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Doll S, Schweizer L, Bollwein C, Steiger K, Pfarr N, Walker M, Wörtler K, Knebel C, von Eisenhart-Rothe R, Hartmann W, Weichert W, Mann M, Kuhn PH, Specht K. Proteomic Characterization of Undifferentiated Small Round Cell Sarcomas With EWSR1 and CIC::DUX4 Translocations Reveals Diverging Tumor Biology and Distinct Diagnostic Markers. Mod Pathol 2024; 37:100511. [PMID: 38705279 DOI: 10.1016/j.modpat.2024.100511] [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: 10/16/2023] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
Undifferentiated small round cell sarcomas (USRS) of bone and soft tissue are a group of tumors with heterogenic genomic alterations sharing similar morphology. In the present study, we performed a comparative large-scale proteomic analysis of USRS (n = 42) with diverse genomic translocations including classic Ewing sarcomas with EWSR1::FLI1 fusions (n = 24) or EWSR1::ERG fusions (n = 4), sarcomas with an EWSR1 rearrangement (n = 2), CIC::DUX4 fusion (n = 8), as well as tumors classified as USRS with no genetic data available (n = 4). Proteins extracted from formalin-fixed, paraffin-embedded pretherapeutic biopsies were analyzed qualitatively and quantitatively using shotgun mass spectrometry (MS). More than 8000 protein groups could be quantified using data-independent acquisition. Unsupervised hierarchical cluster analysis based on proteomic data allowed stratification of the 42 cases into distinct groups reflecting the different molecular genotypes. Protein signatures that significantly correlated with the respective genomic translocations were identified and used to generate a heatmap of all 42 sarcomas with assignment of cases with unknown molecular genetic data to either the EWSR1- or CIC-rearranged groups. MS-based prediction of sarcoma subtypes was molecularly confirmed in 2 cases where next-generation sequencing was technically feasible. MS also detected proteins routinely used in the immunohistochemical approach for the differential diagnosis of USRS. BCL11B highly expressed in Ewing sarcomas, and BACH2 as well as ETS-1 highly expressed in CIC::DUX4-associated sarcomas, were among proteins identified by the present proteomic study, and were chosen for immunohistochemical confirmation of MS data in our study cohort. Differential expressions of these 3 markers in the 2 genetic groups were further validated in an independent cohort of n = 34 USRS. Finally, our proteomic results point toward diverging signaling pathways in the different USRS subgroups.
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Affiliation(s)
- Sophia Doll
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany; OmicEra Diagnostics GmbH, Planegg, Bavaria, Germany
| | - Lisa Schweizer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | | | - Katja Steiger
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Maria Walker
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Klaus Wörtler
- Musculoskeletal Radiology Section, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Carolin Knebel
- Department of Orthopaedic Surgery, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | | | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Peer-Hendrik Kuhn
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Katja Specht
- Institute of Pathology, Technical University of Munich, Munich, Germany.
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2
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Vickridge E, Faraco CCF, Lo F, Rahimian H, Liu Z, Tehrani P, Djerir B, Ramdzan ZM, Leduy L, Maréchal A, Gingras AC, Nepveu A. The function of BCL11B in base excision repair contributes to its dual role as an oncogene and a haplo-insufficient tumor suppressor gene. Nucleic Acids Res 2024; 52:223-242. [PMID: 37956270 PMCID: PMC10783527 DOI: 10.1093/nar/gkad1037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Genetic studies in mice and human cancers established BCL11B as a haploinsufficient tumor suppressor gene. Paradoxically, BCL11B is overexpressed in some human cancers where its knockdown is synthetic lethal. We identified the BCL11B protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro DNA repair assays demonstrated that both BCL11B and a small recombinant BCL11B213-560 protein lacking transcription regulation potential can stimulate the enzymatic activities of two base excision repair (BER) enzymes: NTHL1 and Pol β. In cells, BCL11B is rapidly recruited to sites of DNA damage caused by laser microirradiation. BCL11B knockdown delays, whereas ectopic expression of BCL11B213-560 accelerates, the repair of oxidative DNA damage. Inactivation of one BCL11B allele in TK6 lymphoblastoid cells causes an increase in spontaneous and radiation-induced mutation rates. In turn, ectopic expression of BCL11B213-560 cooperates with the RAS oncogene in cell transformation by reducing DNA damage and cellular senescence. These findings indicate that BCL11B functions as a BER accessory factor, safeguarding normal cells from acquiring mutations. Paradoxically, it also enables the survival of cancer cells that would otherwise undergo senescence or apoptosis due to oxidative DNA damage resulting from the elevated production of reactive oxygen species.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Camila C F Faraco
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Fanny Lo
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Hedyeh Rahimian
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Zi Yang Liu
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Payman S Tehrani
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario Canada
| | - Billel Djerir
- Department of Biology and Cancer Research Institute, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Zubaidah M Ramdzan
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Alexandre Maréchal
- Department of Biology and Cancer Research Institute, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alain Nepveu
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Medicine, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Oncology, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
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3
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Gong H, Xue B, Ru J, Pei G, Li Y. Targeted Therapy for EWS-FLI1 in Ewing Sarcoma. Cancers (Basel) 2023; 15:4035. [PMID: 37627063 PMCID: PMC10452796 DOI: 10.3390/cancers15164035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare and predominantly pediatric malignancy of bone and soft tissue in children and adolescents. Although international collaborations have greatly improved the prognosis of most EwS, the occurrence of macrometastases or relapse remains challenging. The prototypic oncogene EWS-FLI1 acts as an aberrant transcription factor that drives the cellular transformation of EwS. In addition to its involvement in RNA splicing and the DNA damage response, this chimeric protein directly binds to GGAA repeats, thereby modifying the transcriptional profile of EwS. Direct pharmacological targeting of EWS-FLI1 is difficult because of its intrinsically disordered structure. However, targeting the EWS-FLI1 protein complex or downstream pathways provides additional therapeutic options. This review describes the EWS-FLI1 protein partners and downstream pathways, as well as the related target therapies for the treatment of EwS.
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Affiliation(s)
- Helong Gong
- Department of Orthopaedic Surgery, Shengjing Hospital, China Medical University, No. 36 Sanhao Street, Heping District, Shenyang 110004, China;
| | - Busheng Xue
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China;
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Guoqing Pei
- Department of Orthopedics, Xijing Hospital, Air Force Medical University, Xi’an 710032, China;
| | - Yan Li
- Department of Orthopaedic Surgery, Shengjing Hospital, China Medical University, No. 36 Sanhao Street, Heping District, Shenyang 110004, China;
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4
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Abe H, Kamimura K, Okuda S, Watanabe Y, Inoue J, Aoyagi Y, Wakai T, Kominami R, Terai S. BCL11B expression in hepatocellular carcinoma relates to chemosensitivity and clinical prognosis. Cancer Med 2023; 12:15650-15663. [PMID: 37293953 PMCID: PMC10417273 DOI: 10.1002/cam4.6167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
INTRODUCTION B-cell lymphoma/leukemia 11B (BCL11B) is a subunit of SWI/SNF chromatin remodeling complexes and functions in cell cycle regulation and apoptosis upon DNA replication stress and damages via transcription. Many malignancies were reported to exhibit changes in BCL11B gene expression; however, no study has focused on the relationship between BCL11B and hepatocellular carcinoma, which potentially exhibits DNA replication stress and damages upon its oncogenesis. Thus, in this study, we examined the molecular characterization of BCL11B expression in hepatocellular carcinoma. METHODS AND RESULTS The cumulative progression-free survival and overall survival were significantly longer in the clinical cases of BCL11B-negative hepatocellular carcinoma than BCL11B-positve cases. Microarray and real-time PCR analyses in hepatocellular carcinoma cell lines indicated a correlation between BCL11B and GATA6, a gene reported to be correlated with oncogenic activities and resistance to anthracycline, which is often used for hepatocellular carcinoma chemotherapy. Consequently, BCL11B-overexpressing cell lines exhibited resistance to anthracycline in cell growth assays and the resistance has been evidenced by the increased expression of BCL-xL in cell lines. The results were supported by the analyses of human HCC samples showing the correlation between BCL11B and GATA6 expressions. DISCUSSIONS AND CONCLUSION Our results indicated that overexpression of BCL11B amplifies GATA6 expression in hepatocellular carcinoma in vitro and in vivo that leads to anti-apoptotic signal activation, and induces resistance to chemotherapy, which influenced the postoperative prognosis.
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Affiliation(s)
- Hiroyuki Abe
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Kenya Kamimura
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
- Department of General MedicineNiigata University School of MedicineNiigataNiigataJapan
| | - Shujiro Okuda
- Division of Bioinformatics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Yu Watanabe
- Division of Bioinformatics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Jun Inoue
- Department of Agricultural Chemistry, Faculty of Applied BiosciencesTokyo University of AgricultureTokyoJapan
| | - Yutaka Aoyagi
- Department of Gastroenterology and HepatologyNiigata Medical CenterNiigataNiigataJapan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Ryo Kominami
- Department of Molecular Genetics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Shuji Terai
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
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5
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Lu DY, Ellegast JM, Ross KN, Malone CF, Lin S, Mabe NW, Dharia NV, Meyer A, Conway A, Su AH, Selich-Anderson J, Taslim C, Byrum AK, Seong BKA, Adane B, Gray NS, Rivera MN, Lessnick SL, Stegmaier K. The ETS transcription factor ETV6 constrains the transcriptional activity of EWS-FLI to promote Ewing sarcoma. Nat Cell Biol 2023; 25:285-297. [PMID: 36658220 PMCID: PMC9928584 DOI: 10.1038/s41556-022-01059-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 11/24/2022] [Indexed: 01/21/2023]
Abstract
Transcription factors (TFs) are frequently mutated in cancer. Paediatric cancers exhibit few mutations genome-wide but frequently harbour sentinel mutations that affect TFs, which provides a context to precisely study the transcriptional circuits that support mutant TF-driven oncogenesis. A broadly relevant mechanism that has garnered intense focus involves the ability of mutant TFs to hijack wild-type lineage-specific TFs in self-reinforcing transcriptional circuits. However, it is not known whether this specific type of circuitry is equally crucial in all mutant TF-driven cancers. Here we describe an alternative yet central transcriptional mechanism that promotes Ewing sarcoma, wherein constraint, rather than reinforcement, of the activity of the fusion TF EWS-FLI supports cancer growth. We discover that ETV6 is a crucial TF dependency that is specific to this disease because it, counter-intuitively, represses the transcriptional output of EWS-FLI. This work discovers a previously undescribed transcriptional mechanism that promotes cancer.
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Affiliation(s)
- Diana Y Lu
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jana M Ellegast
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth N Ross
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashleigh Meyer
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Conway
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Angela H Su
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Andrea K Byrum
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Bo Kyung A Seong
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Biniam Adane
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Miguel N Rivera
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Division of Pediatric Hematology, Oncology and BMT, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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6
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Apfelbaum AA, Wrenn ED, Lawlor ER. The importance of fusion protein activity in Ewing sarcoma and the cell intrinsic and extrinsic factors that regulate it: A review. Front Oncol 2022; 12:1044707. [PMID: 36505823 PMCID: PMC9727305 DOI: 10.3389/fonc.2022.1044707] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidence shows that despite clonal origins tumors eventually become complex communities comprised of phenotypically distinct cell subpopulations. This heterogeneity arises from both tumor cell intrinsic programs and signals from spatially and temporally dynamic microenvironments. While pediatric cancers usually lack the mutational burden of adult cancers, they still exhibit high levels of cellular heterogeneity that are largely mediated by epigenetic mechanisms. Ewing sarcomas are aggressive bone and soft tissue malignancies with peak incidence in adolescence and the prognosis for patients with relapsed and metastatic disease is dismal. Ewing sarcomas are driven by a single pathognomonic fusion between a FET protein and an ETS family transcription factor, the most common of which is EWS::FLI1. Despite sharing a single driver mutation, Ewing sarcoma cells demonstrate a high degree of transcriptional heterogeneity both between and within tumors. Recent studies have identified differential fusion protein activity as a key source of this heterogeneity which leads to profoundly different cellular phenotypes. Paradoxically, increased invasive and metastatic potential is associated with lower EWS::FLI1 activity. Here, we review what is currently understood about EWS::FLI1 activity, the cell autonomous and tumor microenvironmental factors that regulate it, and the downstream consequences of these activity states on tumor progression. We specifically highlight how transcription factor regulation, signaling pathway modulation, and the extracellular matrix intersect to create a complex network of tumor cell phenotypes. We propose that elucidation of the mechanisms by which these essential elements interact will enable the development of novel therapeutic approaches that are designed to target this complexity and ultimately improve patient outcomes.
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Affiliation(s)
| | | | - Elizabeth R. Lawlor
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute and Department of Pediatrics, University of Washington, Seattle, WA, United States
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7
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Johansson P, Laguna T, Ossowski J, Pancaldi V, Brauser M, Dührsen U, Keuneke L, Queiros A, Richter J, Martín-Subero JI, Siebert R, Schlegelberger B, Küppers R, Dürig J, Murga Penas EM, Carillo-de Santa Pau E, Bergmann AK. Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker. Clin Epigenetics 2022; 14:148. [PMID: 36376973 PMCID: PMC9664638 DOI: 10.1186/s13148-022-01362-z] [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: 04/24/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The molecular pathogenesis of T-cell large granular lymphocytic leukemia (T-LGLL), a mature T-cell leukemia arising commonly from T-cell receptor αβ-positive CD8+ memory cytotoxic T cells, is only partly understood. The role of deregulated methylation in T-LGLL is not well known. We analyzed the epigenetic profile of T-LGLL cells of 11 patients compared to their normal counterparts by array-based DNA methylation profiling. For identification of molecular events driving the pathogenesis of T-LGLL, we compared the differentially methylated loci between the T-LGLL cases and normal T cells with chromatin segmentation data of benign T cells from the BLUEPRINT project. Moreover, we analyzed gene expression data of T-LGLL and benign T cells and validated the results by pyrosequencing in an extended cohort of 17 patients, including five patients with sequential samples. RESULTS We identified dysregulation of DNA methylation associated with altered gene expression in T-LGLL. Since T-LGLL is a rare disease, the samples size is low. But as confirmed for each sample, hypermethylation of T-LGLL cells at various CpG sites located at enhancer regions is a hallmark of this disease. The interaction of BLC11B and C14orf64 as suggested by in silico data analysis could provide a novel pathogenetic mechanism that needs further experimental investigation. CONCLUSIONS DNA methylation is altered in T-LGLL cells compared to benign T cells. In particular, BCL11B is highly significant differentially methylated in T-LGLL cells. Although our results have to be validated in a larger patient cohort, BCL11B could be considered as a potential biomarker for this leukemia. In addition, altered gene expression and hypermethylation of enhancer regions could serve as potential mechanisms for treatment of this disease. Gene interactions of dysregulated genes, like BLC11B and C14orf64, may play an important role in pathogenic mechanisms and should be further analyzed.
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Affiliation(s)
- Patricia Johansson
- grid.5718.b0000 0001 2187 5445Faculty of Medicine, Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Virchowstr. 177, 45122 Essen, Germany
| | - Teresa Laguna
- grid.482878.90000 0004 0500 5302Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, 28049 Madrid, Spain
| | - Julio Ossowski
- grid.9764.c0000 0001 2153 9986Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Campus Kiel, Kiel, Germany ,grid.10423.340000 0000 9529 9877Institute of Human Genetics, Medical School Hannover (MHH), Hannover, Germany
| | - Vera Pancaldi
- grid.468186.5Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, INSERM U1037, 31037 Toulouse, France ,grid.10097.3f0000 0004 0387 1602Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Martina Brauser
- grid.5718.b0000 0001 2187 5445Faculty of Medicine, Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Virchowstr. 177, 45122 Essen, Germany
| | - Ulrich Dührsen
- grid.5718.b0000 0001 2187 5445Department of Hematology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lara Keuneke
- grid.9764.c0000 0001 2153 9986Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Campus Kiel, Kiel, Germany
| | - Ana Queiros
- grid.5841.80000 0004 1937 0247Institut d’Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
| | - Julia Richter
- grid.9764.c0000 0001 2153 9986Institute for Pathology, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Campus Kiel, Kiel, Germany
| | - José I. Martín-Subero
- grid.5841.80000 0004 1937 0247Institut d’Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Reiner Siebert
- grid.9764.c0000 0001 2153 9986Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Campus Kiel, Kiel, Germany ,grid.410712.10000 0004 0473 882XPresent Address: Institute of Human Genetics, University of Ulm and University Medical Center Ulm, Ulm, Germany
| | - Brigitte Schlegelberger
- grid.10423.340000 0000 9529 9877Institute of Human Genetics, Medical School Hannover (MHH), Hannover, Germany
| | - Ralf Küppers
- grid.5718.b0000 0001 2187 5445Faculty of Medicine, Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Virchowstr. 177, 45122 Essen, Germany
| | - Jan Dürig
- grid.500068.bDepartment of Internal Medicine, University Hospital Essen, St. Josef-Krankenhaus, University Medicine Essen, Essen, Germany
| | - Eva M. Murga Penas
- grid.9764.c0000 0001 2153 9986Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Campus Kiel, Kiel, Germany
| | - Enrique Carillo-de Santa Pau
- grid.482878.90000 0004 0500 5302Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, 28049 Madrid, Spain
| | - Anke K. Bergmann
- grid.10423.340000 0000 9529 9877Institute of Human Genetics, Medical School Hannover (MHH), Hannover, Germany
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8
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García-García L, Fernández-Tabanera E, Cervera ST, Melero-Fernández de Mera RM, Josa S, González-González L, Rodríguez-Martín C, Grünewald TGP, Alonso J. The Transcription Factor FEZF1, a Direct Target of EWSR1-FLI1 in Ewing Sarcoma Cells, Regulates the Expression of Neural-Specific Genes. Cancers (Basel) 2021; 13:5668. [PMID: 34830820 PMCID: PMC8616448 DOI: 10.3390/cancers13225668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Ewing sarcoma is a rare pediatric tumor characterized by chromosomal translocations that give rise to aberrant chimeric transcription factors (e.g., EWSR1-FLI1). EWSR1-FLI1 promotes a specific cellular transcriptional program. Therefore, the study of EWSR1-FLI1 target genes is important to identify critical pathways involved in Ewing sarcoma tumorigenesis. In this work, we focused on the transcription factors regulated by EWSR1-FLI1 in Ewing sarcoma. Transcriptomic analysis of the Ewing sarcoma cell line A673 indicated that one of the genes more strongly upregulated by EWSR1-FLI1 was FEZF1 (FEZ family zinc finger protein 1), a transcriptional repressor involved in neural cell identity. The functional characterization of FEZF1 was performed in three Ewing sarcoma cell lines (A673, SK-N-MC, SK-ES-1) through an shRNA-directed silencing approach. FEZF1 knockdown inhibited clonogenicity and cell proliferation. Finally, the analysis of the FEZF1-dependent expression profile in A673 cells showed several neural genes regulated by FEZF1 and concomitantly regulated by EWSR1-FLI1. In summary, FEZF1 is transcriptionally regulated by EWSR1-FLI1 in Ewing sarcoma cells and is involved in the regulation of neural-specific genes, which could explain the neural-like phenotype observed in several Ewing sarcoma tumors and cell lines.
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Affiliation(s)
- Laura García-García
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
| | - Enrique Fernández-Tabanera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Saint T. Cervera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Raquel M. Melero-Fernández de Mera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Santiago Josa
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
| | - Laura González-González
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
| | - Carlos Rodríguez-Martín
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Thomas G. P. Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany;
- Hopp-Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
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9
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Grabarczyk P, Delin M, Rogińska D, Schulig L, Forkel H, Depke M, Link A, Machaliński B, Schmidt CA. Nuclear import of BCL11B is mediated by a classical nuclear localization signal and not the Krüppel-like zinc fingers. J Cell Sci 2021; 134:272659. [PMID: 34714335 DOI: 10.1242/jcs.258655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/24/2021] [Indexed: 11/20/2022] Open
Abstract
The Krüppel-like transcription factor BCL11B is characterized by wide tissue distribution and crucial functions in key developmental and cellular processes and various pathologies including cancer or HIV infection. Although basics of BCL11B activity and relevant interactions with other proteins were uncovered, how this exclusively nuclear protein localizes to its compartment remained unclear. Here, we demonstrate that unlike other KLFs, BCL11B does not require the C-terminal DNA-binding domain to pass through the nuclear envelope but encodes an independent, previously unidentified nuclear localization signal (NLS) which is located distantly from the zinc finger domains and fulfills the essential criteria of an autonomous NLS. First, it can redirect a heterologous cytoplasmic protein to the nucleus. Second, its mutations cause aberrant localization of the protein of origin. Finally, we provide experimental and in silico evidences of the direct interaction with importin alpha. The relative conservation of this motif allows formulating a consensus sequence (K/R)K-X13-14-KR+K++ which can be found in all BCL11B orthologues among vertebrates and in the closely related protein BCL11A.
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Affiliation(s)
- Piotr Grabarczyk
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Martin Delin
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Dorota Rogińska
- Department of General Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lukas Schulig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Hannes Forkel
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Maren Depke
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Andreas Link
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Bogusław Machaliński
- Department of General Pathology, Pomeranian Medical University, Szczecin, Poland
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10
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Cervera ST, Rodríguez-Martín C, Fernández-Tabanera E, Melero-Fernández de Mera RM, Morin M, Fernández-Peñalver S, Iranzo-Martínez M, Amhih-Cardenas J, García-García L, González-González L, Moreno-Pelayo MA, Alonso J. Therapeutic Potential of EWSR1-FLI1 Inactivation by CRISPR/Cas9 in Ewing Sarcoma. Cancers (Basel) 2021; 13:cancers13153783. [PMID: 34359682 PMCID: PMC8345183 DOI: 10.3390/cancers13153783] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 01/14/2023] Open
Abstract
Simple Summary Ewing sarcoma is an aggressive tumor with still unacceptable survival rates, particularly in patients with metastatic disease and for which it is necessary to develop new and innovative therapies. These tumors are characterized by the presence of chromosomal translocations that give rise to chimeric transcription factors (i.e., EWSR1–FLI1) that govern the oncogenic process. In this article, we describe an efficient strategy to permanently inactivate the EWSR1–FLI1 oncogene characteristic of Ewing sarcoma using CRISPR/Cas9 gene editing technology. Although the application of gene therapy in cancer still has many limitations, for example, the strategy for delivery, studies like ours show that gene therapy can be a promising alternative, particularly for those tumors that are highly dependent on a particular oncogene as is the case in Ewing sarcoma. Abstract Ewing sarcoma is an aggressive bone cancer affecting children and young adults. The main molecular hallmark of Ewing sarcoma are chromosomal translocations that produce chimeric oncogenic transcription factors, the most frequent of which is the aberrant transcription factor EWSR1–FLI1. Because this is the principal oncogenic driver of Ewing sarcoma, its inactivation should be the best therapeutic strategy to block tumor growth. In this study, we genetically inactivated EWSR1–FLI1 using CRISPR-Cas9 technology in order to cause permanent gene inactivation. We found that gene editing at the exon 9 of FLI1 was able to block cell proliferation drastically and induce senescence massively in the well-studied Ewing sarcoma cell line A673. In comparison with an extensively used cellular model of EWSR1–FLI1 knockdown (A673/TR/shEF), genetic inactivation was more effective, particularly in its capability to block cell proliferation. In summary, genetic inactivation of EWSR1–FLI1 in A673 Ewing sarcoma cells blocks cell proliferation and induces a senescence phenotype that could be exploited therapeutically. Although efficient and specific in vivo CRISPR-Cas9 editing still presents many challenges today, our data suggest that complete inactivation of EWSR1–FLI1 at the cell level should be considered a therapeutic approach to develop in the future.
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Affiliation(s)
- Saint T. Cervera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Carlos Rodríguez-Martín
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Enrique Fernández-Tabanera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Raquel M. Melero-Fernández de Mera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Matias Morin
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.M.); (S.F.-P.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/0048; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Sergio Fernández-Peñalver
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.M.); (S.F.-P.); (M.A.M.-P.)
| | - Maria Iranzo-Martínez
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
| | - Jorge Amhih-Cardenas
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
| | - Laura García-García
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
| | - Laura González-González
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
| | - Miguel Angel Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.M.); (S.F.-P.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/0048; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), 28029 Madrid, Spain
- Correspondence:
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11
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Unveiling the N-Terminal Homodimerization of BCL11B by Hybrid Solvent Replica-Exchange Simulations. Int J Mol Sci 2021; 22:ijms22073650. [PMID: 33807484 PMCID: PMC8036541 DOI: 10.3390/ijms22073650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/28/2023] Open
Abstract
Transcription factors play a crucial role in regulating biological processes such as cell growth, differentiation, organ development and cellular signaling. Within this group, proteins equipped with zinc finger motifs (ZFs) represent the largest family of sequence-specific DNA-binding transcription regulators. Numerous studies have proven the fundamental role of BCL11B for a variety of tissues and organs such as central nervous system, T cells, skin, teeth, and mammary glands. In a previous work we identified a novel atypical zinc finger domain (CCHC-ZF) which serves as a dimerization interface of BCL11B. This domain and formation of the dimer were shown to be critically important for efficient regulation of the BCL11B target genes and could therefore represent a promising target for novel drug therapies. Here, we report the structural basis for BCL11B-BCL11B interaction mediated by the N-terminal ZF domain. By combining structure prediction algorithms, enhanced sampling molecular dynamics and fluorescence resonance energy transfer (FRET) approaches, we identified amino acid residues indispensable for the formation of the single ZF domain and directly involved in forming the dimer interface. These findings not only provide deep insight into how BCL11B acquires its active structure but also represent an important step towards rational design or selection of potential inhibitors.
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12
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Daher MT, Bausero P, Agbulut O, Li Z, Parlakian A. Bcl11b/Ctip2 in Skin, Tooth, and Craniofacial System. Front Cell Dev Biol 2020; 8:581674. [PMID: 33363142 PMCID: PMC7758212 DOI: 10.3389/fcell.2020.581674] [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: 07/09/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Ctip2/Bcl11b is a zinc finger transcription factor with dual action (repression/activation) that couples epigenetic regulation to gene transcription during the development of various tissues. It is involved in a variety of physiological responses under healthy and pathological conditions. Its role and mechanisms of action are best characterized in the immune and nervous systems. Furthermore, its implication in the development and homeostasis of other various tissues has also been reported. In the present review, we describe its role in skin development, adipogenesis, tooth formation and cranial suture ossification. Experimental data from several studies demonstrate the involvement of Bcl11b in the control of the balance between cell proliferation and differentiation during organ formation and repair, and more specifically in the context of stem cell self-renewal and fate determination. The impact of mutations in the coding sequences of Bcl11b on the development of diseases such as craniosynostosis is also presented. Finally, we discuss genome-wide association studies that suggest a potential influence of single nucleotide polymorphisms found in the 3’ regulatory region of Bcl11b on the homeostasis of the cardiovascular system.
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Affiliation(s)
- Marie-Thérèse Daher
- Biological Adaptation and Ageing, Inserm ERL U1164, UMR CNRS 8256, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Pedro Bausero
- Biological Adaptation and Ageing, Inserm ERL U1164, UMR CNRS 8256, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Onnik Agbulut
- Biological Adaptation and Ageing, Inserm ERL U1164, UMR CNRS 8256, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Zhenlin Li
- Biological Adaptation and Ageing, Inserm ERL U1164, UMR CNRS 8256, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Ara Parlakian
- Biological Adaptation and Ageing, Inserm ERL U1164, UMR CNRS 8256, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
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13
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High Specificity of BCL11B and GLG1 for EWSR1-FLI1 and EWSR1-ERG Positive Ewing Sarcoma. Cancers (Basel) 2020; 12:cancers12030644. [PMID: 32164354 PMCID: PMC7139395 DOI: 10.3390/cancers12030644] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/07/2020] [Accepted: 03/08/2020] [Indexed: 12/15/2022] Open
Abstract
Ewing sarcoma (EwS) is an aggressive cancer displaying an undifferentiated small-round-cell histomorphology that can be easily confused with a broad spectrum of differential diagnoses. Using comparative transcriptomics and immunohistochemistry (IHC), we previously identified BCL11B and GLG1 as potential specific auxiliary IHC markers for EWSR1-FLI1-positive EwS. Herein, we aimed at validating the specificity of both markers in a far larger and independent cohort of EwS (including EWSR1-ERG-positive cases) and differential diagnoses. Furthermore, we evaluated their intra-tumoral expression heterogeneity. Thus, we stained tissue microarrays from 133 molecularly confirmed EwS cases and 320 samples from morphological mimics, as well as a series of patient-derived xenograft (PDX) models for BCL11B, GLG1, and CD99, and systematically assessed the immunoreactivity and optimal cut-offs for each marker. These analyses demonstrated that high BCL11B and/or GLG1 immunoreactivity in CD99-positive cases had a specificity of 97.5% and an accuracy of 87.4% for diagnosing EwS solely by IHC, and that the markers were expressed by EWSR1-ERG-positive EwS. Only little intra-tumoral heterogeneity in immunoreactivity was observed for differential diagnoses. These results indicate that BCL11B and GLG1 may help as specific auxiliary IHC markers in diagnosing EwS in conjunction with CD99, especially if confirmatory molecular diagnostics are not available.
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14
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Lin L, Huang M, Shi X, Mayakonda A, Hu K, Jiang YY, Guo X, Chen L, Pang B, Doan N, Said JW, Xie J, Gery S, Cheng X, Lin Z, Li J, Berman BP, Yin D, Lin DC, Koeffler HP. Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1. Nucleic Acids Res 2019; 47:1255-1267. [PMID: 30496486 PMCID: PMC6379679 DOI: 10.1093/nar/gky1207] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 10/27/2018] [Accepted: 11/21/2018] [Indexed: 02/06/2023] Open
Abstract
As the second most common malignant bone tumor in children and adolescents, Ewing sarcoma is initiated and exacerbated by a chimeric oncoprotein, most commonly, EWS-FLI1. In this study, we apply epigenomic analysis to characterize the transcription dysregulation in this cancer, focusing on the investigation of super-enhancer and its associated transcriptional regulatory mechanisms. We demonstrate that super-enhancer-associated transcripts are significantly enriched in EWS-FLI1 target genes, contribute to the aberrant transcriptional network of the disease, and mediate the exceptional sensitivity of Ewing sarcoma to transcriptional inhibition. Through integrative analysis, we identify MEIS1 as a super-enhancer-driven oncogene, which co-operates with EWS-FLI1 in transcriptional regulation, and plays a key pro-survival role in Ewing sarcoma. Moreover, APCDD1, another super-enhancer-associated gene, acting as a downstream target of both MEIS1 and EWS-FLI1, is also characterized as a novel tumor-promoting factor in this malignancy. These data delineate super-enhancer-mediated transcriptional deregulation in Ewing sarcoma, and uncover numerous candidate oncogenes which can be exploited for further understanding of the molecular pathogenesis for this disease.
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Affiliation(s)
- Lehang Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China.,Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Moli Huang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, P.R. China
| | - Xianping Shi
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Yan-Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Xiao Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Li Chen
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Brendan Pang
- Department of Pathology, National University Hospital Singapore, 119074, Singapore
| | - Ngan Doan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles and David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Jonathan W Said
- Department of Pathology and Laboratory Medicine, University of California Los Angeles and David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Jianjun Xie
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou 515041, P.R. China
| | - Sigal Gery
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xu Cheng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Zhaoyu Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China.,Department of Oral & Maxillofacial Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Jinsong Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China.,Department of Oral & Maxillofacial Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Benjamin P Berman
- Department of Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.,National University Cancer Institute, National University Hospital Singapore, 119074, Singapore
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15
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EWSR1-FLI1 Activation of the Cancer/Testis Antigen FATE1 Promotes Ewing Sarcoma Survival. Mol Cell Biol 2019; 39:MCB.00138-19. [PMID: 31036566 DOI: 10.1128/mcb.00138-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/25/2019] [Indexed: 01/07/2023] Open
Abstract
Ewing sarcoma is characterized by a pathognomonic chromosomal translocation that generates the EWSR1-FLI1 chimeric transcription factor. The transcriptional targets of EWSR1-FLI1 that are essential for tumorigenicity are incompletely defined. Here, we found that EWSR1-FLI1 modulates the expression of cancer/testis (CT) antigen genes, whose expression is biased to the testes but is also activated in cancer. Among these CT antigens, fetal and adult testis expressed 1 (FATE1) is most robustly induced. EWSR1-FLI1 associates with the GGAA repeats in the proximal promoter of FATE1, which exhibits accessible chromatin exclusively in mesenchymal progenitor cells (MPCs) and Ewing sarcoma cells. Expression of EWSR1-FLI1 in non-Ewing sarcoma cells and in MPCs enhances FATE1 mRNA and protein expression. Conversely, depletion of EWSR1-FLI1 in Ewing sarcoma cells leads to a loss of FATE1 expression. Importantly, we found that FATE1 is required for survival and anchorage-independent growth in Ewing sarcoma cells via attenuating the accumulation of BNIP3L, a BH3-only protein that is toxic when stabilized. This action appears to be mediated by the E3 ligase RNF183. We propose that engaging FATE1 function can permit the bypass of cell death mechanisms that would otherwise inhibit tumor progression.
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16
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Liu N, Hargreaves VV, Zhu Q, Kurland JV, Hong J, Kim W, Sher F, Macias-Trevino C, Rogers JM, Kurita R, Nakamura Y, Yuan GC, Bauer DE, Xu J, Bulyk ML, Orkin SH. Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch. Cell 2018; 173:430-442.e17. [PMID: 29606353 DOI: 10.1016/j.cell.2018.03.016] [Citation(s) in RCA: 297] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 01/16/2018] [Accepted: 03/06/2018] [Indexed: 01/06/2023]
Abstract
Fetal hemoglobin (HbF, α2γ2) level is genetically controlled and modifies severity of adult hemoglobin (HbA, α2β2) disorders, sickle cell disease, and β-thalassemia. Common genetic variation affects expression of BCL11A, a regulator of HbF silencing. To uncover how BCL11A supports the developmental switch from γ- to β- globin, we use a functional assay and protein binding microarray to establish a requirement for a zinc-finger cluster in BCL11A in repression and identify a preferred DNA recognition sequence. This motif appears in embryonic and fetal-expressed globin promoters and is duplicated in γ-globin promoters. The more distal of the duplicated motifs is mutated in individuals with hereditary persistence of HbF. Using the CUT&RUN approach to map protein binding sites in erythroid cells, we demonstrate BCL11A occupancy preferentially at the distal motif, which can be disrupted by editing the promoter. Our findings reveal that direct γ-globin gene promoter repression by BCL11A underlies hemoglobin switching.
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Affiliation(s)
- Nan Liu
- Cancer and Blood Disorders Center, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Victoria V Hargreaves
- Cancer and Blood Disorders Center, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Qian Zhu
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jesse V Kurland
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jiyoung Hong
- Cancer and Blood Disorders Center, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Woojin Kim
- Cancer and Blood Disorders Center, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Falak Sher
- Cancer and Blood Disorders Center, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Claudio Macias-Trevino
- Cancer and Blood Disorders Center, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Julia M Rogers
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA
| | - Ryo Kurita
- Cell Engineering Division, RIKEN Bioresource Center, Tsukuba, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN Bioresource Center, Tsukuba, Japan
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Daniel E Bauer
- Cancer and Blood Disorders Center, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas at Southwestern Medical Center, Dallas, TX, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stuart H Orkin
- Cancer and Blood Disorders Center, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA.
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17
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The N-Terminal CCHC Zinc Finger Motif Mediates Homodimerization of Transcription Factor BCL11B. Mol Cell Biol 2018; 38:MCB.00368-17. [PMID: 29203643 DOI: 10.1128/mcb.00368-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/18/2017] [Indexed: 12/14/2022] Open
Abstract
The BCL11B gene encodes a Krüppel-like, sequence-specific zinc finger (ZF) transcription factor that acts as either a repressor or an activator, depending on its posttranslational modifications. The importance of BCL11B in numerous biological processes in multiple organs has been well established in mouse knockout models. The phenotype of the first de novo monoallelic germ line missense mutation in the BCL11B gene (encoding N441K) strongly implies that the mutant protein acts in a dominant-negative manner by neutralizing the unaffected protein through the formation of a nonfunctional dimer. Using a Förster resonance energy transfer-assisted fluorescence-activated cell sorting (FACS-FRET) assay and affinity purification followed by mass spectrometry (AP-MS), we show that the N-terminal CCHC zinc finger motif is necessary and sufficient for the formation of the BCL11B dimer. Mutation of the CCHC ZF in BCL11B abolishes its transcription-regulatory activity. In addition, unlike wild-type BCL11B, this mutant is incapable of inducing cell cycle arrest and protecting against DNA damage-driven apoptosis. Our results confirm the BCL11B dimerization hypothesis and prove its importance for BCL11B function. By mapping the relevant regions to the CCHC domain, we describe a previously unidentified mechanism of transcription factor homodimerization.
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18
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Baldauf MC, Orth MF, Dallmayer M, Marchetto A, Gerke JS, Rubio RA, Kiran MM, Musa J, Knott MML, Ohmura S, Li J, Akpolat N, Akatli AN, Özen Ö, Dirksen U, Hartmann W, de Alava E, Baumhoer D, Sannino G, Kirchner T, Grünewald TGP. Robust diagnosis of Ewing sarcoma by immunohistochemical detection of super-enhancer-driven EWSR1-ETS targets. Oncotarget 2017; 9:1587-1601. [PMID: 29416716 PMCID: PMC5788584 DOI: 10.18632/oncotarget.20098] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 07/23/2017] [Indexed: 12/26/2022] Open
Abstract
Ewing sarcoma is an undifferentiated small-round-cell sarcoma. Although molecular detection of pathognomonic EWSR1-ETS fusions such as EWSR1-FLI1 enables definitive diagnosis, substantial confusion can arise if molecular diagnostics are unavailable. Diagnosis based on the conventional immunohistochemical marker CD99 is unreliable due to its abundant expression in morphological mimics. To identify novel diagnostic immunohistochemical markers for Ewing sarcoma, we performed comparative expression analyses in 768 tumors representing 21 entities including Ewing-like sarcomas, which confirmed that CIC-DUX4-, BCOR-CCNB3-, EWSR1-NFATc2-, and EWSR1-ETS-translocated sarcomas are distinct entities, and revealed that ATP1A1, BCL11B, and GLG1 constitute specific markers for Ewing sarcoma. Their high expression was validated by immunohistochemistry and proved to depend on EWSR1-FLI1-binding to highly active proximal super-enhancers. Automated cut-off-finding and combination-testing in a tissue-microarray comprising 174 samples demonstrated that detection of high BCL11B and/or GLG1 expression is sufficient to reach 96% specificity for Ewing sarcoma. While 88% of tested Ewing-like sarcomas displayed strong CD99-immunoreactivity, none displayed combined strong BCL11B- and GLG1-immunoreactivity. Collectively, we show that ATP1A1, BCL11B, and GLG1 are EWSR1-FLI1 targets, of which BCL11B and GLG1 offer a fast, simple, and cost-efficient way to diagnose Ewing sarcoma by immunohistochemistry. These markers may significantly reduce the number of misdiagnosed patients, and thus improve patient care.
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Affiliation(s)
- Michaela C Baldauf
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marlene Dallmayer
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Julia S Gerke
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Rebeca Alba Rubio
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Merve M Kiran
- Department of Pathology, Medical Faculty, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Julian Musa
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Maximilian M L Knott
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Shunya Ohmura
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jing Li
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Nusret Akpolat
- Department of Pathology, Turgut Ozal Medical Center, Inonu University, Malatya, Turkey
| | - Ayse N Akatli
- Department of Pathology, Turgut Ozal Medical Center, Inonu University, Malatya, Turkey
| | - Özlem Özen
- Department of Pathology, Başkent University Hospital, Ankara, Turkey
| | - Uta Dirksen
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Wolfgang Hartmann
- Gerhard-Domagk-Institute for Pathology, University Hospital Münster, Westfalian Wilhelms University, Münster, Germany
| | - Enrique de Alava
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, CIBERONC, Seville, Spain
| | - Daniel Baumhoer
- Bone Tumour Reference Center, Institute of Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Giuseppina Sannino
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.,Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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19
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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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20
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Harlow ML, Maloney N, Roland J, Guillen Navarro MJ, Easton MK, Kitchen-Goosen SM, Boguslawski EA, Madaj ZB, Johnson BK, Bowman MJ, D'Incalci M, Winn ME, Turner L, Hostetter G, Galmarini CM, Aviles PM, Grohar PJ. Lurbinectedin Inactivates the Ewing Sarcoma Oncoprotein EWS-FLI1 by Redistributing It within the Nucleus. Cancer Res 2016; 76:6657-6668. [PMID: 27697767 DOI: 10.1158/0008-5472.can-16-0568] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 08/31/2016] [Accepted: 09/05/2016] [Indexed: 12/17/2022]
Abstract
There is a great need to develop novel approaches to target oncogenic transcription factors with small molecules. Ewing sarcoma is emblematic of this need, as it depends on the continued activity of the EWS-FLI1 transcription factor to maintain the malignant phenotype. We have previously shown that the small molecule trabectedin interferes with EWS-FLI1. Here, we report important mechanistic advances and a second-generation inhibitor to provide insight into the therapeutic targeting of EWS-FLI1. We discovered that trabectedin functionally inactivated EWS-FLI1 by redistributing the protein within the nucleus to the nucleolus. This effect was rooted in the wild-type functions of the EWSR1, compromising the N-terminal half of the chimeric oncoprotein, which is known to be similarly redistributed within the nucleus in the presence of UV light damage. A second-generation trabectedin analogue lurbinectedin (PM01183) caused the same nuclear redistribution of EWS-FLI1, leading to a loss of activity at the promoter, mRNA, and protein levels of expression. Tumor xenograft studies confirmed this effect, and it was increased in combination with irinotecan, leading to tumor regression and replacement of Ewing sarcoma cells with benign fat cells. The net result of combined lurbinectedin and irinotecan treatment was a complete reversal of EWS-FLI1 activity and elimination of established tumors in 30% to 70% of mice after only 11 days of therapy. Our results illustrate the preclinical safety and efficacy of a disease-specific therapy targeting the central oncogenic driver in Ewing sarcoma. Cancer Res; 76(22); 6657-68. ©2016 AACR.
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Affiliation(s)
- Matt L Harlow
- Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee
| | - Nichole Maloney
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee
| | - Joseph Roland
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | | | | | | | - Ben K Johnson
- Van Andel Research Institute, Grand Rapids, Michigan
| | | | | | - Mary E Winn
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Lisa Turner
- Van Andel Research Institute, Grand Rapids, Michigan
| | | | | | | | - Patrick J Grohar
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee. .,Van Andel Research Institute, Grand Rapids, Michigan.,Helen De Vos Children's Hospital, Grand Rapids, Michigan.,Department of Pediatrics, Michigan State University, Grand Rapids, Michigan
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21
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EWS-FLI1-mediated suppression of the RAS-antagonist Sprouty 1 (SPRY1) confers aggressiveness to Ewing sarcoma. Oncogene 2016; 36:766-776. [PMID: 27375017 DOI: 10.1038/onc.2016.244] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/05/2016] [Accepted: 05/30/2016] [Indexed: 02/07/2023]
Abstract
Ewing sarcoma is characterized by chromosomal translocations fusing the EWS gene with various members of the ETS family of transcription factors, most commonly FLI1. EWS-FLI1 is an aberrant transcription factor driving Ewing sarcoma tumorigenesis by either transcriptionally inducing or repressing specific target genes. Herein, we showed that Sprouty 1 (SPRY1), which is a physiological negative feedback inhibitor downstream of fibroblast growth factor (FGF) receptors (FGFRs) and other RAS-activating receptors, is an EWS-FLI1 repressed gene. EWS-FLI1 knockdown specifically increased the expression of SPRY1, while other Sprouty family members remained unaffected. Analysis of SPRY1 expression in a panel of Ewing sarcoma cells showed that SPRY1 was not expressed in Ewing sarcoma cell lines, suggesting that it could act as a tumor suppressor gene in these cells. In agreement, induction of SPRY1 in three different Ewing sarcoma cell lines functionally impaired proliferation, clonogenic growth and migration. In addition, SPRY1 expression inhibited extracellular signal-related kinase/mitogen-activated protein kinase (MAPK) signaling induced by serum and basic FGF (bFGF). Moreover, treatment of Ewing sarcoma cells with the potent FGFR inhibitor PD-173074 reduced bFGF-induced proliferation, colony formation and in vivo tumor growth in a dose-dependent manner, thus mimicking SPRY1 activity in Ewing sarcoma cells. Although the expression of SPRY1 was low when compared with other tumors, SPRY1 was variably expressed in primary Ewing sarcoma tumors and higher expression levels were significantly associated with improved outcome in a large patient cohort. Taken together, our data indicate that EWS-FLI1-mediated repression of SPRY1 leads to unrestrained bFGF-induced cell proliferation, suggesting that targeting the FGFR/MAPK pathway can constitute a promising therapeutic approach for this devastating disease.
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22
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Kim SK, Park YK. Ewing sarcoma: a chronicle of molecular pathogenesis. Hum Pathol 2016; 55:91-100. [PMID: 27246176 DOI: 10.1016/j.humpath.2016.05.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/25/2016] [Accepted: 05/12/2016] [Indexed: 01/08/2023]
Abstract
Sarcomas have traditionally been classified according to their chromosomal alterations regardless of whether they accompany simple or complex genetic changes. Ewing sarcoma, a classic small round cell bone tumor, is a well-known mesenchymal malignancy that results from simple sarcoma-specific genetic alterations. The genetic alterations are translocations between genes of the TET/FET family (TLS/FUS, EWSR1, and TAF15) and genes of the E26 transformation-specific (ETS) family. In this review, we intend to summarize a chronicle of molecular findings of Ewing sarcoma including recent advances and explain resultant molecular pathogenesis.
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Affiliation(s)
- Sang Kyum Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Yong-Koo Park
- Department of Pathology, Kyung Hee University College of Medicine, Seoul, Korea.
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23
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Gordon DJ, Motwani M, Pellman D. Modeling the initiation of Ewing sarcoma tumorigenesis in differentiating human embryonic stem cells. Oncogene 2015; 35:3092-102. [PMID: 26455317 PMCID: PMC4829493 DOI: 10.1038/onc.2015.368] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 07/12/2015] [Accepted: 08/31/2015] [Indexed: 01/08/2023]
Abstract
Oncogenic transformation in Ewing sarcoma tumors is driven by the fusion oncogene EWS-FLI1. However, despite the well-established role of EWS-FLI1 in tumor initiation, the development of models of Ewing sarcoma in human cells with defined genetic elements has been challenging. Here, we report a novel approach to model the initiation of Ewing sarcoma tumorigenesis that exploits the developmental and pluripotent potential of human embryonic stem cells. The inducible expression of EWS-FLI1 in embryoid bodies, or collections of differentiating stem cells, generates cells with properties of Ewing sarcoma tumors, including characteristics of transformation. These cell lines exhibit anchorage-independent growth, a lack of contact inhibition and a strong Ewing sarcoma gene expression signature. Furthermore, these cells also demonstrate a requirement for the persistent expression of EWS-FLI1 for cell survival and growth, which is a hallmark Ewing sarcoma tumors.
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Affiliation(s)
- D J Gordon
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - M Motwani
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - D Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
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24
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Bauer DE, Orkin SH. Hemoglobin switching's surprise: the versatile transcription factor BCL11A is a master repressor of fetal hemoglobin. Curr Opin Genet Dev 2015; 33:62-70. [PMID: 26375765 DOI: 10.1016/j.gde.2015.08.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 07/23/2015] [Accepted: 08/05/2015] [Indexed: 12/23/2022]
Abstract
The major disorders of β-globin, sickle cell disease and β-thalassemia, may be ameliorated by expression of the fetal gene paralog γ-globin. Uncertainty regarding the mechanisms repressing fetal hemoglobin in the adult stage has served as a puzzle of developmental gene regulation as well as a barrier to rational therapeutic design. Recent genome-wide association studies implicated the zinc-finger transcriptional repressor BCL11A in fetal hemoglobin regulation. Extensive genetic analyses have validated BCL11A as a potent repressor of fetal hemoglobin level. Studies of BCL11A exemplify how contextual gene regulation may often be the substrate for trait-associated common genetic variation. These discoveries have suggested novel rational approaches for the β-hemoglobin disorders including therapeutic genome editing.
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Affiliation(s)
- Daniel E Bauer
- Boston Children's Hospital, Boston, MA 02115, United States; Dana-Farber Cancer Institute, Boston, MA 02115, United States; Harvard Medical School, Boston, MA 02115, United States; Harvard Stem Cell Institute, Cambridge, MA 02138, United States.
| | - Stuart H Orkin
- Boston Children's Hospital, Boston, MA 02115, United States; Dana-Farber Cancer Institute, Boston, MA 02115, United States; Harvard Medical School, Boston, MA 02115, United States; Harvard Stem Cell Institute, Cambridge, MA 02138, United States; Howard Hughes Medical Institute, Boston, MA 02115, United States.
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25
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Sand LGL, Szuhai K, Hogendoorn PCW. Sequencing Overview of Ewing Sarcoma: A Journey across Genomic, Epigenomic and Transcriptomic Landscapes. Int J Mol Sci 2015; 16:16176-215. [PMID: 26193259 PMCID: PMC4519945 DOI: 10.3390/ijms160716176] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 12/17/2022] Open
Abstract
Ewing sarcoma is an aggressive neoplasm occurring predominantly in adolescent Caucasians. At the genome level, a pathognomonic EWSR1-ETS translocation is present. The resulting fusion protein acts as a molecular driver in the tumor development and interferes, amongst others, with endogenous transcription and splicing. The Ewing sarcoma cell shows a poorly differentiated, stem-cell like phenotype. Consequently, the cellular origin of Ewing sarcoma is still a hot discussed topic. To further characterize Ewing sarcoma and to further elucidate the role of EWSR1-ETS fusion protein multiple genome, epigenome and transcriptome level studies were performed. In this review, the data from these studies were combined into a comprehensive overview. Presently, classical morphological predictive markers are used in the clinic and the therapy is dominantly based on systemic chemotherapy in combination with surgical interventions. Using sequencing, novel predictive markers and candidates for immuno- and targeted therapy were identified which were summarized in this review.
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Affiliation(s)
- Laurens G L Sand
- Department of Pathology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
| | - Karoly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
| | - Pancras C W Hogendoorn
- Department of Pathology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
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26
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Liao CK, Fang KM, Chai K, Wu CH, Ho CH, Yang CS, Tzeng SF. Depletion of B cell CLL/Lymphoma 11B Gene Expression Represses Glioma Cell Growth. Mol Neurobiol 2015; 53:3528-3539. [PMID: 26096706 DOI: 10.1007/s12035-015-9231-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/22/2015] [Indexed: 11/29/2022]
Abstract
B cell CLL/lymphoma 11B (Bcl11b), a C2H2 zinc finger transcription factor, not only serves as a critical regulator in development but also plays the controversial role in T cell acute lymphoblastic leukemia (T-ALL). We previously found that the enriched expression of Bcl11b was detected in high tumorigenic C6 glioma cells. However, the role of Bcl11b in glioma malignancy and its mechanisms remains to be uncovered. In this study, using the lentivirus-mediated knockdown (KD) approach, we found that Bcl11b KD in tumorigenic C6 cells reduced the cell proliferation, colony formation, and migratory ability. The results were further verified using two human malignant glioma cell lines, U87 and U251 cells. A cyclin-dependent kinase inhibitor p21, a known Bcl11b target, was significantly upregulated in tumorigenic C6, U87, and U251 cells after Bcl11b KD. Cellular senescence was observed by examination of the β-galactosidase activity in U87 and U251 cells with Bcl11b KD. Reduced expression of stemness gene Sox-2 and its downstream effector Bmi-1 was also observed in U87 and U251 cells with Bcl11b KD. These results suggest that the ablation of Bcl11b gene expression induced glioma cell senescence. Propidium iodide (PI) staining combined with flow cytometry analysis also showed that Bcl11b KD led to the cell cycle arrest of U87 and U251 cells at the G0/G1 or at the S phase, indicating that Bcl11b is required for glioma cell cycle progression. Together, this is the first study to show that the inhibition of Bcl11b suppresses glioma cell growth by regulating the expression of the cell cycle regulator p21 and stemness-associated genes (Sox-2/Bmi-1).
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Affiliation(s)
- Chih-Kai Liao
- Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Kuan-Min Fang
- Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Kitman Chai
- Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Chin-Hsien Wu
- Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Hsin Ho
- Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Chung-Shi Yang
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Shun-Fen Tzeng
- Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
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27
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Sakamaki A, Katsuragi Y, Otsuka K, Tomita M, Obata M, Iwasaki T, Abe M, Sato T, Ochiai M, Sakuraba Y, Aoyagi Y, Gondo Y, Sakimura K, Nakagama H, Mishima Y, Kominami R. Bcl11b SWI/SNF-complex subunit modulates intestinal adenoma and regeneration after γ-irradiation through Wnt/β-catenin pathway. Carcinogenesis 2015; 36:622-31. [PMID: 25827435 DOI: 10.1093/carcin/bgv044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/28/2015] [Indexed: 01/23/2023] Open
Abstract
SWI/SNF chromatin remodeling complexes constitute a highly related family of multi-subunit complexes to modulate transcription, and SWI/SNF subunit genes are collectively mutated in 20% of all human cancers. Bcl11b is a SWI/SNF subunit and acts as a haploinsufficient tumor suppressor in leukemia/lymphomas. Here, we show expression of Bcl11b in intestinal crypt cells and promotion of intestinal tumorigenesis by Bcl11b attenuation in Apc (min/+) mice. Of importance, mutations or allelic loss of BCL11B was detected in one-third of human colon cancers. We also show that attenuated Bcl11b activity in the crypt base columnar (CBC) cells expressing the Lgr5 stem cell marker enhanced regeneration of intestinal epithelial cells after the radiation-induced injury. Interestingly, BCL11B introduction in human cell lines downregulated transcription of β-catenin target genes, whereas Bcl11b attenuation in Lgr5(+) CBCs increased expression of β-catenin targets including c-Myc and cyclin D1. Together, our results argue that Bcl11b impairment promotes tumor development in mouse and human intestine at least in part through deregulation of β-catenin pathway.
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Affiliation(s)
- Akira Sakamaki
- Department of Molecular Genetics, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry, 2-11-1 Iwado-kita, Komae-shi, Tokyo, 201-8511, Japan, Brain Research Institute, Niigata University, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan and RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshinori Katsuragi
- Department of Molecular Genetics, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry, 2-11-1 Iwado-kita, Komae-shi, Tokyo, 201-8511, Japan, Brain Research Institute, Niigata University, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan and RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kensuke Otsuka
- Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry, 2-11-1 Iwado-kita, Komae-shi, Tokyo, 201-8511, Japan
| | - Masanori Tomita
- Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry, 2-11-1 Iwado-kita, Komae-shi, Tokyo, 201-8511, Japan
| | - Miki Obata
- Department of Molecular Genetics, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry, 2-11-1 Iwado-kita, Komae-shi, Tokyo, 201-8511, Japan, Brain Research Institute, Niigata University, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan and RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohiro Iwasaki
- Department of Molecular Genetics, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry, 2-11-1 Iwado-kita, Komae-shi, Tokyo, 201-8511, Japan, Brain Research Institute, Niigata University, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan and RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Manabu Abe
- Brain Research Institute, Niigata University, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan
| | - Toshihiro Sato
- Department of Molecular Genetics, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry, 2-11-1 Iwado-kita, Komae-shi, Tokyo, 201-8511, Japan, Brain Research Institute, Niigata University, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan and RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Masako Ochiai
- Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan and
| | - Yoshiyuki Sakuraba
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yutaka Aoyagi
- Department of Molecular Genetics, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry, 2-11-1 Iwado-kita, Komae-shi, Tokyo, 201-8511, Japan, Brain Research Institute, Niigata University, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan and RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoichi Gondo
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kenji Sakimura
- Brain Research Institute, Niigata University, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan
| | - Hitoshi Nakagama
- Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan and
| | - Yukio Mishima
- Department of Molecular Genetics, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry, 2-11-1 Iwado-kita, Komae-shi, Tokyo, 201-8511, Japan, Brain Research Institute, Niigata University, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan and RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ryo Kominami
- Department of Molecular Genetics, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry, 2-11-1 Iwado-kita, Komae-shi, Tokyo, 201-8511, Japan, Brain Research Institute, Niigata University, Asahimachi 1-757, Chuo-ku, Niigata 951-8510, Japan, Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan and RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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28
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Marques Howarth M, Simpson D, Ngok SP, Nieves B, Chen R, Siprashvili Z, Vaka D, Breese MR, Crompton BD, Alexe G, Hawkins DS, Jacobson D, Brunner AL, West R, Mora J, Stegmaier K, Khavari P, Sweet-Cordero EA. Long noncoding RNA EWSAT1-mediated gene repression facilitates Ewing sarcoma oncogenesis. J Clin Invest 2014; 124:5275-90. [PMID: 25401475 DOI: 10.1172/jci72124] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 10/09/2014] [Indexed: 12/23/2022] Open
Abstract
Chromosomal translocation that results in fusion of the genes encoding RNA-binding protein EWS and transcription factor FLI1 (EWS-FLI1) is pathognomonic for Ewing sarcoma. EWS-FLI1 alters gene expression through mechanisms that are not completely understood. We performed RNA sequencing (RNAseq) analysis on primary pediatric human mesenchymal progenitor cells (pMPCs) expressing EWS-FLI1 in order to identify gene targets of this oncoprotein. We determined that long noncoding RNA-277 (Ewing sarcoma-associated transcript 1 [EWSAT1]) is upregulated by EWS-FLI1 in pMPCs. Inhibition of EWSAT1 expression diminished the ability of Ewing sarcoma cell lines to proliferate and form colonies in soft agar, whereas EWSAT1 inhibition had no effect on other cell types tested. Expression of EWS-FLI1 and EWSAT1 repressed gene expression, and a substantial fraction of targets that were repressed by EWS-FLI1 were also repressed by EWSAT1. Analysis of RNAseq data from primary human Ewing sarcoma further supported a role for EWSAT1 in mediating gene repression. We identified heterogeneous nuclear ribonucleoprotein (HNRNPK) as an RNA-binding protein that interacts with EWSAT1 and found a marked overlap in HNRNPK-repressed genes and those repressed by EWS-FLI1 and EWSAT1, suggesting that HNRNPK participates in EWSAT1-mediated gene repression. Together, our data reveal that EWSAT1 is a downstream target of EWS-FLI1 that facilitates the development of Ewing sarcoma via the repression of target genes.
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MESH Headings
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Down-Regulation/genetics
- Gene Expression Regulation, Neoplastic
- Heterogeneous-Nuclear Ribonucleoprotein K
- Humans
- Oncogene Proteins, Fusion/biosynthesis
- Oncogene Proteins, Fusion/genetics
- Proto-Oncogene Protein c-fli-1/biosynthesis
- Proto-Oncogene Protein c-fli-1/genetics
- RNA, Long Noncoding/biosynthesis
- RNA, Long Noncoding/genetics
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- RNA-Binding Protein EWS/biosynthesis
- RNA-Binding Protein EWS/genetics
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Sarcoma, Ewing/genetics
- Sarcoma, Ewing/metabolism
- Sarcoma, Ewing/pathology
- Sequence Analysis, RNA
- Up-Regulation/genetics
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29
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Bledsoe KL, McGee-Lawrence ME, Camilleri ET, Wang X, Riester SM, van Wijnen AJ, Oliveira AM, Westendorf JJ. RUNX3 facilitates growth of Ewing sarcoma cells. J Cell Physiol 2014; 229:2049-56. [PMID: 24812032 DOI: 10.1002/jcp.24663] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/06/2014] [Indexed: 01/01/2023]
Abstract
Ewing sarcoma is an aggressive pediatric small round cell tumor that predominantly occurs in bone. Approximately 85% of Ewing sarcomas harbor the EWS/FLI fusion protein, which arises from a chromosomal translocation, t(11:22)(q24:q12). EWS/FLI interacts with numerous lineage-essential transcription factors to maintain mesenchymal progenitors in an undifferentiated state. We previously showed that EWS/FLI binds the osteogenic transcription factor RUNX2 and prevents osteoblast differentiation. In this study, we investigated the role of another Runt-domain protein, RUNX3, in Ewing sarcoma. RUNX3 participates in mesenchymal-derived bone formation and is a context dependent tumor suppressor and oncogene. RUNX3 was detected in all Ewing sarcoma cells examined, whereas RUNX2 was detected in only 73% of specimens. Like RUNX2, RUNX3 binds to EWS/FLI via its Runt domain. EWS/FLI prevented RUNX3 from activating the transcription of a RUNX-responsive reporter, p6OSE2. Stable suppression of RUNX3 expression in the Ewing sarcoma cell line A673 delayed colony growth in anchorage independent soft agar assays and reversed expression of EWS/FLI-responsive genes. These results demonstrate an important role for RUNX3 in Ewing sarcoma.
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30
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Le Douce V, Cherrier T, Riclet R, Rohr O, Schwartz C. [CTIP2, a multifunctional protein: cellular physiopathology and therapeutic implications]. Med Sci (Paris) 2014; 30:797-802. [PMID: 25174758 DOI: 10.1051/medsci/20143008019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The transcription factor CTIP2 (BCL11B) is a multifunctional protein involved in numerous cell physiological processes. To date, many molecular mechanisms underlying this process have been discovered, which highlighted the importance of the epigenetic regulation of genes and the regulation of the elongation factor P-TEFb. Furthermore studies of the deregulation of CTIP2 showed the association of CTIP2 to numerous pathologies including cancer and cardiac hypertrophy. A better comprehension of the physiopathology of these diseases might lead to the design of therapeutical strategies intending to prevent CTIP2 deregulation. Moreover, CTIP2 and its associated proteins constitute potential targets in strategies aiming to reduce and/or purge HIV-1 cell reservoirs.
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Affiliation(s)
- Valentin Le Douce
- Institut de parasitologie et de pathologie tropicale, EA7292, université de Strasbourg, Strasbourg, France - IUT de Schiltigheim, 1 allée d'Athènes, Schiltigheim, France
| | - Thomas Cherrier
- Laboratory of protein -interactions and signaling, -université de Liège, Liège, Belgique
| | - Raphaël Riclet
- Institut de parasitologie et de pathologie tropicale, EA7292, université de Strasbourg, Strasbourg, France
| | - Olivier Rohr
- Institut de parasitologie et de pathologie tropicale, EA7292, université de Strasbourg, Strasbourg, France - IUT de Schiltigheim, 1 allée d'Athènes, Schiltigheim, France - Institut universitaire de France, 103, boulevard Saint-Michel, 75005 Paris, France
| | - Christian Schwartz
- Institut de parasitologie et de pathologie tropicale, EA7292, université de Strasbourg, Strasbourg, France - IUT de Schiltigheim, 1 allée d'Athènes, Schiltigheim, France
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31
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Kovar H. Blocking the road, stopping the engine or killing the driver? Advances in targeting EWS/FLI-1 fusion in Ewing sarcoma as novel therapy. Expert Opin Ther Targets 2014; 18:1315-28. [PMID: 25162919 DOI: 10.1517/14728222.2014.947963] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Ewing sarcoma (ES) represents the paradigm of an aberrant E-twenty-six (ETS) oncogene-driven cancer. It is characterized by specific rearrangements of one of five alternative ETS family member genes with EWSR1. There is experimental evidence that the resulting fusion proteins act as aberrant transcription factors driving ES pathogenesis. The transcriptional gene regulatory network driven by EWS-ETS proteins provides the oncogenic engine to the tumor. Therefore, EWS-ETS and their downstream machinery are considered ideal tumor-specific therapeutic targets. AREAS COVERED This review critically discusses the literature on the development of EWS-ETS-directed ES targeting strategies considering current knowledge of EWS-ETS biology and cellular context. It focuses on determinants of EWS-FLI1 function with an emphasis on interactions with chromatin structure. We speculate about the relevance of poorly investigated aspects in ES research such as chromatin remodeling and DNA damage repair for the development of targeted therapies. EXPERT OPINION This review questions the specificity of signature-based screening approaches to the identification of EWS-FLI1-targeted compounds. It challenges the view that targeting the downstream gene regulatory network carries potential for therapeutic breakthroughs because of resistance-inducing network rewiring. Instead, we propose to combine targeting of the fusion protein with epigenetic therapy as a future treatment strategy in ES.
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Affiliation(s)
- Heinrich Kovar
- Children´s Cancer Research Institute, St. Anna Kinderkrebsforschung, and Medical University Vienna, Department of Pediatrics , Zimmermannplatz 10, A1090 Vienna , Austria +43 1 40470 4092 ; +43 1 40470 64092 ;
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32
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Le Douce V, Cherrier T, Riclet R, Rohr O, Schwartz C. The many lives of CTIP2: from AIDS to cancer and cardiac hypertrophy. J Cell Physiol 2014; 229:533-7. [PMID: 24122342 DOI: 10.1002/jcp.24490] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/04/2013] [Indexed: 12/27/2022]
Abstract
CTIP2 is a key transcriptional regulator involved in numerous physiological functions. Initial works have shown the importance of CTIP2 in the establishment and persistence of HIV latency in microglial cells, the main latent/quiescent viral reservoir in the brain. Recent studies have highlighted the importance of CTIP2 in several other pathologies, such as cardiac hypertrophy and various types of human malignancies. Targeting CTIP2 may therefore constitute a new approach in the treatment of these pathologies.
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Affiliation(s)
- Valentin Le Douce
- Institut de Parasitologie et de Pathologie Tropicale, EA7292, Université de Strasbourg, Strasbourg, France; IUT de Schiltigheim, 1 Allée d'Athènes, Schiltigheim, France
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33
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Wiles ET, Bell R, Thomas D, Beckerle M, Lessnick SL. ZEB2 Represses the Epithelial Phenotype and Facilitates Metastasis in Ewing Sarcoma. Genes Cancer 2014; 4:486-500. [PMID: 24386509 DOI: 10.1177/1947601913506115] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/30/2013] [Indexed: 01/06/2023] Open
Abstract
The vast majority of cancer-related deaths are attributable to metastasis. Effective treatment of metastatic disease will be improved by a better understanding of the molecular mechanisms contributing to this phenomenon. Much of the work in this field has focused on metastasis of carcinomas, tumors of epithelial origin, while metastasis of sarcomas, tumors of mesenchymal origin, remains poorly understood. Experimental evidence from studies in carcinomas, coupled with clinical observations, highlights the importance of both epithelial and mesenchymal characteristics in these cancer cells that make them competent for metastasis. We set out to test if similar cellular plasticity contributes to sarcoma metastasis. We found that the transcription factor, ZEB2, repressed epithelial gene expression in Ewing sarcoma cells, and this, in turn, repressed the epithelial phenotype. When ZEB2 was experimentally reduced in these cells, epithelial characteristics including decreased migratory ability and cytoskeleton rearrangements were observed. Furthermore, ZEB2 reduction in Ewing sarcoma cells resulted in a decreased metastatic potential using a mouse metastasis model. Our data show that Ewing sarcoma cells may have more epithelial plasticity than previously appreciated. This coupled with previous data demonstrating Ewing sarcoma cells also have mesenchymal features primes these cells to successfully metastasize. This is clinically relevant for 2 important reasons. First, this may offer a therapeutic opportunity to induce characteristics of one cell type or the other depending on the stage of the disease. Second, and more broadly, this raises questions about the cell of origin in Ewing sarcoma and may inform future animal models of the disease.
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Affiliation(s)
- Elizabeth T Wiles
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA ; Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Russell Bell
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA ; Center for Children's Cancer Research, University of Utah, Salt Lake City, UT, USA
| | - Dafydd Thomas
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mary Beckerle
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA ; Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA ; Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Stephen L Lessnick
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA ; Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA ; Center for Children's Cancer Research, University of Utah, Salt Lake City, UT, USA ; Division of Pediatric Hematology/Oncology, University of Utah, Salt Lake City, UT, USA
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