and mortality was observed across tumor type as well as other demographic and clinicopathological variables, which provide potential suggestion for further adjustment of medical resource.
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Affiliation(s)
- Yao Xu
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Fanqi Shi
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Department of Spinal Surgery, The Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China
| | - Yanting Zhang
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Mengfan Yin
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Department of Orthopedics, The Fifth Central Hospital of Tianjin, Tianjin, China
| | - Xiuxin Han
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Jinyan Feng
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Guowen Wang
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
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31
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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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32
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Chellini L, Scarfò M, Bonvissuto D, Sette C, Paronetto MP. The DNA/RNA helicase DHX9 orchestrates the KDM2B-mediated transcriptional regulation of YAP1 in Ewing sarcoma. Oncogene 2024; 43:225-234. [PMID: 38017132 DOI: 10.1038/s41388-023-02894-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023]
Abstract
Ewing sarcomas (ES) are aggressive paediatric tumours of bone and soft tissues. Resistance to chemotherapy and high propensity to metastasize remain the main causes of treatment failure. Thus, identifying novel targets for alternative therapeutic approaches is urgently needed. DNA/RNA helicases are emerging as crucial regulators of many cellular processes often deregulated in cancer. Among them, DHX9 is up-regulated in ES and collaborates with EWS-FLI1 in ES transformation. We report that DHX9 silencing profoundly impacts on the oncogenic properties of ES cells. Transcriptome profiling combined to bioinformatic analyses disclosed a gene signature commonly regulated by DHX9 and the Lysine Demethylase KDM2B, with the Hippo pathway regulator YAP1 as a prominent target. Mechanistically, we found that DHX9 enhances H3K9 chromatin demethylation by KDM2B and favours RNA Polymerase II recruitment, thus promoting YAP1 expression. Conversely, EWS-FLI1 binding to the promoter represses YAP1 expression. These findings identify the DHX9/KDM2B complex as a new druggable target to counteract ES malignancy.
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Affiliation(s)
- Lidia Chellini
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Santa Lucia Foundation, Rome, Italy.
| | - Marzia Scarfò
- Plaisant Polo Tecnologico s.r.l, Castel Romano, Rome, Italy
| | - Davide Bonvissuto
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Claudio Sette
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
- GSTeP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Santa Lucia Foundation, Rome, Italy.
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.
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Leslie BJ, Lang B, Babu MM. A genome-wide view of disordered proteins. Nat Biotechnol 2024; 42:32-34. [PMID: 37783848 DOI: 10.1038/s41587-023-01955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Affiliation(s)
- Benjamin J Leslie
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Benjamin Lang
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - M Madan Babu
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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34
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Monovich AC, Gurumurthy A, Ryan RJH. The Diverse Roles of ETV6 Alterations in B-Lymphoblastic Leukemia and Other Hematopoietic Cancers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:291-320. [PMID: 39017849 DOI: 10.1007/978-3-031-62731-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Genetic alterations of the repressive ETS family transcription factor gene ETV6 are recurrent in several categories of hematopoietic malignancy, including subsets of B-cell and T-cell acute lymphoblastic leukemias (B-ALL and T-ALL), myeloid neoplasms, and mature B-cell lymphomas. ETV6 is essential for adult hematopoietic stem cells (HSCs), contributes to specific functions of some mature immune cells, and plays a key role in thrombopoiesis as demonstrated by familial ETV6 mutations associated with thrombocytopenia and predisposition to hematopoietic cancers, particularly B-ALL. ETV6 appears to have a tumor suppressor role in several hematopoietic lineages, as demonstrated by recurrent somatic loss-of-function (LoF) and putative dominant-negative alterations in leukemias and lymphomas. ETV6 rearrangements contribute to recurrent fusion oncogenes such as the B-ALL-associated transcription factor (TF) fusions ETV6::RUNX1 and PAX5::ETV6, rare drivers such as ETV6::NCOA6, and a spectrum of tyrosine kinase gene fusions encoding hyperactive signaling proteins that self-associate via the ETV6 N-terminal pointed domain. Another subset of recurrent rearrangements involving the ETV6 gene locus appear to function primarily to drive overexpression of the partner gene. This review surveys what is known about the biochemical and genome regulatory properties of ETV6 as well as our current understanding of how alterations in these functions contribute to hematopoietic and nonhematopoietic cancers.
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Affiliation(s)
- Alexander C Monovich
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Aishwarya Gurumurthy
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Russell J H Ryan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
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35
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Ebegboni VJ, Jones TL, Brownmiller T, Zhao PX, Pehrsson EC, Rajan SS, Caplen NJ. ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572864. [PMID: 38187702 PMCID: PMC10769395 DOI: 10.1101/2023.12.21.572864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The mechanistic basis for the metastasis of Ewing sarcomas remains poorly understood, as these tumors harbor few mutations beyond the chromosomal translocation that initiates the disease. Instead, the epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the EWSR1::FLI1/ERG's repression of transcription factor genes, concentrating on those that exhibit a broader range of expression in tumors than in EWS cell lines. Focusing on one of these target genes, ETS1, we detected EWSR1::FLI1 binding and an H3K27me3 repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1's binding of promoter regions, substantially altering the transcriptome of EWS cells, including the upregulation of the gene encoding TENSIN3 (TNS3), a focal adhesion protein. EWS cell lines expressing ETS1 (CRISPRa) exhibited increased TNS3 expression and enhanced movement compared to control cells. The cytoskeleton of control cells and ETS1-activated EWS cell lines also differed. Specifically, control cells exhibited a distributed vinculin signal and a network-like organization of F-actin. In contrast, ETS1-activated EWS cells showed an accumulation of vinculin and F-actin towards the plasma membrane. Interestingly, the phenotype of ETS1-activated EWS cell lines depleted of TNS3 resembled the phenotype of the control cells. Critically, these findings have clinical relevance as TNS3 expression in EWS tumors positively correlates with that of ETS1.
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Affiliation(s)
- Vernon Justice Ebegboni
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tamara L Jones
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tayvia Brownmiller
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Patrick X Zhao
- Omics Bioinformatics Facility, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Erica C Pehrsson
- Omics Bioinformatics Facility, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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36
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Adibi A, Tokat ÜM, Özgü E, Aydın E, Demiray İ, Demiray M. PARP inhibitor combinations with high-dose vitamin C in the treatment of Ewing sarcoma: two case reports and mechanistic overview. Ther Adv Med Oncol 2023; 15:17588359231213841. [PMID: 38107827 PMCID: PMC10725144 DOI: 10.1177/17588359231213841] [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: 02/28/2023] [Accepted: 10/26/2023] [Indexed: 12/19/2023] Open
Abstract
Ewing's sarcoma (ES) is a bone and soft tissue tumor that mainly occurs at a young age. The underlying cause of Ewing's sarcoma is the formation of fusion proteins between FET family genes and ETS family genes. Tumors with FET/ETS fusion genes can have defects in the DNA damage response and are sensitive to PARP inhibitors (PARPi). However, several studies have shown that PARPi alone is not sufficient to induce a meaningful antitumor response and that combinations of DNA-damaging agents with PARPi are required to achieve efficacy. Accordingly, preclinical studies have reported dramatic responses to PARPi treatment in combination with DNA-damaging agents such as temozolomide or irinotecan. Similarly, it has been previously reported that by generating reactive oxygen species, high-dose intravenous vitamin C (IVC) can induce DNA damage. This suggests that the combination of IVC with PARPi may increase genotoxic stress and enhance the antitumor response. In addition, unlike chemotherapeutic agents, IVC induces DNA damage selectively in cancer cells, and the side effects are significantly milder than those of chemotherapy. As ETS fusion-positive ES is deficient in faithful DNA repair, partly due to the interaction between ETS fusion products and PARP1, a PARPi plus IVC seems to be a logical and effective combination for the treatment of ETS fusion-positive ES. This paper reports significant responses to IVC (1-1.5 g/kg) in combination with PARPi (olaparib 300 mg BID or talazoparib 1 mg/day) in two patients with metastatic Ewing's sarcoma. The observations highlight an unmet therapeutic need for patients with advanced metastatic ES. The combination of PARPi with a selective DNA-damaging agent was effective in these cases. This case experience suggests that IVC may be incorporated into PARPi-based therapeutic strategies. Further studies are needed to confirm the efficacy of this combination in the treatment of Ewing sarcoma with ETS fusions.
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Affiliation(s)
- Ashkan Adibi
- Center of Precision Oncology, Medicana International Hospitals, Istanbul, Türkiye
- Department of Basic Oncology, Division of Cancer Genetics, Institute of Oncology, University of Istanbul, Istanbul, Türkiye
- Institute of Health Sciences, University of Istanbul, Istanbul, Türkiye
| | - Ünal Metin Tokat
- Center of Precision Oncology, Medicana International Hospitals, Istanbul, Türkiye
| | - Eylül Özgü
- Center of Precision Oncology, Medicana International Hospitals, Istanbul, Türkiye
| | - Esranur Aydın
- Center of Precision Oncology, Medicana International Hospitals, Istanbul, Türkiye
| | - İrem Demiray
- Department of Molecular Biology and Genetics, College of Science, Koç University, Istanbul, Türkiye
| | - Mutlu Demiray
- Center of Precision Oncology, Medicana International Hospitals, Küçükbakkalköy, Vedat Günyol Cd. No: 24, Atasehir, Istanbul 34750, Türkiye
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Zhao J, Faryabi RB. Spatial promoter-enhancer hubs in cancer: organization, regulation, and function. Trends Cancer 2023; 9:1069-1084. [PMID: 37599153 PMCID: PMC10840977 DOI: 10.1016/j.trecan.2023.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/14/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
Abstract
Transcriptional dysregulation is a hallmark of cancer and can be driven by altered enhancer landscapes. Recent studies in genome organization have revealed that multiple enhancers and promoters can spatially coalesce to form dynamic topological assemblies, known as promoter-enhancer hubs, which strongly correlate with elevated gene expression. In this review, we discuss the structure and complexity of promoter-enhancer hubs recently identified in multiple cancer types. We further discuss underlying mechanisms driving dysregulation of promoter-enhancer hubs and speculate on their functional role in pathogenesis. Understanding the role of promoter-enhancer hubs in transcriptional dysregulation can provide insight into new therapeutic approaches to target these complex features of genome organization.
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Affiliation(s)
- Jingru Zhao
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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Conover CA, Oxvig C. The Pregnancy-Associated Plasma Protein-A (PAPP-A) Story. Endocr Rev 2023; 44:1012-1028. [PMID: 37267421 DOI: 10.1210/endrev/bnad017] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/01/2023] [Accepted: 05/31/2023] [Indexed: 06/04/2023]
Abstract
Pregnancy-associated plasma protein-A (PAPP-A) was first identified in the early 1970s as a placental protein of unknown function, present at high concentrations in the circulation of pregnant women. In the mid-to-late 1990s, PAPP-A was discovered to be a metzincin metalloproteinase, expressed by many nonplacental cells, that regulates local insulin-like growth factor (IGF) activity through cleavage of high-affinity IGF binding proteins (IGFBPs), in particular IGFBP-4. With PAPP-A as a cell surface-associated enzyme, the reduced affinity of the cleavage fragments results in increased IGF available to bind and activate IGF receptors in the pericellular environment. This proteolytic regulation of IGF activity is important, since the IGFs promote proliferation, differentiation, migration, and survival in various normal and cancer cells. Thus, there has been a steady growth in investigation of PAPP-A structure and function outside of pregnancy. This review provides historical perspective on the discovery of PAPP-A and its structure and cellular function, highlights key studies of the first 50 years in PAPP-A research, and introduces new findings from recent years.
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Affiliation(s)
- Cheryl A Conover
- Division of Endocrinology, Mayo Clinic, Rochester, MN 55905, USA
| | - Claus Oxvig
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
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Mallard HJ, Wan S, Nidhi P, Hanscom-Trofy YD, Mohapatra B, Woods NT, Lopez-Guerrero JA, Llombart-Bosch A, Machado I, Scotlandi K, Kreiling NF, Perry MC, Mirza S, Coulter DW, Band V, Band H, Ghosal G. USP1 Expression Driven by EWS::FLI1 Transcription Factor Stabilizes Survivin and Mitigates Replication Stress in Ewing Sarcoma. Mol Cancer Res 2023; 21:1186-1204. [PMID: 37478161 PMCID: PMC10618738 DOI: 10.1158/1541-7786.mcr-23-0323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/23/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023]
Abstract
In this study, we identify USP1 as a transcriptional target of EWS::FLI1 and demonstrate the requisite function of USP1 in Ewing sarcoma (EWS) cell survival in response to endogenous replication stress. EWS::FLI1 oncogenic transcription factor drives most EWS, a pediatric bone cancer. EWS cells display elevated levels of R-loops and replication stress. The mechanism by which EWS cells override activation of apoptosis or cellular senescence in response to increased replication stress is not known. We show that USP1 is overexpressed in EWS and EWS::FLI1 regulates USP1 transcript levels. USP1 knockdown or inhibition arrests EWS cell growth and induces cell death by apoptosis. Mechanistically, USP1 regulates Survivin (BIRC5/API4) protein stability and the activation of caspase-9 and caspase-3/7 in response to endogenous replication stress. Notably, USP1 inhibition sensitizes cells to doxorubicin and etoposide treatment. Together, our study demonstrates that USP1 is regulated by EWS::FLI1, the USP1-Survivin axis promotes EWS cell survival, and USP1 inhibition sensitizes cells to standard of care chemotherapy. IMPLICATIONS High USP1 and replication stress levels driven by EWS::FLI1 transcription factor in EWS are vulnerabilities that can be exploited to improve existing treatment avenues and overcome drug resistance.
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Affiliation(s)
- Halle J. Mallard
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Shibiao Wan
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Prakriti Nidhi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Yvan D. Hanscom-Trofy
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Bhopal Mohapatra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Nicholas T. Woods
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Antonio Llombart-Bosch
- Department of Pathology, Instituto Valenciano de Oncología and Patologika Laboratory, Hospital QuironSalud, Valencia, Spain
| | - Isidro Machado
- Department of Pathology, Instituto Valenciano de Oncología and Patologika Laboratory, Hospital QuironSalud, Valencia, Spain
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Natasha F. Kreiling
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Megan C. Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Donald W. Coulter
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Hamid Band
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
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Souza BK, Freire NH, Monteiro TS, Herlinger AL, Jaeger M, Dalmolin MGS, de Farias CB, Gregianin L, Brunetto AT, Brunetto AL, Thiele CJ, Roesler R. Histone Methyltransferases G9a/ Ehmt2 and GLP/ Ehmt1 Are Associated with Cell Viability and Poorer Prognosis in Neuroblastoma and Ewing Sarcoma. Int J Mol Sci 2023; 24:15242. [PMID: 37894922 PMCID: PMC10607632 DOI: 10.3390/ijms242015242] [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: 09/01/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Changes in epigenetic programming have been proposed as being key events in the initiation and progression of childhood cancers. HMT euchromatic histone lysine methyltransferase 2 (G9a, EHMT2), which is encoded by the G9a (Ehmt2) gene, as well as its related protein GLP, which is encoded by the GLP/Ehmt1 gene, participate in epigenetic regulation by contributing to a transcriptionally repressed chromatin state. G9a/GLP activation has been reported in several cancer types. Herein, we evaluated the role of G9a in two solid pediatric tumors: neuroblastoma (NB) and Ewing sarcoma (ES). Our results show that G9a/Ehmt2 and GLP/Ehmt1 expression is higher in tumors with poorer prognosis, including St4 International Neuroblastoma Staging System (INSS) stage, MYCN amplified NB, and metastatic ES. Importantly, higher G9a and GLP levels were associated with shorter patient overall survival (OS) in both NB and ES. Moreover, pharmacological inhibition of G9a/GLP reduced cell viability in NB and ES cells. These findings suggest that G9a and GLP are associated with more aggressive NB and ES tumors and should be further investigated as being epigenetic targets in pediatric solid cancers.
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Affiliation(s)
- Barbara Kunzler Souza
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil (A.T.B.)
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- Epigenica Biosciences, Canoas 92035-000, Brazil;
| | - Natalia 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 (A.T.B.)
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, Brazil
| | | | - Alice Laschuk Herlinger
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil (A.T.B.)
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, 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 (A.T.B.)
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, Brazil
| | - Matheus G. S. Dalmolin
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, 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 (A.T.B.)
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, 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 (A.T.B.)
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, 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
| | - 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 (A.T.B.)
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, 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 (A.T.B.)
- National Science and Technology Institute for Children’s Cancer Biology and Pediatric Oncology—INCT BioOncoPed, Porto Alegre 90035-003, Brazil
- Children’s Cancer Institute, Porto Alegre 90620-110, Brazil
| | - Carol J. Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - 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 (A.T.B.)
- 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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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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Thomas NJ, Luck C, Shlimon N, Ponce RK, Kosibaty Z, Okimoto RA. Mapping chromatin state and transcriptional response in CIC-DUX4 undifferentiated round cell sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561932. [PMID: 37873100 PMCID: PMC10592754 DOI: 10.1101/2023.10.11.561932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
CIC-DUX4 is a rare and understudied transcription factor fusion oncoprotein. CIC-DUX4 co-opts native gene targets to drive a lethal form of human sarcoma. The molecular underpinnings that lead to oncogenic reprograming and CIC-DUX4 sarcomagenesis remain largely undefined. Through an integrative ChIP and RNA-Seq analysis using patient-derived CIC-DUX4 cells, we define CIC-DUX4 mediated chromatin states and function. We show that CIC-DUX4 primarily localizes to proximal and distal cis-regulatory elements where it associates with active histone marks. Our findings nominate key signaling pathways and molecular targets that enable CIC-DUX4 to mediate tumor cell survival. Collectively, our data demonstrate how the CIC-DUX4 fusion oncoprotein impacts chromatin state and transcriptional responses to drive an oncogenic program in undifferentiated sarcoma. Significance CIC-DUX4 sarcoma is a rare and lethal sarcoma that affects children, adolescent young adults, and adults. CIC-DUX4 sarcoma is associated with rapid metastatic dissemination and relative insensitivity to chemotherapy. There are no current standard-of-care therapies for CIC-DUX4 sarcoma leading to universally poor outcomes for patients. Through a deep mechanistic understanding of how the CIC-DUX4 fusion oncoprotein reprograms chromatin state and function, we aim to improve outcomes for CIC-DUX4 patients.
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Pozner A, Verma SP, Li L, Wang S, Barrott JJ, Nelson ML, Yu JSE, Negri GL, Colborne S, Hughes CS, Zhu JF, Lambert SL, Carroll LS, Smith-Fry K, Stewart MG, Kannan S, Jensen B, Mortenson KL, John C, Sikdar S, Liu H, Dang NH, Bourdage J, Li J, Vahrenkamp JM, Groundland JS, Wustrack R, Senger DL, Zemp FJ, Mahoney DJ, Gertz J, Zhang X, Lazar AJ, Hirst M, Morin GB, Nielsen TO, Shen PS, Jones KB. ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560242. [PMID: 37873234 PMCID: PMC10592841 DOI: 10.1101/2023.09.29.560242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The t(X,17) chromosomal translocation, generating the ASPSCR1-TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCC), frustrating efforts to identify therapeutic targets for these rare cancers. Proteomic analysis showed that VCP/p97, an AAA+ ATPase with known segregase function, was strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1-TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1-TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributed with ASPSCR1-TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrated the oncogenic transcriptional signature of ASPSCR1-TFE3, by facilitating assembly of higher-order chromatin conformation structures as demonstrated by HiChIP. Finally, ASPSCR1-TFE3 and VCP demonstrated co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCP's potential as a novel therapeutic target.
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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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Frenkel M, Hujoel ML, Morris Z, Raman S. Discovering chromatin dysregulation induced by protein-coding perturbations at scale. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.555752. [PMID: 37781603 PMCID: PMC10541138 DOI: 10.1101/2023.09.20.555752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Although population-scale databases have expanded to millions of protein-coding variants, insight into variant mechanisms has not kept pace. We present PROD-ATAC, a high-throughput method for discovering the effects of protein-coding variants on chromatin. A pooled library of variants is expressed in a disease-agnostic cell line, and single-cell ATAC resolves each variant's effect on chromatin. Using PROD-ATAC, we characterized the effects of >100 oncofusions (a class of cancer-causing chimeric proteins) and controls and revealed that pioneer activity is a common feature of fusions spanning an enormous range of fusion frequencies. Further, fusion-induced dysregulation can be context-agnostic as observed mechanisms often overlapped with cancer and cell-type specific prior knowledge. We also showed that gain-of-function pioneering is common among oncofusions. This work provides a global view of fusion-induced chromatin. We uncovered convergent mechanisms among disparate oncofusions and shared modes of dysregulation across different cancers. PROD-ATAC is generalizable to any set of protein-coding variants.
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Affiliation(s)
- Max Frenkel
- Cellular and Molecular Biology Graduate Program, University of Wisconsin, Madison, Wisconsin, USA
- Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Margaux L.A. Hujoel
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zachary Morris
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, Wisconsin, USA
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46
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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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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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Gong H, Xue B, Ru J, Pei G, Li Y. Targeted Therapy for EWS-FLI1 in Ewing Sarcoma. Cancers (Basel) 2023; 15:4035. [PMID: 37627063 PMCID: PMC10452796 DOI: 10.3390/cancers15164035] [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: 05/28/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare and predominantly pediatric malignancy of bone and soft tissue in children and adolescents. Although international collaborations have greatly improved the prognosis of most EwS, the occurrence of macrometastases or relapse remains challenging. The prototypic oncogene EWS-FLI1 acts as an aberrant transcription factor that drives the cellular transformation of EwS. In addition to its involvement in RNA splicing and the DNA damage response, this chimeric protein directly binds to GGAA repeats, thereby modifying the transcriptional profile of EwS. Direct pharmacological targeting of EWS-FLI1 is difficult because of its intrinsically disordered structure. However, targeting the EWS-FLI1 protein complex or downstream pathways provides additional therapeutic options. This review describes the EWS-FLI1 protein partners and downstream pathways, as well as the related target therapies for the treatment of EwS.
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Affiliation(s)
- Helong Gong
- Department of Orthopaedic Surgery, Shengjing Hospital, China Medical University, No. 36 Sanhao Street, Heping District, Shenyang 110004, China;
| | - Busheng Xue
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China;
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Guoqing Pei
- Department of Orthopedics, Xijing Hospital, Air Force Medical University, Xi’an 710032, China;
| | - Yan Li
- Department of Orthopaedic Surgery, Shengjing Hospital, China Medical University, No. 36 Sanhao Street, Heping District, Shenyang 110004, China;
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Jain K, Henrich IC, Quick L, Young R, Mondal S, Oliveira AM, Blobel GA, Chou MM. Natural Killer Cell Activation by Ubiquitin-specific Protease 6 Mediates Tumor Suppression in Ewing Sarcoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:1615-1627. [PMID: 37615015 PMCID: PMC10443598 DOI: 10.1158/2767-9764.crc-22-0505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/16/2023] [Accepted: 07/18/2023] [Indexed: 08/25/2023]
Abstract
Ewing sarcoma is a rare and deadly pediatric bone cancer for which survival rates and treatment options have stagnated for decades. Ewing sarcoma has not benefited from immunotherapy due to poor understanding of how its immune landscape is regulated. We recently reported that ubiquitin-specific protease 6 (USP6) functions as a tumor suppressor in Ewing sarcoma, and identified it as the first cell-intrinsic factor to modulate the Ewing sarcoma immune tumor microenvironment (TME). USP6 induces intratumoral infiltration and activation of multiple innate immune lineages in xenografted nude mice. Here we report that natural killer (NK) cells are essential for its tumor-inhibitory functions, as NK cell depletion reverses USP6-mediated suppression of Ewing sarcoma xenograft growth. USP6 expression in Ewing sarcoma cells directly stimulates NK cell activation and degranulation in vitro, and functions by increasing surface levels of multiple NK cell-activating ligands. USP6 also induces surface upregulation of the receptor for the apoptosis-inducing ligand tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), providing an additional route for enhanced sensitivity to NK cell killing. Furthermore, USP6-expressing Ewing sarcoma and NK cells participate in a paracrine immunostimulatory feedforward loop, wherein IFNγ secreted by activated NK cells feeds back on USP6/Ewing sarcoma cells to induce synergistic expression of chemokines CXCL9 and CXCL10. Remarkably, expression of USP6 in subcutaneous Ewing sarcoma xenografts induces systemic activation and maturation of NK cells, and induces an abscopal response in which growth of distal tumors is inhibited, coincident with increased infiltration and activation of NK cells. This work reveals how USP6 reprograms the Ewing sarcoma TME to enhance antitumor immunity, and may be exploited for future therapeutic benefit. Significance This study provides novel insights into the immunomodulatory functions of USP6, the only cancer cell-intrinsic factor demonstrated to regulate the immune TME in Ewing sarcoma. We demonstrate that USP6-mediated suppression of Ewing sarcoma tumorigenesis is dependent on NK cells. USP6 directly activates NK cell cytolytic function, inducing both intratumoral and systemic activation of NK cells in an Ewing sarcoma xenograft model.
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Affiliation(s)
- Kanika Jain
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ian C. Henrich
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at University of Pennsylvania, Philadelphia, Pennsylvania
| | - Laura Quick
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Robert Young
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Shreya Mondal
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andre M. Oliveira
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Gerd A. Blobel
- Perelman School of Medicine at University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pediatric Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Margaret M. Chou
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at University of Pennsylvania, Philadelphia, Pennsylvania
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Fernández-Tabanera E, García-García L, Rodríguez-Martín C, Cervera ST, González-González L, Robledo C, Josa S, Martínez S, Chapado L, Monzón S, Melero-Fernández de Mera RM, Alonso J. CD44 Modulates Cell Migration and Invasion in Ewing Sarcoma Cells. Int J Mol Sci 2023; 24:11774. [PMID: 37511533 PMCID: PMC10381016 DOI: 10.3390/ijms241411774] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The chimeric EWSR1::FLI1 transcription factor is the main oncogenic event in Ewing sarcoma. Recently, it has been proposed that EWSR1::FLI1 levels can fluctuate in Ewing sarcoma cells, giving rise to two cell populations. EWSR1::FLI1low cells present a migratory and invasive phenotype, while EWSR1::FLI1high cells are more proliferative. In this work, we described how the CD44 standard isoform (CD44s), a transmembrane protein involved in cell adhesion and migration, is overexpressed in the EWSR1::FLI1low phenotype. The functional characterization of CD44s (proliferation, clonogenicity, migration, and invasion ability) was performed in three doxycycline-inducible Ewing sarcoma cell models (A673, MHH-ES1, and CADO-ES1). As a result, CD44s expression reduced cell proliferation in all the cell lines tested without affecting clonogenicity. Additionally, CD44s increased cell migration in A673 and MHH-ES1, without effects in CADO-ES1. As hyaluronan is the main ligand of CD44s, its effect on migration ability was also assessed, showing that high molecular weight hyaluronic acid (HMW-HA) blocked cell migration while low molecular weight hyaluronic acid (LMW-HA) increased it. Invasion ability was correlated with CD44 expression in A673 and MHH-ES1 cell lines. CD44s, upregulated upon EWSR1::FLI1 knockdown, regulates cell migration and invasion in Ewing sarcoma cells.
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Affiliation(s)
- Enrique Fernández-Tabanera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (U758, CB06/07/1009, CIBERER-ISCIII), 28029 Madrid, Spain
- Universidad Nacional de Educación a Distancia (UNED), 28015 Madrid, Spain
| | - Laura García-García
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Carlos Rodríguez-Martín
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (U758, CB06/07/1009, CIBERER-ISCIII), 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
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (U758, CB06/07/1009, CIBERER-ISCIII), 28029 Madrid, Spain
| | - Laura González-González
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Cristina Robledo
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 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
| | - Selene Martínez
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Luis Chapado
- Bioinformatics Unit, Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Sara Monzón
- Bioinformatics Unit, Instituto de Salud Carlos III (ISCIII), 28220 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
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (U758, CB06/07/1009, CIBERER-ISCIII), 28029 Madrid, Spain
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (U758, CB06/07/1009, CIBERER-ISCIII), 28029 Madrid, Spain
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