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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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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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Zhang S, Pei G, Li B, Li P, Lin Y. Abnormal phase separation of biomacromolecules in human diseases. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1133-1152. [PMID: 37475546 PMCID: PMC10423695 DOI: 10.3724/abbs.2023139] [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: 05/25/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
Membrane-less organelles (MLOs) formed through liquid-liquid phase separation (LLPS) are associated with numerous important biological functions, but the abnormal phase separation will also dysregulate the physiological processes. Emerging evidence points to the importance of LLPS in human health and diseases. Nevertheless, despite recent advancements, our knowledge of the molecular relationship between LLPS and diseases is frequently incomplete. In this review, we outline our current understanding about how aberrant LLPS affects developmental disorders, tandem repeat disorders, cancers and viral infection. We also examine disease mechanisms driven by aberrant condensates, and highlight potential treatment approaches. This study seeks to expand our understanding of LLPS by providing a valuable new paradigm for understanding phase separation and human disorders, as well as to further translate our current knowledge regarding LLPS into therapeutic discoveries.
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Affiliation(s)
- Songhao Zhang
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
| | - Gaofeng Pei
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- Frontier Research Center for Biological StructureTsinghua UniversityBeijing100084China
| | - Boya Li
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
| | - Pilong Li
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- Frontier Research Center for Biological StructureTsinghua UniversityBeijing100084China
| | - Yi Lin
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
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4
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Isoyama S, Tamaki N, Noguchi Y, Okamura M, Yoshimatsu Y, Kondo T, Suzuki T, Yaguchi SI, Dan S. Subtype-selective induction of apoptosis in translocation-related sarcoma cells induced by PUMA and BIM upon treatment with pan-PI3K inhibitors. Cell Death Dis 2023; 14:169. [PMID: 36849535 PMCID: PMC9971170 DOI: 10.1038/s41419-023-05690-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023]
Abstract
Translocation-related sarcomas (TRSs) harbor an oncogenic fusion gene generated by chromosome translocation and account for approximately one-third of all sarcomas; however, effective targeted therapies have yet to be established. We previously reported that a pan-phosphatidylinositol 3-kinase (PI3K) inhibitor, ZSTK474, was effective for the treatment of sarcomas in a phase I clinical trial. We also demonstrated the efficacy of ZSTK474 in a preclinical model, particularly in cell lines from synovial sarcoma (SS), Ewing's sarcoma (ES) and alveolar rhabdomyosarcoma (ARMS), all of which harbor chromosomal translocations. ZSTK474 selectively induced apoptosis in all these sarcoma cell lines, although the precise mechanism underlying the induction of apoptosis remained unclear. In the present study, we aimed to determine the antitumor effect of PI3K inhibitors, particularly with regards to the induction of apoptosis, against various TRS subtypes using cell lines and patient-derived cells (PDCs). All of the cell lines derived from SS (six), ES (two) and ARMS (one) underwent apoptosis accompanied by the cleavage of poly-(ADP-ribose) polymerase (PARP) and the loss of mitochondrial membrane potential. We also observed apoptotic progression in PDCs from SS, ES and clear cell sarcoma (CCS). Transcriptional analyses revealed that PI3K inhibitors triggered the induction of PUMA and BIM and the knockdown of these genes by RNA interference efficiently suppressed apoptosis, suggesting their functional involvement in the progression of apoptosis. In contrast, TRS-derived cell lines/PDCs from alveolar soft part sarcoma (ASPS), CIC-DUX4 sarcoma and dermatofibrosarcoma protuberans failed to undergo apoptosis nor induce PUMA and BIM expression, as well as cell lines derived from non-TRSs and carcinomas. Thus, we conclude that PI3K inhibitors induce apoptosis in selective TRSs such as ES and SS via the induction of PUMA and BIM and the subsequent loss of mitochondrial membrane potential. This represents proof of concept for PI3K-targeted therapy, particularly such TRS patients.
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Affiliation(s)
- Sho Isoyama
- grid.410807.a0000 0001 0037 4131Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550 Japan
| | - Naomi Tamaki
- grid.410807.a0000 0001 0037 4131Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550 Japan
| | - Yutaka Noguchi
- grid.410807.a0000 0001 0037 4131Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550 Japan
| | - Mutsumi Okamura
- grid.410807.a0000 0001 0037 4131Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550 Japan
| | - Yuki Yoshimatsu
- grid.420115.30000 0004 0378 8729Department of Patient-derived Cancer Model, Tochigi Cancer Center, 4-9-13 Yohnan, Utsunomiya, Tochigi, 320-0834 Japan ,grid.272242.30000 0001 2168 5385Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Tadashi Kondo
- grid.272242.30000 0001 2168 5385Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Takeshi Suzuki
- grid.9707.90000 0001 2308 3329Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192 Japan
| | - Shin-ichi Yaguchi
- grid.410807.a0000 0001 0037 4131Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550 Japan ,OHARA Pharmaceutical Co., Ltd., 36F St. Luke’s Tower, 8-1 Akashi-cho, Chuo-ku, Tokyo, 104-6591 Japan
| | - Shingo Dan
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan.
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5
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Cillo AR, Mukherjee E, Bailey NG, Onkar S, Daley J, Salgado C, Li X, Liu D, Ranganathan S, Burgess M, Sembrat J, Weiss K, Watters R, Bruno TC, Vignali DAA, Bailey KM. Ewing Sarcoma and Osteosarcoma Have Distinct Immune Signatures and Intercellular Communication Networks. Clin Cancer Res 2022; 28:4968-4982. [PMID: 36074145 PMCID: PMC9669190 DOI: 10.1158/1078-0432.ccr-22-1471] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/17/2022] [Accepted: 09/06/2022] [Indexed: 01/26/2023]
Abstract
PURPOSE Ewing sarcoma and osteosarcoma are primary bone sarcomas occurring most commonly in adolescents. Metastatic and relapsed disease are associated with dismal prognosis. Although effective for some soft tissue sarcomas, current immunotherapeutic approaches for the treatment of bone sarcomas have been largely ineffective, necessitating a deeper understanding of bone sarcoma immunobiology. EXPERIMENTAL DESIGN Multiplex immunofluorescence analysis of immune infiltration in relapsed versus primary disease was conducted. To better understand immune states and drivers of immune infiltration, especially during disease progression, we performed single-cell RNA sequencing (scRNAseq) of immune populations from paired blood and bone sarcoma tumor samples. RESULTS Our multiplex immunofluorescence analysis revealed increased immune infiltration in relapsed versus primary disease in both Ewing sarcoma and osteosarcoma. scRNAseq analyses revealed terminally exhausted CD8+ T cells expressing co-inhibitory receptors in osteosarcoma and an effector T-cell subpopulation in Ewing sarcoma. In addition, distinct subsets of CD14+CD16+ macrophages were present in Ewing sarcoma and osteosarcoma. To determine pathways driving tumor immune infiltration, we conducted intercellular communication analyses and uncovered shared mechanisms of immune infiltration driven by CD14+CD16+ macrophages and unique pathways of immune infiltration driven by CXCL10 and CXCL12 in osteosarcoma. CONCLUSIONS Our study provides preclinical rationale for future investigation of specific immunotherapeutic targets upon relapse and provides an invaluable resource of immunologic data from bone sarcomas.
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Affiliation(s)
- Anthony R. Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Elina Mukherjee
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nathanael G Bailey
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Sayali Onkar
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA,Program in Microbiology and Immunology, Pittsburgh, PA, USA
| | - Jessica Daley
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Claudia Salgado
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Xiang Li
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA,School of Medicine, Tsinghua University, Beijing, China
| | - Dongyan Liu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA,School of Medicine, Tsinghua University, Beijing, China
| | | | - Melissa Burgess
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John Sembrat
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kurt Weiss
- Department of Orthopedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rebecca Watters
- Department of Orthopedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Tullia C. Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA,Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Dario AA Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh PA, USA,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA,Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Kelly M. Bailey
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
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6
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Sun N, Tran BV, Peng Z, Wang J, Zhang C, Yang P, Zhang TX, Widjaja J, Zhang RY, Xia W, Keir A, She J, Yu H, Shyue J, Zhu H, Agopian VG, Pei R, Tomlinson JS, Toretsky JA, Jonas SJ, Federman N, Lu S, Tseng H, Zhu Y. Coupling Lipid Labeling and Click Chemistry Enables Isolation of Extracellular Vesicles for Noninvasive Detection of Oncogenic Gene Alterations. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105853. [PMID: 35486030 PMCID: PMC9108594 DOI: 10.1002/advs.202105853] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/13/2022] [Indexed: 05/06/2023]
Abstract
Well-preserved molecular cargo in circulating extracellular vesicles (EVs) offers an ideal material for detecting oncogenic gene alterations in cancer patients, providing a noninvasive diagnostic solution for detection of disease status and monitoring treatment response. Therefore, technologies that conveniently isolate EVs with sufficient efficiency are desperately needed. Here, a lipid labeling and click chemistry-based EV capture platform ("Click Beads"), which is ideal for EV message ribonucleic acid (mRNA) assays due to its efficient, convenient, and rapid purification of EVs, enabling downstream molecular quantification using reverse transcription digital polymerase chain reaction (RT-dPCR) is described and demonstrated. Ewing sarcoma protein (EWS) gene rearrangements and kirsten rat sarcoma viral oncogene homolog (KRAS) gene mutation status are detected and quantified using EVs isolated by Click Beads and matched with those identified in biopsy specimens from Ewing sarcoma or pancreatic cancer patients. Moreover, the quantification of gene alterations can be used for monitoring treatment responses and disease progression.
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Affiliation(s)
- Na Sun
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
- Key Laboratory for Nano‐Bio InterfaceSuzhou Institute of Nano‐Tech and Nano‐BionicsUniversity of Chinese Academy of SciencesChinese Academy of SciencesSuzhou215123P. R. China
| | - Benjamin V. Tran
- Department of SurgeryUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Zishan Peng
- Department of PathologyZhongshan HospitalFudan UniversityShanghai200032P. R. China
| | - Jing Wang
- Department of PathologyShanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Ceng Zhang
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Peng Yang
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Tiffany X. Zhang
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Josephine Widjaja
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Ryan Y. Zhang
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Wenxi Xia
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Alexandra Keir
- Department of PediatricsDavid Geffen School of MedicineEli and Edythe Broad Center of Regenerative Medicine and Stem Cell Researchand Children's Discovery and Innovation InstituteUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Jia‐Wei She
- Smart Organic Materials LaboratoryInstitute of ChemistryAcademia SinicaNankangTaipei115Taiwan
| | - Hsiao‐hua Yu
- Smart Organic Materials LaboratoryInstitute of ChemistryAcademia SinicaNankangTaipei115Taiwan
| | - Jing‐Jong Shyue
- Research Center for Applied SciencesAcademia SinicaNankangTaipei115Taiwan
| | - Hongguang Zhu
- Department of PathologyShanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Vatche G. Agopian
- Department of SurgeryUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Renjun Pei
- Key Laboratory for Nano‐Bio InterfaceSuzhou Institute of Nano‐Tech and Nano‐BionicsUniversity of Chinese Academy of SciencesChinese Academy of SciencesSuzhou215123P. R. China
| | - James S. Tomlinson
- Department of SurgeryUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Jeffrey A Toretsky
- Departments of Oncology and PediatricsGeorgetown UniversityWashingtonDC20057USA
| | - Steven J. Jonas
- Department of PediatricsDavid Geffen School of MedicineEli and Edythe Broad Center of Regenerative Medicine and Stem Cell Researchand Children's Discovery and Innovation InstituteUniversity of California, Los AngelesLos AngelesCA90095USA
- California NanoSystems InstituteDepartments of Chemistry and Biochemistry and of Materials Science and EngineeringUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Noah Federman
- Department of PediatricsDavid Geffen School of MedicineEli and Edythe Broad Center of Regenerative Medicine and Stem Cell Researchand Children's Discovery and Innovation InstituteUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Shaohua Lu
- Department of PathologyZhongshan HospitalFudan UniversityShanghai200032P. R. China
| | - Hsian‐Rong Tseng
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Yazhen Zhu
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
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7
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Archer LK, Frame FM, Walker HF, Droop AP, McDonald GLK, Kucko S, Berney DM, Mann VM, Simms MS, Maitland NJ. ETS transcription factor ELF3 (ESE-1) is a cell cycle regulator in benign and malignant prostate. FEBS Open Bio 2022; 12:1365-1387. [PMID: 35472129 PMCID: PMC9249341 DOI: 10.1002/2211-5463.13417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/23/2022] [Accepted: 04/25/2022] [Indexed: 11/07/2022] Open
Abstract
This study aimed to elucidate the role of ELF3, an ETS family member in normal prostate growth and prostate cancer. Silencing ELF3 in both benign prostate (BPH-1) and prostate cancer (PC3) cell lines resulted in decreased colony forming ability, inhibition of cell migration and reduced cell viability due to cell cycle arrest, establishing ELF3 as a cell cycle regulator. Increased ELF3 expression in more advanced prostate tumours was shown by immunostaining of tissue microarrays and from analysis of gene expression and genetic alteration studies. This study indicates that ELF3 functions as part of normal prostate epithelial growth but also as a potential oncogene in advanced prostate cancers.
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Affiliation(s)
- Leanne K. Archer
- Cancer Research UnitDepartment of BiologyUniversity of YorkHeslingtonUK
| | - Fiona M. Frame
- Cancer Research UnitDepartment of BiologyUniversity of YorkHeslingtonUK
| | - Hannah F. Walker
- Cancer Research UnitDepartment of BiologyUniversity of YorkHeslingtonUK
| | | | | | - Samuel Kucko
- Cancer Research UnitDepartment of BiologyUniversity of YorkHeslingtonUK
| | - Daniel M. Berney
- Department of Molecular OncologyBarts Cancer InstituteQueen Mary University of LondonUK
| | - Vincent M. Mann
- Cancer Research UnitDepartment of BiologyUniversity of YorkHeslingtonUK
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8
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Esfandiari Nazzaro E, Sabei FY, Vogel WK, Nazari M, Nicholson KS, Gafken PR, Taratula O, Taratula O, Davare MA, Leid M. Discovery and Validation of a Compound to Target Ewing's Sarcoma. Pharmaceutics 2021; 13:pharmaceutics13101553. [PMID: 34683845 PMCID: PMC8538197 DOI: 10.3390/pharmaceutics13101553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 12/28/2022] Open
Abstract
Ewing’s sarcoma, characterized by pathognomonic t (11; 22) (q24; q12) and related chromosomal ETS family translocations, is a rare aggressive cancer of bone and soft tissue. Current protocols that include cytotoxic chemotherapeutic agents effectively treat localized disease; however, these aggressive therapies may result in treatment-related morbidities including second-site cancers in survivors. Moreover, the five-year survival rate in patients with relapsed, recurrent, or metastatic disease is less than 30%, despite intensive therapy with these cytotoxic agents. By using high-throughput phenotypic screening of small molecule libraries, we identified a previously uncharacterized compound (ML111) that inhibited in vitro proliferation of six established Ewing’s sarcoma cell lines with nanomolar potency. Proteomic studies show that ML111 treatment induced prometaphase arrest followed by rapid caspase-dependent apoptotic cell death in Ewing’s sarcoma cell lines. ML111, delivered via methoxypoly(ethylene glycol)-polycaprolactone copolymer nanoparticles, induced dose-dependent inhibition of Ewing’s sarcoma tumor growth in a murine xenograft model and invoked prometaphase arrest in vivo, consistent with in vitro data. These results suggest that ML111 represents a promising new drug lead for further preclinical studies and is a potential clinical development for the treatment of Ewing’s sarcoma.
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Affiliation(s)
- Ellie Esfandiari Nazzaro
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Fahad Y. Sabei
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan 88723, Saudi Arabia
| | - Walter K. Vogel
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Mohamad Nazari
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Katelyn S. Nicholson
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Philip R. Gafken
- Proteomics & Metabolomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
| | - Olena Taratula
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Oleh Taratula
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
- Correspondence: (O.T.); (M.A.D.)
| | - Monika A. Davare
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA;
- Papé Pediatric Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Correspondence: (O.T.); (M.A.D.)
| | - Mark Leid
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
- Department of Integrative Biosciences, Oregon Health & Science University, Portland, OR 97239, USA
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9
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Oncogenes, Proto-Oncogenes, and Lineage Restriction of Cancer Stem Cells. Int J Mol Sci 2021; 22:ijms22189667. [PMID: 34575830 PMCID: PMC8470404 DOI: 10.3390/ijms22189667] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 01/03/2023] Open
Abstract
In principle, an oncogene is a cellular gene (proto-oncogene) that is dysfunctional, due to mutation and fusion with another gene or overexpression. Generally, oncogenes are viewed as deregulating cell proliferation or suppressing apoptosis in driving cancer. The cancer stem cell theory states that most, if not all, cancers are a hierarchy of cells that arises from a transformed tissue-specific stem cell. These normal counterparts generate various cell types of a tissue, which adds a new dimension to how oncogenes might lead to the anarchic behavior of cancer cells. It is that stem cells, such as hematopoietic stem cells, replenish mature cell types to meet the demands of an organism. Some oncogenes appear to deregulate this homeostatic process by restricting leukemia stem cells to a single cell lineage. This review examines whether cancer is a legacy of stem cells that lose their inherent versatility, the extent that proto-oncogenes play a role in cell lineage determination, and the role that epigenetic events play in regulating cell fate and tumorigenesis.
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10
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The Landscape of Regulatory Noncoding RNAs in Ewing's Sarcoma. Biomedicines 2021; 9:biomedicines9080933. [PMID: 34440137 PMCID: PMC8391329 DOI: 10.3390/biomedicines9080933] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
Ewing’s sarcoma (ES) is a pediatric sarcoma caused by a chromosomal translocation. Unlike in most cancers, the genomes of ES patients are very stable. The translocation product of the EWS-FLI1 fusion is most often the predominant genetic driver of oncogenesis, and it is pertinent to explore the role of epigenetic alterations in the onset and progression of ES. Several types of noncoding RNAs, primarily microRNAs and long noncoding RNAs, are key epigenetic regulators that have been shown to play critical roles in various cancers. The functions of these epigenetic regulators are just beginning to be appreciated in ES. Here, we performed a comprehensive literature review to identify these noncoding RNAs. We identified clinically relevant tumor suppressor microRNAs, tumor promoter microRNAs and long noncoding RNAs. We then explored the known interplay between different classes of noncoding RNAs and described the currently unmet need for expanding the noncoding RNA repertoire of ES. We concluded the review with a discussion of epigenetic regulation of ES via regulatory noncoding RNAs. These noncoding RNAs provide new avenues of exploration to develop better therapeutics and identify novel biomarkers.
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11
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Su S, Chen J, Jiang Y, Wang Y, Vital T, Zhang J, Laggner C, Nguyen KT, Zhu Z, Prevatte AW, Barker NK, Herring LE, Davis IJ, Liu P. SPOP and OTUD7A Control EWS-FLI1 Protein Stability to Govern Ewing Sarcoma Growth. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004846. [PMID: 34060252 PMCID: PMC8292909 DOI: 10.1002/advs.202004846] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/11/2021] [Indexed: 05/08/2023]
Abstract
Chromosomal translocation results in development of an Ewing sarcoma breakpoint region 1-Friend leukemia integration 1 (EWS-FLI1) fusion oncogene in the majority of Ewing sarcoma. The persistent dependence of the tumor for this oncoprotein points to EWS-FLI1 as an ideal drug target. Although EWS-FLI1 transcriptional targets and binding partners are evaluated, the mechanisms regulating EWS-FLI1 protein stability remain elusive. Speckle-type POZ protein (SPOP) and OTU domain-containing protein 7A (OTUD7A) are identified as the bona fide E3 ligase and deubiquitinase, respectively, that control EWS-FLI1 protein turnover in Ewing sarcoma. Casein kinase 1-mediated phosphorylation of the VTSSS degron in the FLI1 domain enhances SPOP activity to degrade EWS-FLI1. Opposing this process, OTUD7A deubiquitinates and stabilizes EWS-FLI1. Depletion of OTUD7A in Ewing sarcoma cell lines reduces EWS-FLI1 protein abundance and impedes Ewing sarcoma growth in vitro and in mice. Performing an artificial-intelligence-based virtual drug screen of a 4-million small molecule library, 7Ai is identified as a potential OTUD7A catalytic inhibitor. 7Ai reduces EWS-FLI1 protein levels and decreases Ewing sarcoma growth in vitro and in a xenograft mouse model. This study supports the therapeutic targeting of OTUD7A as a novel strategy for Ewing sarcoma bearing EWS-FLI1 and related fusions, and may also be applicable to other cancers dependent on aberrant FLI1 expression.
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Affiliation(s)
- Siyuan Su
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Jianfeng Chen
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Yao Jiang
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Present address:
Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Ying Wang
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Tamara Vital
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of GeneticsThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of PediatricsThe University of North Carolina at Chapel HillChapel HillNC 27599USA
| | - Jiaming Zhang
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Present address:
Department of Oral Medicine, Infection, and ImmunityHarvard School of Dental MedicineBostonMA02215USA
| | | | | | - Zhichuan Zhu
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Alex W. Prevatte
- UNC Proteomics Core FacilityDepartment of PharmacologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Natalie K. Barker
- UNC Proteomics Core FacilityDepartment of PharmacologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Laura E. Herring
- UNC Proteomics Core FacilityDepartment of PharmacologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Ian J. Davis
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of GeneticsThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of PediatricsThe University of North Carolina at Chapel HillChapel HillNC 27599USA
| | - Pengda Liu
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
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12
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Panicker S, Venkatabalasubramanian S, Pathak S, Ramalingam S. The impact of fusion genes on cancer stem cells and drug resistance. Mol Cell Biochem 2021; 476:3771-3783. [PMID: 34095988 DOI: 10.1007/s11010-021-04203-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022]
Abstract
With ever increasing evidences on the role of fusion genes as the oncogenic protagonists in myriad cancers, it's time to explore if fusion genes can be the next generational drug targets in meeting the current demands of higher drug efficacy. Eliminating cancer stem cells (CSC) has become the current focus; however, we have reached a standstill in drug development owing to the lack of effective strategies to eradicate CSC. We believe that fusion genes could be the novel targets to overcome this limitation. The intriguing feature of fusion genes is that it dominantly impacts every aspect of CSC including self-renewal, differentiation, lineage commitment, tumorigenicity and stemness. Given the clinical success of fusion gene-based drugs in hematological cancers, our attempt to target fusion genes in eradicating CSC can be rewarding. As fusion genes are expressed explicitly in cancer cells, eradicating CSC by targeting fusion genes provides yet an another advantage of negligible patient side effects since normal cells remain unaffected by the drug. We hereby delineate the latest evidences on how fusion genes regulate CSC and drug resistance.
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Affiliation(s)
- Saurav Panicker
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kanchipuram, 603203, Tamil Nadu, India
| | | | - Surajit Pathak
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, Chennai, 603103, Tamil Nadu, India
| | - Satish Ramalingam
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kanchipuram, 603203, Tamil Nadu, India.
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13
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Kannan S, Lock I, Ozenberger BB, Jones KB. Genetic drivers and cells of origin in sarcomagenesis. J Pathol 2021; 254:474-493. [DOI: 10.1002/path.5617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/01/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Sarmishta Kannan
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
| | - Ian Lock
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
| | - Benjamin B Ozenberger
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
| | - Kevin B Jones
- Departments of Orthopaedics and Oncological Sciences Huntsman Cancer Institute, University of Utah School of Medicine Salt Lake City UT USA
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14
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To YH, Orme L, Lewin J. The Role of Systemic Therapies in the Management of Bone Sarcoma. Sarcoma 2021. [DOI: 10.1007/978-981-15-9414-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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15
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Martinez-Lage M, Torres-Ruiz R, Puig-Serra P, Moreno-Gaona P, Martin MC, Moya FJ, Quintana-Bustamante O, Garcia-Silva S, Carcaboso AM, Petazzi P, Bueno C, Mora J, Peinado H, Segovia JC, Menendez P, Rodriguez-Perales S. In vivo CRISPR/Cas9 targeting of fusion oncogenes for selective elimination of cancer cells. Nat Commun 2020; 11:5060. [PMID: 33033246 PMCID: PMC7544871 DOI: 10.1038/s41467-020-18875-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/16/2020] [Indexed: 12/16/2022] Open
Abstract
Fusion oncogenes (FOs) are common in many cancer types and are powerful drivers of tumor development. Because their expression is exclusive to cancer cells and their elimination induces cell apoptosis in FO-driven cancers, FOs are attractive therapeutic targets. However, specifically targeting the resulting chimeric products is challenging. Based on CRISPR/Cas9 technology, here we devise a simple, efficient and non-patient-specific gene-editing strategy through targeting of two introns of the genes involved in the rearrangement, allowing for robust disruption of the FO specifically in cancer cells. As a proof-of-concept of its potential, we demonstrate the efficacy of intron-based targeting of transcription factors or tyrosine kinase FOs in reducing tumor burden/mortality in in vivo models. The FO targeting approach presented here might open new horizons for the selective elimination of cancer cells.
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Affiliation(s)
- M Martinez-Lage
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - R Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain.
| | - P Puig-Serra
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - P Moreno-Gaona
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - M C Martin
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - F J Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - O Quintana-Bustamante
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
- Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - S Garcia-Silva
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - A M Carcaboso
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - P Petazzi
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - C Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - J Mora
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - H Peinado
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - J C Segovia
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
- Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - P Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys, 08010, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - S Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
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16
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Theisen ER, Selich-Anderson J, Miller KR, Tanner JM, Taslim C, Pishas KI, Sharma S, Lessnick SL. Chromatin profiling reveals relocalization of lysine-specific demethylase 1 by an oncogenic fusion protein. Epigenetics 2020; 16:405-424. [PMID: 32842875 PMCID: PMC7993145 DOI: 10.1080/15592294.2020.1805678] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Paediatric cancers commonly harbour quiet mutational landscapes and are instead characterized by single driver events such as the mutation of critical chromatin regulators, expression of oncohistones, or expression of oncogenic fusion proteins. These events ultimately promote malignancy through disruption of normal gene regulation and development. The driver protein in Ewing sarcoma, EWS/FLI, is an oncogenic fusion and transcription factor that reshapes the enhancer landscape, resulting in widespread transcriptional dysregulation. Lysine-specific demethylase 1 (LSD1) is a critical functional partner for EWS/FLI as inhibition of LSD1 reverses the transcriptional activity of EWS/FLI. However, how LSD1 participates in fusion-directed epigenomic regulation and aberrant gene activation is unknown. We now show EWS/FLI causes dynamic rearrangement of LSD1 and we uncover a role for LSD1 in gene activation through colocalization at EWS/FLI binding sites throughout the genome. LSD1 is integral to the establishment of Ewing sarcoma super-enhancers at GGAA-microsatellites, which ubiquitously overlap non-microsatellite loci bound by EWS/FLI. Together, we show that EWS/FLI induces widespread changes to LSD1 distribution in a process that impacts the enhancer landscape throughout the genome.
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Affiliation(s)
- Emily R Theisen
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Kyle R Miller
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Jason M Tanner
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Kathleen I Pishas
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Cancer Genomics and Genetics, Peter MacCallum Cancer Centre, Melbourne, VIC, USA
| | - Sunil Sharma
- Applied Cancer Research and Drug Discovery, Translational Genomics Research Institute (Tgen), Phoenix, AX, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Division of Pediatric Hematology/Oncology/Blood and Marrow Transplant, The Ohio State University, Columbus, OH, USA
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17
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Han C, Sun LY, Wang WT, Sun YM, Chen YQ. Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications. J Mol Cell Biol 2020; 11:886-898. [PMID: 31361891 PMCID: PMC6884712 DOI: 10.1093/jmcb/mjz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 12/25/2022] Open
Abstract
Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.
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Affiliation(s)
- Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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18
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García-Domínguez DJ, Hontecillas-Prieto L, León EA, Sánchez-Molina S, Rodríguez-Núñez P, Morón FJ, Hajji N, Mackintosh C, de Álava E. An inducible ectopic expression system of EWSR1-FLI1 as a tool for understanding Ewing sarcoma oncogenesis. PLoS One 2020; 15:e0234243. [PMID: 32502203 PMCID: PMC7274397 DOI: 10.1371/journal.pone.0234243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
The presence of the chimeric EWSR1-FLI1 oncoprotein is the main and initiating event defining Ewing sarcoma (ES). The dysregulation of epigenomic and proteomic homeostasis induced by the oncoprotein contributes to a wide variety of events involved in oncogenesis and tumor progression. Attempts at studying the effects of EWSR1-FLI1 in non-tumor cells to understand the mechanisms underlying sarcomagenesis have been unsuccessful to date, as ectopic expression of EWSR1-FLI1 blocks cell cycle progression and induces apoptosis in the tested cell lines. Therefore, it is essential to find a permissive cell type for EWSR1-FLI1 expression that allows its endogenous molecular functions to be studied. Here we have demonstrated that HeLa cell lines are permissive to EWSR1-FLI1 ectopic expression, and that our model substantially recapitulates the endogenous activity of the EWSR1-FLI1 fusion protein. This model could contribute to better understanding ES sarcomagenesis by helping to understand the molecular mechanisms induced by the EWSR1-FLI1 oncoprotein.
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Affiliation(s)
- Daniel J. García-Domínguez
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla/CIBERONC, Seville, Spain
- * E-mail: (DJGD); (EDA)
| | - Lourdes Hontecillas-Prieto
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla/CIBERONC, Seville, Spain
| | - Eduardo Andrés León
- Bioinformatics Unit, Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Sara Sánchez-Molina
- Developmental Tumor Biology Laboratory, Institut de Recerca Pediàtrica—Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Pablo Rodríguez-Núñez
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla/CIBERONC, Seville, Spain
| | - Francisco J. Morón
- Genomics Core Facility, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, Sevilla, Spain
| | - Nabil Hajji
- Division of Brain Sciences, The John Fulcher Molecular Neuro-Oncology Laboratory, Imperial College London, London, England, United Kingdom
| | | | - Enrique de Álava
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla/CIBERONC, Seville, Spain
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, Seville, Spain
- * E-mail: (DJGD); (EDA)
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19
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Cadena Castaneda D, Brachet G, Goupille C, Ouldamer L, Gouilleux-Gruart V. The neonatal Fc receptor in cancer FcRn in cancer. Cancer Med 2020; 9:4736-4742. [PMID: 32368865 PMCID: PMC7333860 DOI: 10.1002/cam4.3067] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/25/2022] Open
Abstract
Since the neonatal IgG Fc receptor (FcRn) was discovered, it was found to be involved in immunoglobulin recycling and biodistribution, immune complexes routing, antigen presentation, humoral immune response, and cancer immunosurveillance. The latest data show that FcRn plays a part in cancer pathophysiology. In various types of cancers, such as lung and colorectal cancer, FcRn has been described as an early marker for prognosis. Dysregulation of FcRn expression by cancer cells allows them to increase their metabolism, and this process could be exploited for passive targeting of cytotoxic drugs. However, the roles of this receptor depend on whether the studied cell population is the tumor tissue or the infiltrating cells, bringing forward the need for further studies.
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Affiliation(s)
| | | | - Caroline Goupille
- CHRU de Tours, Tours, France.,Université de Tours, INSERM, Tours, France
| | - Lobna Ouldamer
- CHRU de Tours, Tours, France.,Université de Tours, INSERM, Tours, France
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20
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Breakthrough Technologies Reshape the Ewing Sarcoma Molecular Landscape. Cells 2020; 9:cells9040804. [PMID: 32225029 PMCID: PMC7226764 DOI: 10.3390/cells9040804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022] Open
Abstract
Ewing sarcoma is a highly aggressive round cell mesenchymal neoplasm, most often occurring in children and young adults. At the molecular level, it is characterized by the presence of recurrent chromosomal translocations. In the last years, next-generation technologies have contributed to a more accurate diagnosis and a refined classification. Moreover, the application of these novel technologies has highlighted the relevance of intertumoral and intratumoral molecular heterogeneity and secondary genetic alterations. Furthermore, they have shown evidence that genomic features can change as the tumor disseminates and are influenced by treatment as well. Similarly, next-generation technologies applied to liquid biopsies will significantly impact patient management by allowing the early detection of relapse and monitoring response to treatment. Finally, the use of these novel technologies has provided data of great value in order to discover new druggable pathways. Thus, this review provides concise updates on the latest progress of these breakthrough technologies, underscoring their importance in the generation of key knowledge, prognosis, and potential treatment of Ewing Sarcoma.
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21
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Conn E, Hour S, Allegakoen D, Graham G, Petro J, Kouassi-Brou M, Hong SH, Selvanathan S, Çelik H, Toretsky J, Üren A. Development of an Ewing sarcoma cell line with resistance to EWS‑FLI1 inhibitor YK‑4‑279. Mol Med Rep 2020; 21:1667-1675. [PMID: 32016454 PMCID: PMC8371434 DOI: 10.3892/mmr.2020.10948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/28/2019] [Indexed: 01/01/2023] Open
Abstract
Despite Ewing sarcoma (ES) being the second most common pediatric malignancy of bone and soft tissue, few novel therapeutic approaches have been introduced over the past few decades. ES contains a pathognomonic chromosomal translocation that leads to a fusion protein between EWSR1 and an ets family member, most often FLI1. EWS‑FLI1 is the most common type of fusion protein and is a well‑vetted therapeutic target. A small molecule inhibitor of EWS‑FLI1, YK‑4‑279 (YK) was developed with the intention to serve as a targeted therapy option for patients with ES. The present study investigated resistance mechanisms by developing an ES cell line specifically resistant to YK. The ES cell line A4573 was treated with YK to create resistant cells by long term continuous exposure. The results revealed that resistance in A4573 was robust and sustainable, with a >27‑fold increase in IC50 lasting up to 16 weeks in the absence of the compound. Resistant ES cells were still sensitive to standard of care drugs, including doxorubicin, vincristine and etoposide, which may be valuable in future combination treatments in the clinic. Resistant ES cells revealed an increased expression of CD99. RNA sequencing and qPCR validation of resistant ES cells confirmed an increased expression of ANO1, BRSK2 and IGSF21, and a reduced expression of COL24A1, PRSS23 and RAB38 genes. A functional association between these genes and mechanism of resistance remains to be investigated. The present study created a cell line to investigate YK resistance.
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Affiliation(s)
- Erin Conn
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Sarah Hour
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - David Allegakoen
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Garrett Graham
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Jeff Petro
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Marilyn Kouassi-Brou
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Sung Hyeok Hong
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Saravana Selvanathan
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Haydar Çelik
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Jeffrey Toretsky
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Aykut Üren
- Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
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22
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Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2020; 578:102-111. [PMID: 32025015 PMCID: PMC7054214 DOI: 10.1038/s41586-020-1965-x] [Citation(s) in RCA: 342] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 12/02/2019] [Indexed: 01/28/2023]
Abstract
The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
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Affiliation(s)
- Esther Rheinbay
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Morten Muhlig Nielsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | | | - Jeremiah A Wala
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA
| | - Ofer Shapira
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Grace Tiao
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Henrik Hornshøj
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Julian M Hess
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Randi Istrup Juul
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Ziao Lin
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard University, Cambridge, MA, USA
| | - Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Radhakrishnan Sabarinathan
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tobias Madsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Loris Mularoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Shimin Shuai
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Andrés Lanzós
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Carl Herrmann
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bioquant Center, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Yosef E Maruvka
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Ciyue Shen
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- cBio Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Samirkumar B Amin
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Pratiti Bandopadhayay
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johanna Bertl
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Keith A Boroevich
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - John Busanovich
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joana Carlevaro-Fita
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Dimple Chakravarty
- Department of Genitourinary Medical Oncology - Research, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Urology, Icahn school of Medicine at Mount Sinai, New York, NY, USA
| | - Calvin Wing Yiu Chan
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - David Craft
- Department of Radiation Oncology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Priyanka Dhingra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Klev Diamanti
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Nuno A Fonseca
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Qianyun Guo
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Mark P Hamilton
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nicholas J Haradhvala
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Chen Hong
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Keren Isaev
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Todd A Johnson
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Malene Juul
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Andre Kahles
- Division of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abdullah Kahraman
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Youngwook Kim
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jan Komorowski
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Kiran Kumar
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sushant Kumar
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Donghoon Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Kjong-Van Lehmann
- Division of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yilong Li
- SBGD Inc, Cambridge, MA, USA
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eric Minwei Liu
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lucas Lochovsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Keunchil Park
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicola D Roberts
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Gordon Saksena
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven E Schumacher
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikos Sidiropoulos
- Biotech Research & Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lina Sieverling
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | | | - Chip Stewart
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Tamborero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jose M C Tubio
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo, Spain
| | - Husen M Umer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Liis Uusküla-Reimand
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Ontario, Canada
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lina Wadi
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Cheng-Zhong Zhang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jing Zhang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | - Asger Hobolth
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, and Englander Institute for Precision Medicine, and Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Manolis Kellis
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Michael S Lawrence
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Chris Sander
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- cBio Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Lincoln D Stein
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Joshua M Stuart
- Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Rory Johnson
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Ekta Khurana
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Rameen Beroukhim
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | | | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark.
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark.
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
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23
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Neckles C, Boer RE, Aboreden N, Cross AM, Walker RL, Kim BH, Kim S, Schneekloth JS, Caplen NJ. HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction. RNA (NEW YORK, N.Y.) 2019; 25:1731-1750. [PMID: 31511320 PMCID: PMC6859848 DOI: 10.1261/rna.072454.119] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/08/2019] [Indexed: 05/05/2023]
Abstract
The primary oncogenic event in ∼85% of Ewing sarcomas is a chromosomal translocation that generates a fusion oncogene encoding an aberrant transcription factor. The exact genomic breakpoints within the translocated genes, EWSR1 and FLI1, vary; however, in EWSR1, breakpoints typically occur within introns 7 or 8. We previously found that in Ewing sarcoma cells harboring EWSR1 intron 8 breakpoints, the RNA-binding protein HNRNPH1 facilitates a splicing event that excludes EWSR1 exon 8 from the EWS-FLI1 pre-mRNA to generate an in-frame mRNA. Here, we show that the processing of distinct EWS-FLI1 pre-mRNAs by HNRNPH1, but not other homologous family members, resembles alternative splicing of transcript variants of EWSR1 We demonstrate that HNRNPH1 recruitment is driven by guanine-rich sequences within EWSR1 exon 8 that have the potential to fold into RNA G-quadruplex structures. Critically, we demonstrate that an RNA mimetic of one of these G-quadruplexes modulates HNRNPH1 binding and induces a decrease in the growth of an EWSR1 exon 8 fusion-positive Ewing sarcoma cell line. Finally, we show that EWSR1 exon 8 fusion-positive cell lines are more sensitive to treatment with the pan-quadruplex binding molecule, pyridostatin (PDS), than EWSR1 exon 8 fusion-negative lines. Also, the treatment of EWSR1 exon 8 fusion-positive cells with PDS decreases EWS-FLI1 transcriptional activity, reversing the transcriptional deregulation driven by EWS-FLI1. Our findings illustrate that modulation of the alternative splicing of EWS-FLI1 pre-mRNA is a novel strategy for future therapeutics against the EWSR1 exon 8 containing fusion oncogenes present in a third of Ewing sarcoma.
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Affiliation(s)
- Carla Neckles
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Robert E Boer
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Nicholas Aboreden
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Allison M Cross
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Robert L Walker
- Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Bong-Hyun Kim
- CCR Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702, USA
| | - Suntae Kim
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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24
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Andersson MK, Åman P, Stenman G. IGF2/IGF1R Signaling as a Therapeutic Target in MYB-Positive Adenoid Cystic Carcinomas and Other Fusion Gene-Driven Tumors. Cells 2019; 8:cells8080913. [PMID: 31426421 PMCID: PMC6721700 DOI: 10.3390/cells8080913] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 12/12/2022] Open
Abstract
Chromosome rearrangements resulting in pathogenetically important gene fusions are a common feature of many cancers. They are often potent oncogenic drivers and have key functions in central cellular processes and pathways and encode transcription factors, transcriptional co-regulators, growth factor receptors, tyrosine kinases, and chromatin modifiers. In addition to being useful diagnostic biomarkers, they are also targets for development of new molecularly targeted therapies. Studies in recent decades have shown that several oncogenic gene fusions interact with the insulin-like growth factor (IGF) signaling pathway. For example, the MYB-NFIB fusion in adenoid cystic carcinoma is regulated by IGF1R through an autocrine loop, and IGF1R is a downstream target of the EWSR1-WT1 and PAX3-FKHR fusions in desmoplastic small round cell tumors and alveolar rhabdomyosarcoma, respectively. Here, we will discuss the mechanisms behind the interactions between oncogenic gene fusions and the IGF signaling pathway. We will also discuss the role of therapeutic inhibition of IGF1R in fusion gene driven malignancies.
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Affiliation(s)
- Mattias K Andersson
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, 405 30 Gothenburg, Sweden.
| | - Pierre Åman
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Göran Stenman
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, 405 30 Gothenburg, Sweden
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25
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A Gammaherpesvirus MicroRNA Targets EWSR1 (Ewing Sarcoma Breakpoint Region 1) In Vivo To Promote Latent Infection of Germinal Center B Cells. mBio 2019; 10:mBio.00996-19. [PMID: 31363027 PMCID: PMC6667617 DOI: 10.1128/mbio.00996-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV), directly contribute to the genesis of multiple types of malignancies. In vivo, these viruses infect B cells and manipulate B cell biology to establish lifelong infection. To accomplish this, gammaherpesviruses employ an array of gene products, including miRNAs, short noncoding RNAs that bind to and repress protein synthesis from specific target mRNAs. The in vivo relevance of repression of targets of gammaherpesvirus miRNAs remains highly elusive. Here, we identified a murine gammaherpesvirus miRNA as critical for in vivo infection and validated the host mRNA EWSR1 (Ewing sarcoma breakpoint region 1) as the predominant target for this miRNA. Using a novel technology, we demonstrated that repression of EWSR1 was essential for in vivo infection of the critical B cell reservoir. These findings provide the first in vivo demonstration of the significance of repression of a specific host mRNA by a gammaherpesvirus miRNA. Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), directly contribute to the genesis of multiple types of malignancies, including B cell lymphomas. In vivo, these viruses infect B cells and manipulate B cell biology to establish lifelong latent infection. To accomplish this, gammaherpesviruses employ an array of gene products, including microRNAs (miRNAs). Although numerous host mRNA targets of gammaherpesvirus miRNAs have been identified, the in vivo relevance of repression of these targets remains elusive due to species restriction. Murine gammaherpesvirus 68 (MHV68) provides a robust virus-host system to dissect the in vivo function of conserved gammaherpesvirus genetic elements. We identified here MHV68 mghv-miR-M1-7-5p as critical for in vivo infection and then validated host EWSR1 (Ewing sarcoma breakpoint region 1) as the predominant target for this miRNA. Using novel, target-specific shRNA-expressing viruses, we determined that EWSR1 repression in vivo was essential for germinal center B cell infection. These findings provide the first in vivo demonstration of the biological significance of repression of a specific host mRNA by a gammaherpesvirus miRNA.
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26
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Okimoto RA, Wu W, Nanjo S, Olivas V, Lin YK, Ponce RK, Oyama R, Kondo T, Bivona TG. CIC-DUX4 oncoprotein drives sarcoma metastasis and tumorigenesis via distinct regulatory programs. J Clin Invest 2019; 129:3401-3406. [PMID: 31329165 DOI: 10.1172/jci126366] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Abstract
Transcription factor fusion genes create oncoproteins that drive oncogenesis and represent challenging therapeutic targets. Understanding the molecular targets by which such fusion oncoproteins promote malignancy offers an approach to develop rational treatment strategies to improve clinical outcomes. Capicua-double homeobox 4 (CIC-DUX4) is a transcription factor fusion oncoprotein that defines certain undifferentiated round cell sarcomas with high metastatic propensity and poor clinical outcomes. The molecular targets regulated by the CIC-DUX4 oncoprotein that promote this aggressive malignancy remain largely unknown. We demonstrated that increased expression of ETS variant 4 (ETV4) and cyclin E1 (CCNE1) occurs via neomorphic, direct effects of CIC-DUX4 and drives tumor metastasis and survival, respectively. We uncovered a molecular dependence on the CCNE-CDK2 cell cycle complex that renders CIC-DUX4-expressing tumors sensitive to inhibition of the CCNE-CDK2 complex, suggesting a therapeutic strategy for CIC-DUX4-expressing tumors. Our findings highlight a paradigm of functional diversification of transcriptional repertoires controlled by a genetically aberrant transcriptional regulator, with therapeutic implications.
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Affiliation(s)
- Ross A Okimoto
- Department of Medicine.,Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | | | | | | | | | | | - Rieko Oyama
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Trever G Bivona
- Department of Medicine.,Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA.,Cellular and Molecular Pharmacology, UCSF, San Francisco, California, USA
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27
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Kang J, Lim L, Lu Y, Song J. A unified mechanism for LLPS of ALS/FTLD-causing FUS as well as its modulation by ATP and oligonucleic acids. PLoS Biol 2019; 17:e3000327. [PMID: 31188823 PMCID: PMC6590835 DOI: 10.1371/journal.pbio.3000327] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 06/24/2019] [Accepted: 05/30/2019] [Indexed: 12/22/2022] Open
Abstract
526-residue Fused in sarcoma (FUS) undergoes liquid-liquid phase separation (LLPS) for its functions, which can further transit into pathological aggregation. ATP and nucleic acids, the universal cellular actors, were shown to modulate LLPS of FUS in a unique manner: enhancement and then dissolution. Currently, the driving force for LLPS of FUS is still under debate, while the mechanism for the modulation remains completely undefined. Here, by NMR and differential interference contrast (DIC) imaging, we characterized conformations, dynamics, and LLPS of FUS and its domains and subsequently their molecular interactions with oligonucleic acids, including one RNA and two single-stranded DNA (ssDNA) molecules, as well as ATP, Adenosine monophosphate (AMP), and adenosine. The results reveal 1) both a prion-like domain (PLD) rich in Tyr but absent of Arg/Lys and a C-terminal domain (CTD) abundant in Arg/Lys fail to phase separate. By contrast, the entire N-terminal domain (NTD) containing the PLD and an Arg-Gly (RG)-rich region efficiently phase separate, indicating that the π-cation interaction is the major driving force; 2) despite manifesting distinctive NMR observations, ATP has been characterized to modulate LLPS by specific binding as oligonucleic acids but with much lower affinity. Our results together establish a unified mechanism in which the π-cation interaction acts as the major driving force for LLPS of FUS and also serves as the target for modulation by ATP and oligonucleic acids through specific binding. This mechanism predicts that a myriad of proteins unrelated to RNA-binding proteins (RBPs) but with Arg/Lys-rich disordered regions could be modulated by ATP and nucleic acids, thus rationalizing the pathological association of Amyotrophic lateral sclerosis (ALS)-causing C9ORF72 dipeptides with any nucleic acids to manifest cytotoxicity.
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Affiliation(s)
- Jian Kang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Yimei Lu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
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28
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Abstract
Among the various genes that can be rearranged in soft tissue neoplasms associated with nonrandom chromosomal translocations, EWSR1 is the most frequent one to partner with other genes to generate recurrent fusion genes. This leads to a spectrum of clinically and pathologically diverse mesenchymal and nonmesenchymal neoplasms, variably manifesting as small round cell, spindle cell, clear cell or adipocytic tumors, or tumors with distinctive myxoid stroma. This review summarizes the growing list of mesenchymal neoplasms that are associated with EWSR1 gene rearrangements.
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Affiliation(s)
- Khin Thway
- Sarcoma Unit, Royal Marsden Hospital, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK.
| | - Cyril Fisher
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital NHS Foundation Trust, Robert Aitken Institute for Clinical Research, University of Birmingham, Birmingham B15 2TT, UK
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29
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PET-CT imaging features that differentiate between positive and negative EWSR1 translocation in Ewing sarcoma. Nucl Med Commun 2019; 40:827-834. [PMID: 31107830 DOI: 10.1097/mnm.0000000000001031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Ewing sarcoma breakpoint region 1 (EWSR1) translocation-negative tumors represent a minor portion of small round cell tumors consistent with Ewing sarcoma morphology. The purpose of this study was to differentiate EWSR1 translocation-positive tumors from EWSR1 translocation-negative tumors using PET-computed tomography features. MATERIALS AND METHODS In this retrospective study 27, Ewing sarcoma patients (December 2011 to November 2016) were divided into two groups, EWSR1 translocation-positive and EWSR1 translocation-negative based on cytogenetic analysis. Pretreatment standardized uptake value maximum (SUVmax) and Hounsfield Units (HU) were measured in the primary tumor in the axial slice with the largest tumor diameter.The associations between SUVmax, HU and the presence of EWSR1 translocation were evaluated. Receiver operating characteristic curve analysis was used to determine cut-off levels of SUVmax and HU suggestive of EWSR1-negative tumors. RESULTS Twenty-one patients were classified as EWSR1-positive and six as EWSR1-negative. Eighteen had SUVmax and 21 had HU measurements. EWSR1-negative tumors had significantly higher SUVmax values (P = 0.003) and significantly lower HU values (P = 0.008). Receiver operating characteristic curve analysis showed that SUVmax had diagnostic ability to discriminate between EWSR1-negative and EWSR1-positive tumors (area under the curve = 0.964, P = 0.006). A SUVmax of at least 10 had a sensitivity of 100% and specificity of 85.7% for EWSR1-negative tumors. HU had lower diagnostic ability than SUVmax (area under the curve = 0.881, P = 0.012). A HU up to 57 had a sensitivity of 81.3% and specificity of 80.0% for EWSR1-negative tumors. CONCLUSION Higher SUVmax and lower HU may differentiate between EWSR1-positive and EWSR1-negative tumors. This may reflect EWSR1-negative tumor aggressiveness.
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30
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Theisen ER, Miller KR, Showpnil IA, Taslim C, Pishas KI, Lessnick SL. Transcriptomic analysis functionally maps the intrinsically disordered domain of EWS/FLI and reveals novel transcriptional dependencies for oncogenesis. Genes Cancer 2019; 10:21-38. [PMID: 30899417 PMCID: PMC6420793 DOI: 10.18632/genesandcancer.188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
EWS/FLI is the pathognomic fusion oncoprotein that drives Ewing sarcoma. The amino-terminal EWS portion coordinates transcriptional regulation and the carboxy-terminal FLI portion contains an ETS DNA-binding domain. EWS/FLI acts as an aberrant transcription factor, orchestrating a complex mix of gene activation and repression, from both high affinity ETS motifs and repetitive GGAA-microsatellites. Our overarching hypothesis is that executing multi-faceted transcriptional regulation requires EWS/FLI to use distinct molecular mechanisms at different loci. Many attempts have been made to map distinct functions to specific features of the EWS domain, but described deletion mutants are either fully active or completely "dead" and other approaches have been limited by the repetitive and disordered nature of the EWS domain. Here, we use transcriptomic approaches to show an EWS/FLI mutant, called DAF, previously thought to be nonfunctional, displays context-dependent and partial transcriptional activity but lacks transforming capacity. Using transcriptomic and phenotypic anchorage-independent growth profiles of other EWS/FLI mutants coupled with reported EWS/FLI localization data, we have mapped the critical structure-function requirements of the EWS domain for EWS/FLI-mediated oncogenesis. This approach defined unique classes of EWS/FLI response elements and revealed novel structure-function relationships required for EWS/FLI activation at these response elements.
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Affiliation(s)
- Emily R Theisen
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Kyle R Miller
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Iftekhar A Showpnil
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH, USA
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Kathleen I Pishas
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH, USA.,Division of Pediatric Hematology/Oncology/Blood & Marrow Transplant, The Ohio State University, Columbus, OH, USA
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31
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Myelolytic Treatments Enhance Oncolytic Herpes Virotherapy in Models of Ewing Sarcoma by Modulating the Immune Microenvironment. MOLECULAR THERAPY-ONCOLYTICS 2018; 11:62-74. [PMID: 30505937 PMCID: PMC6249791 DOI: 10.1016/j.omto.2018.10.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/13/2018] [Indexed: 12/27/2022]
Abstract
Ewing sarcoma is a highly aggressive cancer that promotes the infiltration and activation of pro-tumor M2-like macrophages. Oncolytic virotherapy that selectively infects and destroys cancer cells is a promising option for treating Ewing sarcoma. The effect of tumor macrophages on oncolytic virus therapy, however, is variable among solid tumors and is unknown in Ewing sarcoma. We tested the effects of macrophage reduction using liposomal clodronate (Clodrosome) and trabectedin on the antitumor efficacy of intratumoral oncolytic herpes simplex virus, rRp450, in two Ewing sarcoma xenograft models. Both agents enhanced antitumor efficacy without increasing virus replication. The most profound effects were in A673 with only a transient effect on response rates in TC71. Interestingly, A673 was more dependent than TC71 on macrophages for its tumorigenesis. We found Clodrosome and virus together induced expression of antitumorigenic genes and reduced expression of protumorigenic genes in both the tumor-associated macrophages and the overall tumor stroma. Trabectedin reduced intratumoral natural killer (NK) cells, myeloid-derived suppressor cells, and M2-like macrophages, and prevented their increase following virotherapy. Our data suggest that a combination of trabectedin and oncolytic herpes virotherapy warrants testing in the clinical setting.
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32
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Namatame N, Tamaki N, Yoshizawa Y, Okamura M, Nishimura Y, Yamazaki K, Tanaka M, Nakamura T, Semba K, Yamori T, Yaguchi SI, Dan S. Antitumor profile of the PI3K inhibitor ZSTK474 in human sarcoma cell lines. Oncotarget 2018; 9:35141-35161. [PMID: 30416685 PMCID: PMC6205545 DOI: 10.18632/oncotarget.26216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/26/2018] [Indexed: 11/25/2022] Open
Abstract
Treatment of patients with advanced sarcoma remains challenging due to lack of effective medicine, with the development of novel drugs being of keen interest. A pan-PI3K inhibitor, ZSTK474, has been evaluated in clinical trials against a range of advanced solid tumors, with clinical benefit shown in sarcoma patients. In the present study, we developed a panel of 14 human sarcoma cell lines and investigated the antitumor effect of 24 anticancer agents including ZSTK474, other PI3K inhibitors, and those clinically used for sarcoma treatment. ZSTK474 exhibited a similar antiproliferative profile to other PI3K inhibitors but was clearly different from the other drugs examined. Indeed, ZSTK474 inhibited PI3K-downstream pathways, in parallel to growth inhibition, in all cell lines examined, showing proof-of-concept of PI3K inhibition. In addition, ZSTK474 induced apoptosis selectively in Ewing's sarcoma (RD-ES and A673), alveolar rhabdomyosarcoma (SJCRH30) and synovial sarcoma (SYO-1, Aska-SS and Yamato-SS) cell lines, all of which harbor chromosomal translocation and resulting oncogenic fusion genes, EWSR1-FLI1, PAX3-FOXO1 and SS18-SSX, respectively. Finally, animal experiments confirmed the antitumor activity of ZSTK474 in vivo, with superior efficacy observed in translocation-positive cells. These results suggest that ZSTK474 could be a promising drug candidate for treating sarcomas, especially those harboring chromosomal translocation.
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Affiliation(s)
- Nachi Namatame
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,R&D Center, Zenyaku Kogyo Co. Ltd, Tokyo, Japan
| | - Naomi Tamaki
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuya Yoshizawa
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mutsumi Okamura
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yumiko Nishimura
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kanami Yamazaki
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Miwa Tanaka
- Division of Carcinogenesis, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takuro Nakamura
- Division of Carcinogenesis, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Takao Yamori
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Present address: Center for Product Evaluation, Pharmaceuticals and Medical Devices Agency, Tokyo, Japan
| | - Shin-Ichi Yaguchi
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,R&D Center, Zenyaku Kogyo Co. Ltd, Tokyo, Japan
| | - Shingo Dan
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
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33
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Lui GYL, Grandori C, Kemp CJ. CDK12: an emerging therapeutic target for cancer. J Clin Pathol 2018; 71:957-962. [PMID: 30104286 DOI: 10.1136/jclinpath-2018-205356] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 12/20/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12) belongs to the cyclin-dependent kinase (CDK) family of serine/threonine protein kinases that regulate transcriptional and post-transcriptional processes, thereby modulating multiple cellular functions. Early studies characterised CDK12 as a transcriptional CDK that complexes with cyclin K to mediate gene transcription by phosphorylating RNA polymerase II. CDK12 has been demonstrated to specifically upregulate the expression of genes involved in response to DNA damage, stress and heat shock. More recent studies have implicated CDK12 in regulating mRNA splicing, 3' end processing, pre-replication complex assembly and genomic stability during embryonic development. Genomic alterations in CDK12 have been detected in oesophageal, stomach, breast, endometrial, uterine, ovarian, bladder, colorectal and pancreatic cancers, ranging from 5% to 15% of sequenced cases. An increasing number of studies point to CDK12 inhibition as an effective strategy to inhibit tumour growth, and synthetic lethal interactions have been described with MYC, EWS/FLI and PARP/CHK1 inhibition. Herein, we discuss the present literature on CDK12 in cell function and human cancer, highlighting important roles for CDK12 as a clinical biomarker for treatment response and potential as an effective therapeutic target.
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Affiliation(s)
- Goldie Y L Lui
- Fred Hutchinson Cancer Research Center, Human Biology Division, Seattle, Washington, USA
| | | | - Christopher J Kemp
- Fred Hutchinson Cancer Research Center, Human Biology Division, Seattle, Washington, USA
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34
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Yoon Y, Park H, Kim S, Nguyen PT, Hyeon SJ, Chung S, Im H, Lee J, Lee SB, Ryu H. Genetic Ablation of EWS RNA Binding Protein 1 (EWSR1) Leads to Neuroanatomical Changes and Motor Dysfunction in Mice. Exp Neurobiol 2018; 27:103-111. [PMID: 29731676 PMCID: PMC5934541 DOI: 10.5607/en.2018.27.2.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 12/23/2022] Open
Abstract
A recent study reveals that missense mutations of EWSR1 are associated with neurodegenerative disorders such as amyotrophic lateral sclerosis, but the function of wild-type (WT) EWSR1 in the central nervous system (CNS) is not known yet. Herein, we investigated the neuroanatomical and motor function changes in Ewsr1 knock out (KO) mice. First, we quantified neuronal nucleus size in the motor cortex, dorsal striatum and hippocampus of three different groups: WT, heterozygous Ewsr1 KO (+/−), and homozygous Ewsr1 KO (−/−) mice. The neuronal nucleus size was significantly smaller in the motor cortex and striatum of homozygous Ewsr1 KO (−/−) mice than that of WT. In addition, in the hippocampus, the neuronal nucleus size was significantly smaller in both heterozygous Ewsr1 KO (+/−) and homozygous Ewsr1 KO (−/−) mice. We then assessed motor function of Ewsr1 KO (−/−) and WT mice by a tail suspension test. Both forelimb and hindlimb movements were significantly increased in Ewsr1 KO (−/−) mice. Lastly, we performed immunohistochemistry to examine the expression of TH, DARPP-32, and phosphorylated (p)-DARPP-32 (Thr75) in the striatum and substantia nigra, which are associated with dopaminergic signaling. The immunoreactivity of TH and DARPP-32 was decreased in Ewsr1 KO (−/−) mice. Together, our results suggest that EWSR1 plays a significant role in neuronal morphology, dopaminergic signaling pathways, and motor function in the CNS of mice.
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Affiliation(s)
- Yeojun Yoon
- Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hasang Park
- Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sangyeon Kim
- Yonsei University College of Medicine, Seoul 03722, Korea
| | - Phuong T Nguyen
- Center for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Seung Jae Hyeon
- Center for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Sooyoung Chung
- Center for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Hyeonjoo Im
- Center for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Junghee Lee
- VA Boston Healthcare System, Boston, MA 02130, USA.,Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sean Bong Lee
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Hoon Ryu
- Center for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea.,VA Boston Healthcare System, Boston, MA 02130, USA.,Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
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35
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Tsafou K, Tiwari PB, Forman-Kay JD, Metallo SJ, Toretsky JA. Targeting Intrinsically Disordered Transcription Factors: Changing the Paradigm. J Mol Biol 2018; 430:2321-2341. [PMID: 29655986 DOI: 10.1016/j.jmb.2018.04.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/21/2018] [Accepted: 04/05/2018] [Indexed: 12/21/2022]
Abstract
Increased understanding of intrinsically disordered proteins (IDPs) and protein regions has revolutionized our view of the relationship between protein structure and function. Data now support that IDPs can be functional in the absence of a single, fixed, three-dimensional structure. Due to their dynamic morphology, IDPs have the ability to display a range of kinetics and affinity depending on what the system requires, as well as the potential for large-scale association. Although several studies have shed light on the functional properties of IDPs, the class of intrinsically disordered transcription factors (TFs) is still poorly characterized biophysically due to their combination of ordered and disordered sequences. In addition, TF modulation by small molecules has long been considered a difficult or even impossible task, limiting functional probe development. However, with evolving technology, it is becoming possible to characterize TF structure-function relationships in unprecedented detail and explore avenues not available or not considered in the past. Here we provide an introduction to the biophysical properties of intrinsically disordered TFs and we discuss recent computational and experimental efforts toward understanding the role of intrinsically disordered TFs in biology and disease. We describe a series of successful TF targeting strategies that have overcome the perception of the "undruggability" of TFs, providing new leads on drug development methodologies. Lastly, we discuss future challenges and opportunities to enhance our understanding of the structure-function relationship of intrinsically disordered TFs.
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Affiliation(s)
- K Tsafou
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - P B Tiwari
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - J D Forman-Kay
- Molecular Medicine, The Hospital for Sick Children, Toronto M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto M5G 1X8, Canada
| | - S J Metallo
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - J A Toretsky
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA.
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36
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Minas TZ, Surdez D, Javaheri T, Tanaka M, Howarth M, Kang HJ, Han J, Han ZY, Sax B, Kream BE, Hong SH, Çelik H, Tirode F, Tuckermann J, Toretsky JA, Kenner L, Kovar H, Lee S, Sweet-Cordero EA, Nakamura T, Moriggl R, Delattre O, Üren A. Combined experience of six independent laboratories attempting to create an Ewing sarcoma mouse model. Oncotarget 2018; 8:34141-34163. [PMID: 27191748 PMCID: PMC5470957 DOI: 10.18632/oncotarget.9388] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 05/05/2016] [Indexed: 12/17/2022] Open
Abstract
Ewing sarcoma (ES) involves a tumor-specific chromosomal translocation that produces the EWS-FLI1 protein, which is required for the growth of ES cells both in vitro and in vivo. However, an EWS-FLI1-driven transgenic mouse model is not currently available. Here, we present data from six independent laboratories seeking an alternative approach to express EWS-FLI1 in different murine tissues. We used the Runx2, Col1a2.3, Col1a3.6, Prx1, CAG, Nse, NEFL, Dermo1, P0, Sox9 and Osterix promoters to target EWS-FLI1 or Cre expression. Additional approaches included the induction of an endogenous chromosomal translocation, in utero knock-in, and the injection of Cre-expressing adenovirus to induce EWS-FLI1 expression locally in multiple lineages. Most models resulted in embryonic lethality or developmental defects. EWS-FLI1-induced apoptosis, promoter leakiness, the lack of potential cofactors, and the difficulty of expressing EWS-FLI1 in specific sites were considered the primary reasons for the failed attempts to create a transgenic mouse model of ES.
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Affiliation(s)
- Tsion Zewdu Minas
- Department of Oncology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Didier Surdez
- Genetics and Biology of Cancers Unit, Institut Curie Research Center, PSL Research University, Île-de-France, Paris, France.,INSERM U830, Institut Curie Research Center, Île-de-France, Paris, France
| | | | - Miwa Tanaka
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Michelle Howarth
- Division of Hematology and Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Hong-Jun Kang
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States of America
| | - Jenny Han
- Department of Oncology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Zhi-Yan Han
- Genetics and Biology of Cancers Unit, Institut Curie Research Center, PSL Research University, Île-de-France, Paris, France.,INSERM U830, Institut Curie Research Center, Île-de-France, Paris, France
| | - Barbara Sax
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
| | - Barbara E Kream
- Department of Medicine, and Genetics and Genome Sciences, University of Connecticut Health Science Center, Farmington, CT, United States of America
| | - Sung-Hyeok Hong
- Department of Oncology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Haydar Çelik
- Department of Oncology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Franck Tirode
- Genetics and Biology of Cancers Unit, Institut Curie Research Center, PSL Research University, Île-de-France, Paris, France.,INSERM U830, Institut Curie Research Center, Île-de-France, Paris, France
| | - Jan Tuckermann
- Institute of Comparative Molecular Endocrinology (CME), University of Ulm, Ulm, Germany
| | - Jeffrey A Toretsky
- Department of Oncology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Lukas Kenner
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria.,Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria.,Department of Pathology of Laboratory Animals (UPLA), University of Veterinary Medicine, Vienna, Austria
| | - Heinrich Kovar
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria.,Children´s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Sean Lee
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States of America
| | - E Alejandro Sweet-Cordero
- Division of Hematology and Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Takuro Nakamura
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Richard Moriggl
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria.,Medical University of Vienna, Vienna, Austria
| | - Olivier Delattre
- Genetics and Biology of Cancers Unit, Institut Curie Research Center, PSL Research University, Île-de-France, Paris, France.,INSERM U830, Institut Curie Research Center, Île-de-France, Paris, France.,Unité de génétique somatique, Institut Curie, Île-de-France, Paris, France
| | - Aykut Üren
- Department of Oncology, Georgetown University Medical Center, Washington, DC, United States of America
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Abstract
PURPOSE OF REVIEW Building upon preclinical advances, we are uncovering immunotherapy strategies that are translating into improved outcomes in tumor subsets. Advanced pediatric solid tumors carry poor prognoses and resultant robust efforts to apply immunotherapy advances to pediatric solid tumors are in progress. Here, we discuss recent developments in the field using mAb and mAb-based therapies including checkpoint blockade and chimeric antigen receptors (CARs). RECENT FINDINGS The pediatric solid tumor mAb experience targeting the diganglioside, GD2, for patients with neuroblastoma has been the most compelling to date. GD2 and alternative antigen-specific mAbs are now being incorporated into antibody-drug conjugates, bispecific antibodies and CARs for treatment of solid tumors. CARs in pediatric solid tumors have not yet achieved comparative responses to the hematologic CAR experience; however, novel strategies such as bispecific targeting, intratumoral administration and improved understanding of T-cell biology may yield enhanced CAR-efficacy. Therapeutic effect using single-agent checkpoint blocking antibodies in pediatric solid tumors also remains limited to date. Combinatorial strategies continue to hold promise and the clinical effect in tumor subsets with high antigenic burden is being explored. SUMMARY Pediatric immunotherapy remains at early stages of translation, yet we anticipate that with advanced technology, we will achieve widespread, efficacious use of immunotherapy for pediatric solid tumors.
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Jacques C, Lamoureux F, Baud'huin M, Rodriguez Calleja L, Quillard T, Amiaud J, Tirode F, Rédini F, Bradner JE, Heymann D, Ory B. Targeting the epigenetic readers in Ewing sarcoma inhibits the oncogenic transcription factor EWS/Fli1. Oncotarget 2018; 7:24125-40. [PMID: 27006472 PMCID: PMC5029689 DOI: 10.18632/oncotarget.8214] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/02/2016] [Indexed: 11/25/2022] Open
Abstract
Ewing Sarcoma is a rare bone and soft tissue malignancy affecting children and young adults. Chromosomal translocations in this cancer produce fusion oncogenes as characteristic molecular signatures of the disease. The most common case is the translocation t (11; 22) (q24;q12) which yields the EWS-Fli1 chimeric transcription factor. Finding a way to directly target EWS-Fli1 remains a central therapeutic approach to eradicate this aggressive cancer. Here we demonstrate that treating Ewing Sarcoma cells with JQ1(+), a BET bromodomain inhibitor, represses directly EWS-Fli1 transcription as well as its transcriptional program. Moreover, the Chromatin Immuno Precipitation experiments demonstrate for the first time that these results are a consequence of the depletion of BRD4, one of the BET bromodomains protein from the EWS-Fli1 promoter. In vitro, JQ1(+) treatment reduces the cell viability, impairs the cell clonogenic and the migratory abilities, and induces a G1-phase blockage as well as a time- and a dose-dependent apoptosis. Furthermore, in our in vivo model, we observed a tumor burden delay, an inhibition of the global vascularization and an increase of the mice overall survival. Taken together, our data indicate that inhibiting the BET bromodomains interferes with EWS-FLi1 transcription and could be a promising strategy in the Ewing tumors context.
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Affiliation(s)
- Camille Jacques
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | - François Lamoureux
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | - Marc Baud'huin
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France.,Nantes University Hospital, Nantes, France
| | - Lidia Rodriguez Calleja
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | - Thibaut Quillard
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | - Jérôme Amiaud
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | | | - Françoise Rédini
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Dominique Heymann
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France.,Nantes University Hospital, Nantes, France
| | - Benjamin Ory
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
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Lee T, Pelletier J. The biology of DHX9 and its potential as a therapeutic target. Oncotarget 2018; 7:42716-42739. [PMID: 27034008 PMCID: PMC5173168 DOI: 10.18632/oncotarget.8446] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
DHX9 is member of the DExD/H-box family of helicases with a “DEIH” sequence at its eponymous DExH-box motif. Initially purified from human and bovine cells and identified as a homologue of the Drosophila Maleless (MLE) protein, it is an NTP-dependent helicase consisting of a conserved helicase core domain, two double-stranded RNA-binding domains at the N-terminus, and a nuclear transport domain and a single-stranded DNA-binding RGG-box at the C-terminus. With an ability to unwind DNA and RNA duplexes, as well as more complex nucleic acid structures, DHX9 appears to play a central role in many cellular processes. Its functions include regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. Because of its central role in gene regulation and RNA metabolism, there are growing implications for DHX9 in human diseases and their treatment. This review will provide an overview of the structure, biochemistry, and biology of DHX9, its role in cancer and other human diseases, and the possibility of targeting DHX9 in chemotherapy.
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Affiliation(s)
- Teresa Lee
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
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40
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Kedage V, Selvaraj N, Nicholas TR, Budka JA, Plotnik JP, Jerde TJ, Hollenhorst PC. An Interaction with Ewing's Sarcoma Breakpoint Protein EWS Defines a Specific Oncogenic Mechanism of ETS Factors Rearranged in Prostate Cancer. Cell Rep 2017; 17:1289-1301. [PMID: 27783944 DOI: 10.1016/j.celrep.2016.10.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 09/15/2016] [Accepted: 09/28/2016] [Indexed: 12/22/2022] Open
Abstract
More than 50% of prostate tumors have a chromosomal rearrangement resulting in aberrant expression of an oncogenic ETS family transcription factor. However, mechanisms that differentiate the function of oncogenic ETS factors expressed in prostate tumors from non-oncogenic ETS factors expressed in normal prostate are unknown. Here, we find that four oncogenic ETS (ERG, ETV1, ETV4, and ETV5), and no other ETS, interact with the Ewing's sarcoma breakpoint protein, EWS. This EWS interaction was necessary and sufficient for oncogenic ETS functions including gene activation, cell migration, clonogenic survival, and transformation. Significantly, the EWS interacting region of ERG has no homology with that of ETV1, ETV4, and ETV5. Therefore, this finding may explain how divergent ETS factors have a common oncogenic function. Strikingly, EWS is fused to various ETS factors by the chromosome translocations that cause Ewing's sarcoma. Therefore, these findings link oncogenic ETS function in both prostate cancer and Ewing's sarcoma.
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Affiliation(s)
- Vivekananda Kedage
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | | | - Taylor R Nicholas
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Justin A Budka
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Joshua P Plotnik
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Travis J Jerde
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Peter C Hollenhorst
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA.
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Dasgupta A, Trucco M, Rainusso N, Bernardi RJ, Shuck R, Kurenbekova L, Loeb DM, Yustein JT. Metabolic modulation of Ewing sarcoma cells inhibits tumor growth and stem cell properties. Oncotarget 2017; 8:77292-77308. [PMID: 29100387 PMCID: PMC5652780 DOI: 10.18632/oncotarget.20467] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022] Open
Abstract
Ewing sarcoma (EWS) is a highly aggressive and metabolically active malignant tumor. Metabolic activity can broadly be characterized by features of glycolytic activity and oxidative phosphorylation. We have further characterized metabolic features of EWS cells to identify potential therapeutic targets. EWS cells had significantly more glycolytic activity compared to their non-malignant counterparts. Thus, metabolic inhibitors of glycolysis such as 2-deoxy-D-glucose (2DG) and of the mitochondrial respiratory pathway, such as metformin, were evaluated as potential therapeutic agents against a panel of EWS cell lines in vitro. Results indicate that 2DG alone or in combination with metformin was effective at inducing cell death in EWS cell lines. The predominant mechanism of cell death appears to be through stimulating apoptosis leading into necrosis with concomitant activation of AMPK-α. Furthermore, we demonstrate that the use of metabolic modulators can target putative EWS stem cells, both in vitro and in vivo, and potentially overcome chemotherapeutic resistance in EWS. Based on these data, clinical strategies using drugs targeting tumor cell metabolism present a viable therapeutic modality against EWS.
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Affiliation(s)
- Atreyi Dasgupta
- The Faris D. Virani Ewing Sarcoma Center at The Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matteo Trucco
- Sylvester Comprehensive Cancer Center, Department of Pediatrics, Hematology-Oncology, University of Miami-Miller School of Medicine, Miami, FL 33136, USA
| | - Nino Rainusso
- The Faris D. Virani Ewing Sarcoma Center at The Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ronald J Bernardi
- The Faris D. Virani Ewing Sarcoma Center at The Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan Shuck
- The Faris D. Virani Ewing Sarcoma Center at The Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lyazat Kurenbekova
- The Faris D. Virani Ewing Sarcoma Center at The Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David M Loeb
- Sydney Kimmel Comprehensive Cancer Center at Johns Hopkins Hospital, Baltimore, MD 21231, USA
| | - Jason T Yustein
- The Faris D. Virani Ewing Sarcoma Center at The Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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42
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Monteleone NJ, Lutz CS. miR-708-5p: a microRNA with emerging roles in cancer. Oncotarget 2017; 8:71292-71316. [PMID: 29050362 PMCID: PMC5642637 DOI: 10.18632/oncotarget.19772] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/16/2017] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate gene expression post-transcriptionally. They are crucial for normal development and maintaining homeostasis. Researchers have discovered that dysregulated miRNA expression contributes to many pathological conditions, including cancer. miRNAs can augment or suppress tumorigenesis based on their expression and transcribed targetome in various cell types. In recent years, researchers have begun to identify miRNAs commonly dysregulated in cancer. One recently identified miRNA, miR-708-5p, has been shown to have profound roles in promoting or suppressing oncogenesis in a myriad of solid and hematological tumors. This review highlights the diverse, sometimes controversial findings reported for miR-708-5p in cancer, and the importance of further exploring this exciting miRNA.
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Affiliation(s)
- Nicholas J Monteleone
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, and the School of Graduate Studies, Health Sciences Campus - Newark, Newark, NJ 07103, USA
| | - Carol S Lutz
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, and the School of Graduate Studies, Health Sciences Campus - Newark, Newark, NJ 07103, USA
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43
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Eastley N, Ottolini B, Garrido C, Shaw JA, McCulloch TA, Ashford RU, Royle NJ. Telomere maintenance in soft tissue sarcomas. J Clin Pathol 2017; 70:371-377. [PMID: 28183782 PMCID: PMC5484030 DOI: 10.1136/jclinpath-2016-204151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/15/2016] [Indexed: 01/27/2023]
Abstract
Soft tissue sarcomas (STS) are a diverse group of heterogeneous malignant tumours derived from mesenchymal tissues. Over 50 different STS subtypes are recognised by WHO, which show a wide range of different biological behaviours and prognoses. At present, clinicians managing this complex group of tumours face several challenges. This is reflected by the relatively poor outcome of patients with STSs compared with many other solid malignant tumours. These include difficulties securing accurate diagnoses, a lack of effective systemic treatments and absence of any sensitive circulating biomarkers to monitor patients throughout their treatment and follow-up. In order to progress STS's cells must evade the usual cellular proliferative checkpoints, and then activate a telomere maintenance mechanism in order to achieve replicative immortality. The purpose of this review is to provide an overview of STS genetics focusing particularly on these mechanisms. We will also highlight some of the key barriers to improving outcome for patients with STS, and hypothesise how a better understanding of these genetic characteristics may impact on future STS management.
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Affiliation(s)
| | - Barbara Ottolini
- Department of Cancer Studies, University of Leicester, Leicester, UK
| | - Carmen Garrido
- Department of Genetics, University of Leicester, Leicester, UK
| | - Jacqueline A Shaw
- Department of Cancer Studies, University of Leicester, Leicester, UK
| | | | | | - Nicola J Royle
- Department of Genetics, University of Leicester, Leicester, UK
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44
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Theisen ER, Pishas KI, Saund RS, Lessnick SL. Therapeutic opportunities in Ewing sarcoma: EWS-FLI inhibition via LSD1 targeting. Oncotarget 2017; 7:17616-30. [PMID: 26848860 PMCID: PMC4951237 DOI: 10.18632/oncotarget.7124] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/23/2016] [Indexed: 11/25/2022] Open
Abstract
Ewing sarcoma is an aggressive primary pediatric bone tumor, often diagnosed in adolescents and young adults. A pathognomonic reciprocal chromosomal translocation results in a fusion gene coding for a protein which derives its N-terminus from a FUS/EWS/TAF15 (FET) protein family member, commonly EWS, and C-terminus containing the DNA-binding domain of an ETS transcription factor, commonly FLI1. Nearly 85% of cases express the EWS-FLI protein which functions as a transcription factor and drives oncogenesis. As the primary genomic lesion and a protein which is not expressed in normal cells, disrupting EWS-FLI function is an attractive therapeutic strategy for Ewing sarcoma. However, transcription factors are notoriously difficult targets for the development of small molecules. Improved understanding of the oncogenic mechanisms employed by EWS-FLI to hijack normal cellular programming has uncovered potential novel approaches to pharmacologically block EWS-FLI function. In this review we examine targeting the chromatin regulatory enzymes recruited to conspire in oncogenesis with a focus on the histone lysine specific demethylase 1 (LSD1). LSD1 inhibitors are being aggressively investigated in acute myeloid leukemia and the results of early clinical trials will help inform the future use of LSD1 inhibitors in sarcoma. High LSD1 expression is observed in Ewing sarcoma patient samples and mechanistic and preclinical data suggest LSD1 inhibition globally disrupts the function of EWS-ETS proteins.
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Affiliation(s)
- Emily R Theisen
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kathleen I Pishas
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Cancer Therapeutics Laboratory, Centre for Personalized Cancer Medicine, Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Ranajeet S Saund
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Division of Pediatric Hematology/Oncology/Bone Marrow Transplant at The Ohio State University, Columbus, Ohio, USA
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Archer LK, Frame FM, Maitland NJ. Stem cells and the role of ETS transcription factors in the differentiation hierarchy of normal and malignant prostate epithelium. J Steroid Biochem Mol Biol 2017; 166:68-83. [PMID: 27185499 DOI: 10.1016/j.jsbmb.2016.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/25/2016] [Accepted: 05/07/2016] [Indexed: 12/18/2022]
Abstract
Prostate cancer is the most common cancer of men in the UK and accounts for a quarter of all new cases. Although treatment of localised cancer can be successful, there is no cure for patients presenting with invasive prostate cancer and there are less treatment options. They are generally treated with androgen-ablation therapies but eventually the tumours become hormone resistant and patients develop castration-resistant prostate cancer (CRPC) for which there are no further successful or curative treatments. This highlights the need for new treatment strategies. In order to prevent prostate cancer recurrence and treatment resistance, all the cell populations in a heterogeneous prostate tumour must be targeted, including the rare cancer stem cell (CSC) population. The ETS transcription factor family members are now recognised as a common feature in multiple cancers including prostate cancer; with aberrant expression, loss of tumour suppressor function, inactivating mutations and the formation of fusion genes observed. Most notably, the TMPRSS2-ERG gene fusion is present in approximately 50% of prostate cancers and in prostate CSCs. However, the role of other ETS transcription factors in prostate cancer is less well understood. This review will describe the prostate epithelial cell hierarchy and discuss the evidence behind prostate CSCs and their inherent resistance to conventional cancer therapies. The known and proposed roles of the ETS family of transcription factors in prostate epithelial cell differentiation and regulation of the CSC phenotype will be discussed, as well as how they might be targeted for therapy.
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Affiliation(s)
- Leanne K Archer
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Fiona M Frame
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Norman J Maitland
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom.
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He T, Surdez D, Rantala JK, Haapa-Paananen S, Ban J, Kauer M, Tomazou E, Fey V, Alonso J, Kovar H, Delattre O, Iljin K. High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability. Gene 2016; 596:137-146. [PMID: 27760381 DOI: 10.1016/j.gene.2016.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/21/2016] [Accepted: 10/14/2016] [Indexed: 12/31/2022]
Abstract
A translocation leading to the formation of an oncogenic EWS-ETS fusion protein defines Ewing sarcoma. The most frequent gene fusion, present in 85 percent of Ewing sarcomas, is EWS-FLI1. Here, a high-throughput RNA interference screen was performed to identify genes whose function is critical for EWS-FLI1 driven cell viability. In total, 6781 genes were targeted by siRNA molecules and the screen was performed both in presence and absence of doxycycline-inducible expression of the EWS-FLI1 shRNA in A673/TR/shEF Ewing sarcoma cells. The Leucine rich repeats and WD repeat Domain containing 1 (LRWD1) targeting siRNA pool was the strongest hit reducing cell viability only in EWS-FLI1 expressing Ewing sarcoma cells. LRWD1 had been previously described as a testis specific gene with only limited information on its function. Analysis of LRWD1 mRNA levels in patient samples indicated that high expression associated with poor overall survival in Ewing sarcoma. Gene ontology analysis of LRWD1 co-expressed genes in Ewing tumors revealed association with DNA replication and analysis of differentially expressed genes in LRWD1 depleted Ewing sarcoma cells indicated a role in connective tissue development and cellular morphogenesis. Moreover, EWS-FLI1 repressed genes with repressive H3K27me3 chromatin marks were highly enriched among LRWD1 target genes in A673/TR/shEF Ewing sarcoma cells, suggesting that LRWD1 contributes to EWS-FLI1 driven transcriptional regulation. Taken together, we have identified LRWD1 as a novel regulator of EWS-FLI1 driven cell viability in A673/TR/shEF Ewing sarcoma cells, shown association between high LRWD1 mRNA expression and aggressive disease and identified processes by which LRWD1 may promote oncogenesis in Ewing sarcoma.
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Affiliation(s)
- Tao He
- VTT Technical Research Centre of Finland, Turku, Finland
| | - Didier Surdez
- Institut Curie, Unité de génétique somatique, Paris, France; Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France; INSERM U830, Institut Curie Research Center, Paris, France
| | | | | | - Jozef Ban
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Maximilian Kauer
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Eleni Tomazou
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Vidal Fey
- VTT Technical Research Centre of Finland, Turku, Finland
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Heinrich Kovar
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria; Department of Pediatrics, Medical University, Vienna, Austria
| | - Olivier Delattre
- Institut Curie, Unité de génétique somatique, Paris, France; Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France; INSERM U830, Institut Curie Research Center, Paris, France; Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, Paris, France
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Lee CJ, Ahn H, Lee SB, Shin JY, Park WY, Kim JI, Lee J, Ryu H, Kim S. Integrated analysis of omics data using microRNA-target mRNA network and PPI network reveals regulation of Gnai1 function in the spinal cord of Ews/Ewsr1 KO mice. BMC Med Genomics 2016; 9 Suppl 1:33. [PMID: 27534535 PMCID: PMC4989891 DOI: 10.1186/s12920-016-0195-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background Multifunctional transcription factor (TF) gene EWS/EWSR1 is involved in various cellular processes such as transcription regulation, noncoding RNA regulation, splicing regulation, genotoxic stress response, and cancer generation. Role of a TF gene can be effectively studied by measuring genome-wide gene expression, i.e., transcriptome, in an animal model of Ews/Ewsr1 knockout (KO). However, when a TF gene has complex multi-functions, conventional approaches such as differentially expressed genes (DEGs) analysis are not successful to characterize the role of the EWS gene. In this regard, network-based analyses that consider associations among genes are the most promising approach. Methods Networks are constructed and used to show associations among biological entities at various levels, thus different networks represent association at different levels. Taken together, in this paper, we report contributions on both computational and biological sides. Results Contribution on the computational side is to develop a novel computational framework that combines miRNA-gene network and protein-protein interaction network information to characterize the multifunctional role of EWS gene. On the biological side, we report that EWS regulates G-protein, Gnai1, in the spinal cord of Ews/Ewsr1 KO mice using the two biological network integrated analysis method. Neighbor proteins of Gnai1, G-protein complex subunits Gnb1, Gnb2 and Gnb4 were also down-regulated at their gene expression level. Interestingly, up-regulated genes, such as Rgs1 and Rgs19, are linked to the inhibition of Gnai1 activities. We further verified the altered expression of Gnai1 by qRT-PCR in Ews/Ewsr1 KO mice. Conclusions Our integrated analysis of miRNA-transcriptome network and PPI network combined with qRT-PCR verifies that Gnai1 function is impaired in the spinal cord of Ews/Ewsr1 KO mice. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0195-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chai-Jin Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Hongryul Ahn
- Department of Computer Science and Engineering, Seoul National University, Seoul, 151-744, Republic of Korea
| | - Sean Bong Lee
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Jong-Yeon Shin
- Genome Medicine Institute and Department of Biochemistry, Seoul National University College of Medicine, Seoul, 110-799, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center and Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 135-710, Republic of Korea
| | - Jong-Il Kim
- Genome Medicine Institute and Department of Biochemistry, Seoul National University College of Medicine, Seoul, 110-799, Republic of Korea
| | - Junghee Lee
- VA Boston Healthcare System, Boston, MA, 02130, USA.,Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Hoon Ryu
- VA Boston Healthcare System, Boston, MA, 02130, USA. .,Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA. .,Center for Neuromedicine, Brain Science Institute, Korea Institute of Science and Technology, Seoul, 136-791, Republic of Korea.
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea. .,Department of Computer Science and Engineering, Seoul National University, Seoul, 151-744, Republic of Korea. .,Bioinformatics Institute, Seoul National University, Seoul, 151-747, Republic of Korea.
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48
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Song W, Li W, Li L, Zhang S, Yan X, Wen X, Zhang X, Tian H, Li A, Hu JF, Cui J. Friend leukemia virus integration 1 activates the Rho GTPase pathway and is associated with metastasis in breast cancer. Oncotarget 2016; 6:23764-75. [PMID: 26156017 PMCID: PMC4695150 DOI: 10.18632/oncotarget.4350] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/11/2015] [Indexed: 01/22/2023] Open
Abstract
Breast cancer is the most prevalent malignant disease in women worldwide. In patients with breast cancer, metastasis to distant sites directly determines the survival outcome. However, the molecular mechanism underlying metastasis in breast cancer remains to be defined. In this report, we found that Friend leukemia virus integration 1 (FLI1) proto-oncogene was differentially expressed between the aggressive MDA-MB231 and the non-aggressive MCF-7 breast cancer cells. Congruently, immunohistochemical staining of clinical samples revealed that FLI1 was overexpressed in breast cancers as compared with the adjacent tissues. The abundance of FLI1 protein was strongly correlated with the advanced stage, poor differentiation, and lymph node metastasis in breast cancer patients. Knockdown of FLI1 with small interfering RNAs significantly attenuated the potential of migration and invasion in highly metastatic human breast cancer cells. FLI1 oncoprotein activated the Rho GTPase pathway that is known to play a role in tumor metastasis. This study for the first time identifies FLI1 as a clinically and functionally important target gene of metastasis, providing a rationale for developing FLI1 inhibitors in the treatment of breast cancer.
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Affiliation(s)
- Wei Song
- Cancer Center, the First Hospital of Jilin University, Changchun, China
| | - Wei Li
- Cancer Center, the First Hospital of Jilin University, Changchun, China
| | - Lingyu Li
- Cancer Center, the First Hospital of Jilin University, Changchun, China
| | - Shilin Zhang
- Cancer Center, the First Hospital of Jilin University, Changchun, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Xu Yan
- Cancer Center, the First Hospital of Jilin University, Changchun, China
| | - Xue Wen
- Cancer Center, the First Hospital of Jilin University, Changchun, China
| | - Xiaoying Zhang
- Cancer Center, the First Hospital of Jilin University, Changchun, China
| | - Huimin Tian
- Cancer Center, the First Hospital of Jilin University, Changchun, China
| | - Ailing Li
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
| | - Ji-Fan Hu
- Cancer Center, the First Hospital of Jilin University, Changchun, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Jiuwei Cui
- Cancer Center, the First Hospital of Jilin University, Changchun, China
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49
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Celli R, Cai G. Ewing Sarcoma/Primitive Neuroectodermal Tumor of the Kidney: A Rare and Lethal Entity. Arch Pathol Lab Med 2016; 140:281-5. [PMID: 26927724 DOI: 10.5858/arpa.2014-0367-rs] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ewing sarcoma/primitive neuroectodermal tumor represents a spectrum of undifferentiated tumors with similar biology that together represent the second most common sarcoma in the pediatric-young adult age range. Very rarely, this tumor presents as a primary neoplasm of the kidney. The clinical presentation of this tumor is not specific, and other renal tumors may present with a similar histologic appearance. Establishing the correct diagnosis is critical because renal Ewing sarcoma/primitive neuroectodermal tumor carries a strikingly dismal prognosis and thus dictates a specific treatment strategy. A low threshold for the use of ancillary molecular tests is recommended, particularly in diagnostically problematic cases. Important considerations with regards to morphology, immunohistochemistry, and molecular alterations will be reviewed here and should be taken into account before rendering this rare and lethal diagnosis.
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Affiliation(s)
- Romulo Celli
- From the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
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50
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Grohar PJ, Kim S, Rangel Rivera GO, Sen N, Haddock S, Harlow ML, Maloney NK, Zhu J, O'Neill M, Jones TL, Huppi K, Grandin M, Gehlhaus K, Klumpp-Thomas CA, Buehler E, Helman LJ, Martin SE, Caplen NJ. Functional Genomic Screening Reveals Splicing of the EWS-FLI1 Fusion Transcript as a Vulnerability in Ewing Sarcoma. Cell Rep 2016; 14:598-610. [PMID: 26776507 PMCID: PMC4755295 DOI: 10.1016/j.celrep.2015.12.063] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/30/2015] [Accepted: 12/13/2015] [Indexed: 10/22/2022] Open
Abstract
Ewing sarcoma cells depend on the EWS-FLI1 fusion transcription factor for cell survival. Using an assay of EWS-FLI1 activity and genome-wide RNAi screening, we have identified proteins required for the processing of the EWS-FLI1 pre-mRNA. We show that Ewing sarcoma cells harboring a genomic breakpoint that retains exon 8 of EWSR1 require the RNA-binding protein HNRNPH1 to express in-frame EWS-FLI1. We also demonstrate the sensitivity of EWS-FLI1 fusion transcripts to the loss of function of the U2 snRNP component, SF3B1. Disrupted splicing of the EWS-FLI1 transcript alters EWS-FLI1 protein expression and EWS-FLI1-driven expression. Our results show that the processing of the EWS-FLI1 fusion RNA is a potentially targetable vulnerability in Ewing sarcoma cells.
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MESH Headings
- Base Sequence
- Binding Sites
- Calmodulin-Binding Proteins/antagonists & inhibitors
- Calmodulin-Binding Proteins/genetics
- Calmodulin-Binding Proteins/metabolism
- Cell Line, Tumor
- Cell Survival
- Exons
- Gene Expression Regulation, Neoplastic
- Heterogeneous-Nuclear Ribonucleoprotein Group F-H/antagonists & inhibitors
- Heterogeneous-Nuclear Ribonucleoprotein Group F-H/genetics
- Heterogeneous-Nuclear Ribonucleoprotein Group F-H/metabolism
- Humans
- Microfilament Proteins/antagonists & inhibitors
- Microfilament Proteins/genetics
- Microfilament Proteins/metabolism
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Phosphoproteins/antagonists & inhibitors
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Proto-Oncogene Protein c-fli-1/antagonists & inhibitors
- Proto-Oncogene Protein c-fli-1/genetics
- Proto-Oncogene Protein c-fli-1/metabolism
- RNA Interference
- RNA Precursors/metabolism
- RNA Splicing
- RNA Splicing Factors
- RNA, Small Interfering/metabolism
- RNA-Binding Protein EWS/antagonists & inhibitors
- RNA-Binding Protein EWS/genetics
- RNA-Binding Protein EWS/metabolism
- RNA-Binding Proteins/antagonists & inhibitors
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Ribonucleoprotein, U2 Small Nuclear/antagonists & inhibitors
- Ribonucleoprotein, U2 Small Nuclear/genetics
- Ribonucleoprotein, U2 Small Nuclear/metabolism
- Sarcoma, Ewing/pathology
- Trans-Activators
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Patrick J Grohar
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Suntae Kim
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Guillermo O Rangel Rivera
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; NIH Academy, Office of Intramural Training and Education, NIH, Bethesda, MD 20892, USA
| | - Nirmalya Sen
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sara Haddock
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Matt L Harlow
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Nichole K Maloney
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jack Zhu
- Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Maura O'Neill
- Protein Characterization Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Tamara L Jones
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Konrad Huppi
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Magdalena Grandin
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Kristen Gehlhaus
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Carleen A Klumpp-Thomas
- Trans-NIH RNAi Screening Facility, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Eugen Buehler
- Trans-NIH RNAi Screening Facility, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Lee J Helman
- Molecular Oncology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Scott E Martin
- Trans-NIH RNAi Screening Facility, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Natasha J Caplen
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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