1
|
Feng X, Tao J, Wang Y, Long AY, He LJ, Zhang N. [Clinicopathological and molecular characteristics of angiomatoid fibrous histiocytoma in children]. Zhonghua Bing Li Xue Za Zhi 2024; 53:483-485. [PMID: 38678331 DOI: 10.3760/cma.j.cn112151-20231026-00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
MESH Headings
- Humans
- Female
- Child
- Male
- Child, Preschool
- Histiocytoma, Malignant Fibrous/pathology
- Histiocytoma, Malignant Fibrous/metabolism
- Histiocytoma, Malignant Fibrous/genetics
- Histiocytoma, Malignant Fibrous/diagnosis
- Histiocytoma, Malignant Fibrous/surgery
- Actins/metabolism
- RNA-Binding Protein EWS/genetics
- RNA-Binding Protein EWS/metabolism
- 12E7 Antigen/metabolism
- In Situ Hybridization, Fluorescence
- Anaplastic Lymphoma Kinase/genetics
- Anaplastic Lymphoma Kinase/metabolism
- Soft Tissue Neoplasms/pathology
- Soft Tissue Neoplasms/genetics
- Soft Tissue Neoplasms/metabolism
- Soft Tissue Neoplasms/surgery
- Antigens, CD/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Cell Adhesion Molecules/metabolism
- Cell Adhesion Molecules/genetics
Collapse
Affiliation(s)
- X Feng
- Department of Pathology, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - J Tao
- Department of Pathology, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Y Wang
- Department of Pathology, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - A Y Long
- Department of Pathology, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - L J He
- Department of Pathology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - N Zhang
- Department of Pathology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| |
Collapse
|
2
|
Magrath JW, Sampath SS, Flinchum DA, Hartono AB, Goldberg IN, Boehling JR, Savkovic SD, Lee SB. Comprehensive Transcriptomic Analysis of EWSR1::WT1 Targets Identifies CDK4/6 Inhibitors as an Effective Therapy for Desmoplastic Small Round Cell Tumors. Cancer Res 2024; 84:1426-1442. [PMID: 38588409 PMCID: PMC11063761 DOI: 10.1158/0008-5472.can-23-3334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/28/2023] [Accepted: 02/07/2024] [Indexed: 04/10/2024]
Abstract
Desmoplastic small round cell tumors (DSRCT) are a type of aggressive, pediatric sarcoma characterized by the EWSR1::WT1 fusion oncogene. Targeted therapies for DSRCT have not been developed, and standard multimodal therapy is insufficient, leading to a 5-year survival rate of only 15% to 25%. Here, we depleted EWSR1::WT1 in DSRCT and established its essentiality in vivo. Transcriptomic analysis revealed that EWSR1::WT1 induces unique transcriptional alterations compared with WT1 and other fusion oncoproteins and that EWSR1::WT1 binding directly mediates gene upregulation. The E-KTS isoform of EWSR1::WT1 played a dominant role in transcription, and it bound to the CCND1 promoter and stimulated DSRCT growth through the cyclin D-CDK4/6-RB axis. Treatment with the CDK4/6 inhibitor palbociclib successfully reduced growth in two DSRCT xenograft models. As palbociclib has been approved by the FDA for the treatment of breast cancer, these findings demonstrate the sensitivity of DSRCT to palbociclib and support immediate clinical investigation of palbociclib for treating this aggressive pediatric cancer. SIGNIFICANCE EWSR1::WT1 is essential for desmoplastic small round cell tumors and upregulates the cyclin D-CDK4/6-RB axis that can be targeted with palbociclib, providing a targeted therapeutic strategy for treating this deadly tumor type.
Collapse
Affiliation(s)
- Justin W. Magrath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Shruthi Sanjitha Sampath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Dane A. Flinchum
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Alifiani B. Hartono
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Ilon N. Goldberg
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Julia R. Boehling
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Suzana D. Savkovic
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Sean B. Lee
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| |
Collapse
|
3
|
Johnson CN, Sojitra KA, Sohn EJ, Moreno-Romero AK, Baudin A, Xu X, Mittal J, Libich DS. Insights into Molecular Diversity within the FUS/EWS/TAF15 Protein Family: Unraveling Phase Separation of the N-Terminal Low-Complexity Domain from RNA-Binding Protein EWS. J Am Chem Soc 2024; 146:8071-8085. [PMID: 38492239 DOI: 10.1021/jacs.3c12034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
The FET protein family, comprising FUS, EWS, and TAF15, plays crucial roles in mRNA maturation, transcriptional regulation, and DNA damage response. Clinically, they are linked to Ewing family tumors and neurodegenerative diseases such as amyotrophic lateral sclerosis. The fusion protein EWS::FLI1, the causative mutation of Ewing sarcoma, arises from a genomic translocation that fuses a portion of the low-complexity domain (LCD) of EWS (EWSLCD) with the DNA binding domain of the ETS transcription factor FLI1. This fusion protein modifies transcriptional programs and disrupts native EWS functions, such as splicing. The exact role of the intrinsically disordered EWSLCD remains a topic of active investigation, but its ability to phase separate and form biomolecular condensates is believed to be central to EWS::FLI1's oncogenic properties. Here, we used paramagnetic relaxation enhancement NMR, microscopy, and all-atom molecular dynamics (MD) simulations to better understand the self-association and phase separation tendencies of the EWSLCD. Our NMR data and mutational analysis suggest that a higher density and proximity of tyrosine residues amplify the likelihood of condensate formation. MD simulations revealed that the tyrosine-rich termini exhibit compact conformations with unique contact networks and provided critical input on the relationship between contacts formed within a single molecule (intramolecular) and inside the condensed phase (intermolecular). These findings enhance our understanding of FET proteins' condensate-forming capabilities and underline differences between EWS, FUS, and TAF15.
Collapse
Affiliation(s)
- Courtney N Johnson
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Kandarp A Sojitra
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Erich J Sohn
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Alma K Moreno-Romero
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Antoine Baudin
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Xiaoping Xu
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843, United States
| | - David S Libich
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| |
Collapse
|
4
|
Ruzanov P, Evdokimova V, Pachva MC, Minkovich A, Zhang Z, Langman S, Gassmann H, Thiel U, Orlic-Milacic M, Zaidi SH, Peltekova V, Heisler LE, Sharma M, Cox ME, McKee TD, Zaidi M, Lapouble E, McPherson JD, Delattre O, Radvanyi L, Burdach SE, Stein LD, Sorensen PH. Oncogenic ETS fusions promote DNA damage and proinflammatory responses via pericentromeric RNAs in extracellular vesicles. J Clin Invest 2024; 134:e169470. [PMID: 38530366 PMCID: PMC11060741 DOI: 10.1172/jci169470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
Aberrant expression of the E26 transformation-specific (ETS) transcription factors characterizes numerous human malignancies. Many of these proteins, including EWS:FLI1 and EWS:ERG fusions in Ewing sarcoma (EwS) and TMPRSS2:ERG in prostate cancer (PCa), drive oncogenic programs via binding to GGAA repeats. We report here that both EWS:FLI1 and ERG bind and transcriptionally activate GGAA-rich pericentromeric heterochromatin. The respective pathogen-like HSAT2 and HSAT3 RNAs, together with LINE, SINE, ERV, and other repeat transcripts, are expressed in EwS and PCa tumors, secreted in extracellular vesicles (EVs), and are highly elevated in plasma of patients with EwS with metastatic disease. High human satellite 2 and 3 (HSAT2,3) levels in EWS:FLI1- or ERG-expressing cells and tumors were associated with induction of G2/M checkpoint, mitotic spindle, and DNA damage programs. These programs were also activated in EwS EV-treated fibroblasts, coincident with accumulation of HSAT2,3 RNAs, proinflammatory responses, mitotic defects, and senescence. Mechanistically, HSAT2,3-enriched cancer EVs induced cGAS-TBK1 innate immune signaling and formation of cytosolic granules positive for double-strand RNAs, RNA-DNA, and cGAS. Hence, aberrantly expressed ETS proteins derepress pericentromeric heterochromatin, yielding pathogenic RNAs that transmit genotoxic stress and inflammation to local and distant sites. Monitoring HSAT2,3 plasma levels and preventing their dissemination may thus improve therapeutic strategies and blood-based diagnostics.
Collapse
Affiliation(s)
- Peter Ruzanov
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Manideep C. Pachva
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alon Minkovich
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Zhenbo Zhang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sofya Langman
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hendrik Gassmann
- Department of Pediatrics, Children’s Cancer Research Center, Kinderklinik München Schwabing, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Uwe Thiel
- Department of Pediatrics, Children’s Cancer Research Center, Kinderklinik München Schwabing, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | | | - Syed H. Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vanya Peltekova
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Manju Sharma
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Michael E. Cox
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Trevor D. McKee
- STTARR Innovation Centre, Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Pathomics Inc., Toronto, Ontario, Canada
| | - Mark Zaidi
- Pathomics Inc., Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Eve Lapouble
- Unité Génétique Somatique (UGS), Institut Curie, Centre Hospitalier Paris, France
| | - John D. McPherson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Olivier Delattre
- Unité Génétique Somatique (UGS), Institut Curie, Centre Hospitalier Paris, France
- Diversity and Plasticity of Childhood tumors, INSERM U830, Institut Curie Research Center, PSL Research University, Paris, France
| | - Laszlo Radvanyi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Stefan E.G. Burdach
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pediatrics, Children’s Cancer Research Center, Kinderklinik München Schwabing, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- CCC München Comprehensive Cancer Center, DKTK German Cancer Consortium, Munich, Germany
- Institute of Pathology, Translation Pediatric Cancer Research Action, School of Medicine, Technical University of Munich, Munich, Germany
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Poul H. Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
5
|
Sundara Rajan S, Ebegboni VJ, Pichling P, Ludwig KR, Jones TL, Chari R, Tran A, Kruhlak MJ, Loncarek J, Caplen NJ. Endogenous EWSR1 Exists in Two Visual Modalities That Reflect Its Associations with Nucleic Acids and Concentration at Sites of Active Transcription. Mol Cell Biol 2024; 44:103-122. [PMID: 38506112 PMCID: PMC10986767 DOI: 10.1080/10985549.2024.2315425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 03/21/2024] Open
Abstract
EWSR1 is a member of the FET family of nucleic acid binding proteins that includes FUS and TAF15. Here, we report the systematic analysis of endogenous EWSR1's cellular organization in human cells. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.
Collapse
Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Vernon J. Ebegboni
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Patricio Pichling
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, Maryland, USA
| | - Andy Tran
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael J. Kruhlak
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jadranka Loncarek
- Centrosome Biology Section, Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
6
|
Warmke LM, Perret R, Ledoux P, Michot A, Italiano A, Zou YS, Matoso A, Argani P, Ulbright TM, Baumhoer D, Ameline B, Gross JM. EWSR1::WT1 Fusions in Neoplasms Other Than Conventional Desmoplastic Small Round Cell Tumor: Three Tumors Occurring Outside the Female Genital Tract. Mod Pathol 2024; 37:100418. [PMID: 38158126 DOI: 10.1016/j.modpat.2023.100418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/07/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Desmoplastic small round cell tumor (DSRCT) is a high-grade, primitive round cell sarcoma classically associated with prominent desmoplastic stroma, coexpression of keratin and desmin, and a characteristic EWSR1::WT1 gene fusion. DSRCT typically arises in the abdominopelvic cavity of young males with diffuse peritoneal spread and poor overall survival. Although originally considered to be pathognomonic for DSRCT, EWSR1::WT1 gene fusions have recently been detected in rare tumors lacking the characteristic morphologic and immunohistochemical features of DSRCT. Here, we report 3 additional cases of neoplasms other than conventional DSCRCT with EWSR1::WT1 gene fusions that occurred outside the female genital tract. Two occurred in the abdominopelvic cavities of a 27-year-old man and a 12-year-old girl, whereas the third arose in the axillary soft tissue of an 85-year-old man. All cases lacked prominent desmoplastic stroma and were instead solid and cystic with peripheral fibrous pseudocapsules and occasional intervening fibrous septa. Necrosis was either absent (1/3) or rare (2/3), and mitotic activity was low (<1 to 3 per 10 hpf). In immunohistochemical studies, there was expression of smooth muscle actin (3/3) and desmin (3/3), rare to focal reactivity for EMA (2/3), and variable expression of CK AE1/AE3 (1/3). Myogenin and MyoD1 were negative, and C-terminus-specific WT1 was positive in both cases tested (2/2). All 3 tumors followed a more indolent clinical course with 2 cases demonstrating no evidence of disease at 20 and 44 months after resection. The patient from case 3 died of other causes at 14 months with no evidence of recurrence. DNA methylation profiling showed that the 3 cases clustered with DSRCT; however, they demonstrated fewer copy number variations with 2 cases having a flat profile (0% copy number variation). Differential methylation analysis with hierarchical clustering further showed variation between the 3 cases and conventional DSRCT. Although further study is needed, our results, in addition to previous reports, suggest that EWSR1::WT1 gene fusions occur in rare and seemingly distinctive tumors other than conventional DSRCT with indolent behavior. Proper classification of these unusual soft tissue tumors with EWSR1::WT1 gene fusions requires direct correlation with tumor morphology and clinical behavior, which is essential to avoid overtreatment with aggressive chemotherapy.
Collapse
Affiliation(s)
- Laura M Warmke
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Raul Perret
- Department of Biopathology, Institut Bergonié, Comprehensive Cancer Center, Bordeaux, France; Bordeaux Institute of Oncology, BRIC, INSERM, Bordeaux University, Bergonié Institute, Bordeaux, France
| | - Pauline Ledoux
- Department of Diagnostic and Interventional Oncological Imaging, Institut Bergonié, Regional Comprehensive Cancer of Nouvelle-Aquitaine, Bordeaux, France
| | - Audrey Michot
- Plastic and Reconstructive Surgery Department, Bergonié Institute, Bordeaux, France
| | - Antoine Italiano
- Sarcoma Unit, Institut Bergonié, Bordeaux, Gironde, France; Faculty of Medicine, University of Bordeaux, Bordeaux, Gironde, France
| | - Ying S Zou
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland
| | - Andres Matoso
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland
| | - Pedram Argani
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland
| | - Thomas M Ulbright
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Daniel Baumhoer
- Bone Tumor Reference Center at the Institute of Pathology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Baptiste Ameline
- Bone Tumor Reference Center at the Institute of Pathology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - John M Gross
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland
| |
Collapse
|
7
|
Elkin R, Oh JH, Dela Cruz F, Norton L, Deasy JO, Kung AL, Tannenbaum AR. Dynamic network curvature analysis of gene expression reveals novel potential therapeutic targets in sarcoma. Sci Rep 2024; 14:488. [PMID: 38177639 PMCID: PMC10766622 DOI: 10.1038/s41598-023-49930-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
Network properties account for the complex relationship between genes, making it easier to identify complex patterns in their interactions. In this work, we leveraged these network properties for dual purposes. First, we clustered pediatric sarcoma tumors using network information flow as a similarity metric, computed by the Wasserstein distance. We demonstrate that this approach yields the best concordance with histological subtypes, validated against three state-of-the-art methods. Second, to identify molecular targets that would be missed by more conventional methods of analysis, we applied a novel unsupervised method to cluster gene interactomes represented as networks in pediatric sarcoma. RNA-Seq data were mapped to protein-level interactomes to construct weighted networks that were then subjected to a non-Euclidean, multi-scale geometric approach centered on a discrete notion of curvature. This provides a measure of the functional association among genes in the context of their connectivity. In confirmation of the validity of this method, hierarchical clustering revealed the characteristic EWSR1-FLI1 fusion in Ewing sarcoma. Furthermore, assessing the effects of in silico edge perturbations and simulated gene knockouts as quantified by changes in curvature, we found non-trivial gene associations not previously identified.
Collapse
Affiliation(s)
- Rena Elkin
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, 10065, USA.
| | - Jung Hun Oh
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Filemon Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Joseph O Deasy
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Allen R Tannenbaum
- Departments of Computer Science and Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, USA
| |
Collapse
|
8
|
Wrenn ED, Apfelbaum AA, Rudzinski ER, Deng X, Jiang W, Sud S, Van Noord RA, Newman EA, Garcia NM, Miyaki A, Hoglund VJ, Bhise SS, Kanaan SB, Waltner OG, Furlan SN, Lawlor ER. Cancer-Associated Fibroblast-Like Tumor Cells Remodel the Ewing Sarcoma Tumor Microenvironment. Clin Cancer Res 2023; 29:5140-5154. [PMID: 37471463 PMCID: PMC10801911 DOI: 10.1158/1078-0432.ccr-23-1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
PURPOSE Despite limited genetic and histologic heterogeneity, Ewing sarcoma (EwS) tumor cells are transcriptionally heterogeneous and display varying degrees of mesenchymal lineage specification in vitro. In this study, we investigated if and how transcriptional heterogeneity of EwS cells contributes to heterogeneity of tumor phenotypes in vivo. EXPERIMENTAL DESIGN Single-cell proteogenomic-sequencing of EwS cell lines was performed and integrated with patient tumor transcriptomic data. Cell subpopulations were isolated by FACS for assessment of gene expression and phenotype. Digital spatial profiling and human whole transcriptome analysis interrogated transcriptomic heterogeneity in EwS xenografts. Tumor cell subpopulations and matrix protein deposition were evaluated in xenografts and patient tumors using multiplex immunofluorescence staining. RESULTS We identified CD73 as a biomarker of highly mesenchymal EwS cell subpopulations in tumor models and patient biopsies. CD73+ tumor cells displayed distinct transcriptional and phenotypic properties, including selective upregulation of genes that are repressed by EWS::FLI1, and increased migratory potential. CD73+ cells were distinguished in vitro and in vivo by increased expression of matrisomal genes and abundant deposition of extracellular matrix (ECM) proteins. In epithelial-derived malignancies, ECM is largely deposited by cancer-associated fibroblasts (CAF), and we thus labeled CD73+ EwS cells, CAF-like tumor cells. Marked heterogeneity of CD73+ EwS cell frequency and distribution was detected in tumors in situ, and CAF-like tumor cells and associated ECM were observed in peri-necrotic regions and invasive foci. CONCLUSIONS EwS tumor cells can adopt CAF-like properties, and these distinct cell subpopulations contribute to tumor heterogeneity by remodeling the tumor microenvironment. See related commentary by Kuo and Amatruda, p. 5002.
Collapse
Affiliation(s)
- Emma D. Wrenn
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - April A. Apfelbaum
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Cancer Biology PhD Program, University of Michigan, Ann Arbor, Michigan
| | - Erin R. Rudzinski
- Pathology Department, Seattle Children’s Hospital, Seattle, Washington
| | - Xuemei Deng
- Pathology Department, Seattle Children’s Hospital, Seattle, Washington
| | - Wei Jiang
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Sudha Sud
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | | | - Erika A. Newman
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Nicolas M. Garcia
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Aya Miyaki
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Virginia J. Hoglund
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Shruti S. Bhise
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Sami B. Kanaan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Olivia G. Waltner
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Scott N. Furlan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Elizabeth R. Lawlor
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, WA
| |
Collapse
|
9
|
Koshyk O, Dehner CA, van den Hout MFCM, Bempt IV, Sciot R, Huang HY, Agaimy A, Din NU, Klubíčková N, Mosaieby E, Skálová A, Michalová K, Schöffski P, Oliveira AM, Halling KC, Gupta S, Gross JM, Nin JWM, Michal M, Folpe AL, Kosemehmetoglu K, Torres-Mora J, Michal M. EWSR1::POU2AF3(COLCA2) Sarcoma: An Aggressive, Polyphenotypic Sarcoma With a Head and Neck Predilection. Mod Pathol 2023; 36:100337. [PMID: 37742928 DOI: 10.1016/j.modpat.2023.100337] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/25/2023] [Accepted: 09/15/2023] [Indexed: 09/26/2023]
Abstract
EWSR1::POU2AF3 (COLCA2) sarcomas are a recently identified group of undifferentiated round/spindle cell neoplasms with a predilection for the head and neck region. Herein, we report our experience with 8 cases, occurring in 5 men and 3 women (age range, 37-74 years; median, 60 years). Tumors involved the head/neck (4 cases), and one each the thigh, thoracic wall, fibula, and lung. Seven patients received multimodal therapy; 1 patient was treated only with surgery. Clinical follow-up (8 patients; range, 4-122 months; median, 32 months) showed 5 patients with metastases (often multifocal, with a latency ranging from 7 to 119 months), and 3 of them also with local recurrence. The median local recurrence-free and metastasis-free survival rates were 24 months and 29 months, respectively. Of the 8 patients, 1 died of an unknown cause, 4 were alive with metastatic disease, 1 was alive with unresectable local disease, and 2 were without disease. The tumors were composed of 2 morphologic subgroups: (1) relatively bland tumors consisting of spindled to stellate cells with varying cellularity and fibromyxoid stroma (2 cases) and (2) overtly malignant tumors composed of nests of "neuroendocrine-appearing" round cells surrounded by spindled cells (6 cases). Individual cases in the second group showed glandular, osteogenic, or rhabdomyoblastic differentiation. Immunohistochemical results included CD56 (4/4 cases), GFAP (5/8), SATB2 (4/6), keratin (AE1/AE3) (5/8), and S100 protein (4/7). RNA sequencing identified EWSR1::POU2AF3 gene fusion in all cases. EWSR1 gene rearrangement was confirmed by fluorescence in situ hybridization in 5 cases. Our findings confirm the head/neck predilection and aggressive clinical behavior of EWSR1::POU2AF3 sarcomas and widen the morphologic spectrum of these rare lesions to include relatively bland spindle cell tumors and tumors with divergent differentiation.
Collapse
Affiliation(s)
- Olena Koshyk
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Medical Laboratory CSD, Ltd, Kyiv, Ukraine
| | - Carina A Dehner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Mari F C M van den Hout
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Isabelle Vanden Bempt
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Raf Sciot
- Department of Pathology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Hsuan-Ying Huang
- Department of Anatomical Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung City, Taiwan
| | - Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
| | - Nasir Ud Din
- Section of Histopathology, Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Natálie Klubíčková
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic
| | - Elaheh Mosaieby
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic
| | - Alena Skálová
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic
| | - Květoslava Michalová
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic
| | - Patrick Schöffski
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium; Department of Oncology, KU Leuven, Laboratory of Experimental Oncology, Leuven, Belgium
| | - Andre M Oliveira
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - John M Gross
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Johanna W M Nin
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Michal Michal
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Jorge Torres-Mora
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Michael Michal
- Department of Pathology, Charles University, Faculty of Medicine in Plzeň, Czech Republic; Bioptical Laboratory, Ltd, Plzeň, Czech Republic.
| |
Collapse
|
10
|
Greulich BM, Rajendran S, Downing NF, Nicholas TR, Hollenhorst PC. A complex with poly(A)-binding protein and EWS facilitates the transcriptional function of oncogenic ETS transcription factors in prostate cells. J Biol Chem 2023; 299:105453. [PMID: 37956771 PMCID: PMC10704431 DOI: 10.1016/j.jbc.2023.105453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
The ETS transcription factor ERG is aberrantly expressed in approximately 50% of prostate tumors due to chromosomal rearrangements such as TMPRSS2/ERG. The ability of ERG to drive oncogenesis in prostate epithelial cells requires interaction with distinct coactivators, such as the RNA-binding protein EWS. Here, we find that ERG has both direct and indirect interactions with EWS, and the indirect interaction is mediated by the poly-A RNA-binding protein PABPC1. PABPC1 directly bound both ERG and EWS. ERG expression in prostate cells promoted PABPC1 localization to the nucleus and recruited PABPC1 to ERG/EWS-binding sites in the genome. Knockdown of PABPC1 in prostate cells abrogated ERG-mediated phenotypes and decreased the ability of ERG to activate transcription. These findings define a complex including ERG and the RNA-binding proteins EWS and PABPC1 that represents a potential therapeutic target for ERG-positive prostate cancer and identify a novel nuclear role for PABPC1.
Collapse
Affiliation(s)
| | - Saranya Rajendran
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, USA
| | - Nicholas F Downing
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, USA
| | - Taylor R Nicholas
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, USA
| | - Peter C Hollenhorst
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, USA.
| |
Collapse
|
11
|
Mallard HJ, Wan S, Nidhi P, Hanscom-Trofy YD, Mohapatra B, Woods NT, Lopez-Guerrero JA, Llombart-Bosch A, Machado I, Scotlandi K, Kreiling NF, Perry MC, Mirza S, Coulter DW, Band V, Band H, Ghosal G. USP1 Expression Driven by EWS::FLI1 Transcription Factor Stabilizes Survivin and Mitigates Replication Stress in Ewing Sarcoma. Mol Cancer Res 2023; 21:1186-1204. [PMID: 37478161 PMCID: PMC10618738 DOI: 10.1158/1541-7786.mcr-23-0323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/23/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023]
Abstract
In this study, we identify USP1 as a transcriptional target of EWS::FLI1 and demonstrate the requisite function of USP1 in Ewing sarcoma (EWS) cell survival in response to endogenous replication stress. EWS::FLI1 oncogenic transcription factor drives most EWS, a pediatric bone cancer. EWS cells display elevated levels of R-loops and replication stress. The mechanism by which EWS cells override activation of apoptosis or cellular senescence in response to increased replication stress is not known. We show that USP1 is overexpressed in EWS and EWS::FLI1 regulates USP1 transcript levels. USP1 knockdown or inhibition arrests EWS cell growth and induces cell death by apoptosis. Mechanistically, USP1 regulates Survivin (BIRC5/API4) protein stability and the activation of caspase-9 and caspase-3/7 in response to endogenous replication stress. Notably, USP1 inhibition sensitizes cells to doxorubicin and etoposide treatment. Together, our study demonstrates that USP1 is regulated by EWS::FLI1, the USP1-Survivin axis promotes EWS cell survival, and USP1 inhibition sensitizes cells to standard of care chemotherapy. IMPLICATIONS High USP1 and replication stress levels driven by EWS::FLI1 transcription factor in EWS are vulnerabilities that can be exploited to improve existing treatment avenues and overcome drug resistance.
Collapse
Affiliation(s)
- Halle J. Mallard
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Shibiao Wan
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Prakriti Nidhi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Yvan D. Hanscom-Trofy
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Bhopal Mohapatra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Nicholas T. Woods
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Antonio Llombart-Bosch
- Department of Pathology, Instituto Valenciano de Oncología and Patologika Laboratory, Hospital QuironSalud, Valencia, Spain
| | - Isidro Machado
- Department of Pathology, Instituto Valenciano de Oncología and Patologika Laboratory, Hospital QuironSalud, Valencia, Spain
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Natasha F. Kreiling
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Megan C. Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Donald W. Coulter
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Hamid Band
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| |
Collapse
|
12
|
Dorwal P, Lambie D, Dettrick A, Goh AFN, Kumar B, Manders P. A novel FET-ETS family fusion (FUS::FLI1) in a case of Ewing sarcoma. Pathol Int 2023; 73:563-565. [PMID: 37606217 DOI: 10.1111/pin.13373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023]
Affiliation(s)
- Pranav Dorwal
- Monash Health, Clayton, VIC, Australia
- Department of Medicine, Monash University, Clayton, VIC, Australia
| | - Duncan Lambie
- Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
- Diamantina Institute, University of Queensland, St Lucia, QLD, Australia
| | - Andrew Dettrick
- Pathology Queensland, Sunshine Coast University Hospital, Birtinya, QLD, Australia
- Department of Medicine, The University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | | | - Beena Kumar
- Monash Health, Clayton, VIC, Australia
- Department of Medicine, Monash University, Clayton, VIC, Australia
| | - Peter Manders
- Department of Medicine, The University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast University Hospital, Birtinya, QLD, Australia
| |
Collapse
|
13
|
Yasir M, Park J, Chun W. EWS/FLI1 Characterization, Activation, Repression, Target Genes and Therapeutic Opportunities in Ewing Sarcoma. Int J Mol Sci 2023; 24:15173. [PMID: 37894854 PMCID: PMC10607184 DOI: 10.3390/ijms242015173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Despite their clonal origins, tumors eventually develop into complex communities made up of phenotypically different cell subpopulations, according to mounting evidence. Tumor cell-intrinsic programming and signals from geographically and temporally changing microenvironments both contribute to this variability. Furthermore, the mutational load is typically lacking in childhood malignancies of adult cancers, and they still exhibit high cellular heterogeneity levels largely mediated by epigenetic mechanisms. Ewing sarcomas represent highly aggressive malignancies affecting both bone and soft tissue, primarily afflicting adolescents. Unfortunately, the outlook for patients facing relapsed or metastatic disease is grim. These tumors are primarily fueled by a distinctive fusion event involving an FET protein and an ETS family transcription factor, with the most prevalent fusion being EWS/FLI1. Despite originating from a common driver mutation, Ewing sarcoma cells display significant variations in transcriptional activity, both within and among tumors. Recent research has pinpointed distinct fusion protein activities as a principal source of this heterogeneity, resulting in markedly diverse cellular phenotypes. In this review, we aim to characterize the role of the EWS/FLI fusion protein in Ewing sarcoma by exploring its general mechanism of activation and elucidating its implications for tumor heterogeneity. Additionally, we delve into potential therapeutic opportunities to target this aberrant fusion protein in the context of Ewing sarcoma treatment.
Collapse
Affiliation(s)
| | | | - Wanjoo Chun
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea; (M.Y.); (J.P.)
| |
Collapse
|
14
|
Wang Y, Yu C, Pei G, Jia W, Li T, Li P. Dissolution of oncofusion transcription factor condensates for cancer therapy. Nat Chem Biol 2023; 19:1223-1234. [PMID: 37400539 DOI: 10.1038/s41589-023-01376-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
Cancer-associated chromosomal rearrangements can result in the expression of numerous pathogenic fusion proteins. The mechanisms by which fusion proteins contribute to oncogenesis are largely unknown, and effective therapies for fusion-associated cancers are lacking. Here we comprehensively scrutinized fusion proteins found in various cancers. We found that many fusion proteins are composed of phase separation-prone domains (PSs) and DNA-binding domains (DBDs), and these fusions have strong correlations with aberrant gene expression patterns. Furthermore, we established a high-throughput screening method, named DropScan, to screen drugs capable of modulating aberrant condensates. One of the drugs identified via DropScan, LY2835219, effectively dissolved condensates in reporter cell lines expressing Ewing sarcoma fusions and partially rescued the abnormal expression of target genes. Our results indicate that aberrant phase separation is likely a common mechanism for these PS-DBD fusion-related cancers and suggest that modulating aberrant phase separation is a potential route to treat these diseases.
Collapse
Affiliation(s)
- Yuan Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing, China
| | - Chunyu Yu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing, China
| | - Wen Jia
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China.
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing, China.
| |
Collapse
|
15
|
Chatzopoulos K, Davila JI, Fadra N, Jackson RA, Minn KT, Sotiriou S, Oliveira AM, Erickson LA, Halling KC, Rumilla KM, Rivera M. Transcriptomic and immunophenotypic characterization of two cases of adamantinoma-like Ewing sarcoma of the thyroid gland. Histopathology 2023; 83:426-434. [PMID: 37195579 DOI: 10.1111/his.14961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/22/2023] [Accepted: 05/08/2023] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Adamantinoma-like Ewing sarcoma (ALES) is a rare aggressive malignancy occasionally diagnosed in the thyroid gland. ALES shows basaloid cytomorphology, expresses keratins, p63, p40, frequently CD99, and harbours the t(11;22) EWSR1::FLI1 translocation. There is debate on whether ALES resembles more sarcoma or carcinoma. METHODS We performed RNA sequencing from two ALES cases and compared findings with skeletal Ewing's sarcomas and nonneoplastic thyroid tissue. ALES was investigated by in situ hybridization (ISH) for high-risk human papillomavirus (HPV) DNA and immunohistochemistry for the following antigens: keratin 7, keratin 20, keratin 5, keratins (AE1/AE3 and CAM5.2), CD45, CD20, CD5, CD99, chromogranin, synaptophysin, calcitonin, thyroglobulin, PAX8, TTF1, S100, p40, p63, p16, NUT, desmin, ER, FLI1, INI1, and myogenin. RESULTS An uncommon EWSR1::FLI transcript with retained EWSR1 exon 8 was detected in both ALES cases. Regulators of EWSR1::FLI1 splicing (HNRNPH1, SUPT6H, SF3B1) necessary for production of a functional fusion oncoprotein, as well as 53 genes (including TNNT1, NKX2.2) activated downstream to the EWSR1::FLI1 cascade, were overexpressed. Eighty-six genes were uniquely overexpressed in ALES, most of which were related to squamous differentiation. Immunohistochemically, ALES strongly expressed keratins 5, AE1/AE3 and CAM5.2, p63, p40, p16, and focally CD99. INI1 was retained. The remaining immunostains and HPV DNA ISH were negative. CONCLUSION Comparative transcriptomic profiling reveals overlapping features of ALES with skeletal Ewing's sarcoma and an epithelial carcinoma, as evidenced by immunohistochemical expression of keratin 5, p63, p40, CD99, the transcriptome profile, and detection of EWSR1::FLI1 fusion transcript by RNA sequencing.
Collapse
Affiliation(s)
- Kyriakos Chatzopoulos
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Department of General and Anatomic Pathology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Jaime I Davila
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Numrah Fadra
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rory A Jackson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- NeoGenomics Laboratories, Aliso Viejo, CA, USA
| | - Kay T Minn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sotiris Sotiriou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Department of General and Anatomic Pathology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andre M Oliveira
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Lori A Erickson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kandelaria M Rumilla
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Michael Rivera
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
16
|
Kitagawa R, Niikura Y, Becker A, Houghton PJ, Kitagawa K. EWSR1 maintains centromere identity. Cell Rep 2023; 42:112568. [PMID: 37243594 PMCID: PMC10758295 DOI: 10.1016/j.celrep.2023.112568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 04/03/2023] [Accepted: 05/11/2023] [Indexed: 05/29/2023] Open
Abstract
The centromere is essential for ensuring high-fidelity transmission of chromosomes. CENP-A, the centromeric histone H3 variant, is thought to be the epigenetic mark of centromere identity. CENP-A deposition at the centromere is crucial for proper centromere function and inheritance. Despite its importance, the precise mechanism responsible for maintenance of centromere position remains obscure. Here, we report a mechanism to maintain centromere identity. We demonstrate that CENP-A interacts with EWSR1 (Ewing sarcoma breakpoint region 1) and EWSR1-FLI1 (the oncogenic fusion protein in Ewing sarcoma). EWSR1 is required for maintaining CENP-A at the centromere in interphase cells. EWSR1 and EWSR1-FLI1 bind CENP-A through the SYGQ2 region within the prion-like domain, important for phase separation. EWSR1 binds to R-loops through its RNA-recognition motif in vitro. Both the domain and motif are required for maintaining CENP-A at the centromere. Therefore, we conclude that EWSR1 guards CENP-A in centromeric chromatins by binding to centromeric RNA.
Collapse
Affiliation(s)
- Risa Kitagawa
- Greehey Children's Cancer Research Institute, Mays Cancer Center, Department of Molecular Medicine, UT Health Science Center San Antonio, 8403 Floyd Curl Drive, San Antonio, TX 78229-3000, USA
| | - Yohei Niikura
- Greehey Children's Cancer Research Institute, Mays Cancer Center, Department of Molecular Medicine, UT Health Science Center San Antonio, 8403 Floyd Curl Drive, San Antonio, TX 78229-3000, USA
| | - Argentina Becker
- Greehey Children's Cancer Research Institute, Mays Cancer Center, Department of Molecular Medicine, UT Health Science Center San Antonio, 8403 Floyd Curl Drive, San Antonio, TX 78229-3000, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, Mays Cancer Center, Department of Molecular Medicine, UT Health Science Center San Antonio, 8403 Floyd Curl Drive, San Antonio, TX 78229-3000, USA
| | - Katsumi Kitagawa
- Greehey Children's Cancer Research Institute, Mays Cancer Center, Department of Molecular Medicine, UT Health Science Center San Antonio, 8403 Floyd Curl Drive, San Antonio, TX 78229-3000, USA.
| |
Collapse
|
17
|
Selig EE, Bhura R, White MR, Akula S, Hoffman RD, Tovar CN, Xu X, Booth RE, Libich DS. Biochemical and biophysical characterization of the nucleic acid binding properties of the RNA/DNA binding protein EWS. Biopolymers 2023; 114:e23536. [PMID: 36929870 PMCID: PMC10233817 DOI: 10.1002/bip.23536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023]
Abstract
EWS is a member of the FET family of RNA/DNA binding proteins that regulate crucial phases of nucleic acid metabolism. EWS comprises an N-terminal low-complexity domain (LCD) and a C-terminal RNA-binding domain (RBD). The RBD is further divided into three RG-rich regions, which flank an RNA-recognition motif (RRM) and a zinc finger (ZnF) domain. Recently, EWS was shown to regulate R-loops in Ewing sarcoma, a pediatric bone and soft-tissue cancer in which a chromosomal translocation fuses the N-terminal LCD of EWS to the C-terminal DNA binding domain of the transcription factor FLI1. Though EWS was shown to directly bind R-loops, the binding mechanism was not elucidated. In the current study, the RBD of EWS was divided into several constructs, which were subsequently assayed for binding to various nucleic acid structures expected to form at R-loops, including RNA stem-loops, DNA G-quadruplexes, and RNA:DNA hybrids. EWS interacted with all three nucleic acid structures with varying affinities and multiple domains contributed to binding each substrate. The RRM and RG2 region appear to bind nucleic acids promiscuously while the ZnF displayed more selectivity for single-stranded structures. With these results, the structural underpinnings of EWS recognition and binding of R-loops and other nucleic acid structures is better understood.
Collapse
Affiliation(s)
- Emily E Selig
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
| | - Roohi Bhura
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Matthew R White
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Shivani Akula
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Renee D Hoffman
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Carmel N Tovar
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Xiaoping Xu
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
| | - Rachell E Booth
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - David S Libich
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
| |
Collapse
|
18
|
Sanalkumar R, Dong R, Lee L, Xing YH, Iyer S, Letovanec I, La Rosa S, Finzi G, Musolino E, Papait R, Chebib I, Nielsen GP, Renella R, Cote GM, Choy E, Aryee M, Stegmaier K, Stamenkovic I, Rivera MN, Riggi N. Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity. Sci Adv 2023; 9:eabo3789. [PMID: 37000878 DOI: 10.1126/sciadv.abo3789] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 01/18/2023] [Indexed: 06/19/2023]
Abstract
Cell fate transitions observed in embryonic development involve changes in three-dimensional genomic organization that provide proper lineage specification. Whether similar events occur within tumor cells and contribute to cancer evolution remains largely unexplored. We modeled this process in the pediatric cancer Ewing sarcoma and investigated high-resolution looping and large-scale nuclear conformation changes associated with the oncogenic fusion protein EWS-FLI1. We show that chromatin interactions in tumor cells are dominated by highly connected looping hubs centered on EWS-FLI1 binding sites, which directly control the activity of linked enhancers and promoters to establish oncogenic expression programs. Conversely, EWS-FLI1 depletion led to the disassembly of these looping networks and a widespread nuclear reorganization through the establishment of new looping patterns and large-scale compartment configuration matching those observed in mesenchymal stem cells, a candidate Ewing sarcoma progenitor. Our data demonstrate that major architectural features of nuclear organization in cancer cells can depend on single oncogenes and are readily reversed to reestablish latent differentiation programs.
Collapse
Affiliation(s)
- Rajendran Sanalkumar
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Rui Dong
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Lukuo Lee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Yu-Hang Xing
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sowmya Iyer
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Igor Letovanec
- Department of Histopathology, Central Institute, Valais Hospital, Sion, Switzerland
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stefano La Rosa
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Giovanna Finzi
- Department of Pathology, ASST Sette Laghi, Varese, Italy
| | - Elettra Musolino
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Roberto Papait
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- IRCSS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Ivan Chebib
- Department of Pathology and Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - G Petur Nielsen
- Department of Pathology and Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raffaele Renella
- Department Woman-Mother-Child, Division of Pediatrics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gregory M Cote
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Edwin Choy
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Martin Aryee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Kimberly Stegmaier
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Ivan Stamenkovic
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Miguel N Rivera
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Nicolò Riggi
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
19
|
Lee OW, Rodrigues C, Lin SH, Luo W, Jones K, Brown DW, Zhou W, Karlins E, Khan SM, Baulande S, Raynal V, Surdez D, Reynaud S, Rubio RA, Zaidi S, Grossetête S, Ballet S, Lapouble E, Laurence V, Pierron G, Gaspar N, Corradini N, Marec-Bérard P, Rothman N, Dagnall CL, Burdett L, Manning M, Wyatt K, Yeager M, Chari R, Leisenring WM, Kulozik AE, Kriebel J, Meitinger T, Strauch K, Kirchner T, Dirksen U, Mirabello L, Tucker MA, Tirode F, Armstrong GT, Bhatia S, Robison LL, Yasui Y, Romero-Pérez L, Hartmann W, Metzler M, Diver WR, Lori A, Freedman ND, Hoover RN, Morton LM, Chanock SJ, Grünewald TGP, Delattre O, Machiela MJ. Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding. Am J Hum Genet 2023; 110:427-441. [PMID: 36787739 PMCID: PMC10027473 DOI: 10.1016/j.ajhg.2023.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare bone and soft tissue malignancy driven by chromosomal translocations encoding chimeric transcription factors, such as EWSR1-FLI1, that bind GGAA motifs forming novel enhancers that alter nearby expression. We propose that germline microsatellite variation at the 6p25.1 EwS susceptibility locus could impact downstream gene expression and EwS biology. We performed targeted long-read sequencing of EwS blood DNA to characterize variation and genomic features important for EWSR1-FLI1 binding. We identified 50 microsatellite alleles at 6p25.1 and observed that EwS-affected individuals had longer alleles (>135 bp) with more GGAA repeats. The 6p25.1 GGAA microsatellite showed chromatin features of an EWSR1-FLI1 enhancer and regulated expression of RREB1, a transcription factor associated with RAS/MAPK signaling. RREB1 knockdown reduced proliferation and clonogenic potential and reduced expression of cell cycle and DNA replication genes. Our integrative analysis at 6p25.1 details increased binding of longer GGAA microsatellite alleles with acquired EWSR-FLI1 to promote Ewing sarcomagenesis by RREB1-mediated proliferation.
Collapse
Affiliation(s)
- Olivia W Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Calvin Rodrigues
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wen Luo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Sairah M Khan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sylvain Baulande
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Virginie Raynal
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Didier Surdez
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Stephanie Reynaud
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Rebeca Alba Rubio
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Sakina Zaidi
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Sandrine Grossetête
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Stelly Ballet
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Eve Lapouble
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | | | - Gaelle Pierron
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Nathalie Gaspar
- Department of Oncology for Child and Adolescent, Institut Gustave Roussy, 94800 Villejuif, France
| | - Nadège Corradini
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Perrine Marec-Bérard
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Michelle Manning
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Raj Chari
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Genome Modification Core Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andreas E Kulozik
- University Children's Hospital of Heidelberg, 69120 Heidelberg, Germany
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 80333 Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, 80539 Munich, Germany
| | - Thomas Kirchner
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Uta Dirksen
- University Children's Hospital of Essen, 45147 Essen, Germany
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Franck Tirode
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama, Birmingham, AL 35294, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard- Domagk Institute of Pathology, University Hospital of Münster, 48149 Münster, Germany
| | - Markus Metzler
- University Children's Hospital of Erlangen, 91054 Erlangen, Germany
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olivier Delattre
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
| |
Collapse
|
20
|
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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
21
|
Dasgupta A, Kurenbekova L, Patel TD, Rajapakshe K, Ghosal G, Nirala B, Coarfa C, Yustein J. Modeling Ewing Sarcoma Lung Metastasis. Curr Protoc 2023; 3:e670. [PMID: 36799651 PMCID: PMC9942121 DOI: 10.1002/cpz1.670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Ewing Sarcoma (EwS) is the second most common malignant bone tumor in adolescents and young adults. The single-most powerful predictor of outcome in EwS is presence of metastatic burden at the time of diagnosis. Patients with metastatic Ewing Sarcoma have an abysmal 5-year survival rate of 10%-25%, which has not changed over the past 30-40 years. Thus, unraveling underlying mechanisms of EwS metastasis are imperative for developing effective therapeutic measures. Investigations towards this goal are limited by the lack of reliable genetically engineered mouse models and specialized metastatic models. Using two established cell lines, A673 and TC71, we generated lung specific metastatic cell lines by serial orthotopic intra-tibial injection followed by isolation of cells from lung metastases. The lung metastatic lines generated exhibit distinct differential molecular signatures from the parental cells when analyzed using a multi-omics approach. These signatures overlapped with EwS patient primary bone and metastatic lung specimens supporting the clinical relevance of these preclinical models of EwS. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Intra-Tibial injection in NSG mice Basic Protocol 2: Development and characterization of lung metastatic cell line.
Collapse
Affiliation(s)
- Atreyi Dasgupta
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas. 1102 Bates Street, Suite 1070.07, Houston. TX
| | - Lyazat Kurenbekova
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas. 1102 Bates Street, Suite 1070.07, Houston. TX
| | - Tajhal D. Patel
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas. 1102 Bates Street, Suite 1070.07, Houston. TX
| | - Kimal Rajapakshe
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX: 77030
| | - Gargi Ghosal
- College of Medicine, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE: 68198
| | - Bikesh Nirala
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas. 1102 Bates Street, Suite 1070.07, Houston. TX
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, TX
| | - Jason Yustein
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas. 1102 Bates Street, Suite 1070.07, Houston. TX
| |
Collapse
|
22
|
Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Exploration of Flavonoids as Lead Compounds against Ewing Sarcoma through Molecular Docking, Pharmacogenomics Analysis, and Molecular Dynamics Simulations. Molecules 2023; 28:molecules28010414. [PMID: 36615603 PMCID: PMC9823950 DOI: 10.3390/molecules28010414] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023]
Abstract
Ewing sarcoma (ES) is a highly malignant carcinoma prevalent in children and most frequent in the second decade of life. It mostly occurs due to t(11;22) (q24;q12) translocation. This translocation encodes the oncogenic fusion protein EWS/FLI (Friend leukemia integration 1 transcription factor), which acts as an aberrant transcription factor to deregulate target genes essential for cancer. Traditionally, flavonoids from plants have been investigated against viral and cancerous diseases and have shown some promising results to combat these disorders. In the current study, representative flavonoid compounds from various subclasses are selected and used to disrupt the RNA-binding motif of EWS, which is required for EWS/FLI fusion. By blocking the RNA-binding motif of EWS, it might be possible to combat ES. Therefore, molecular docking experiments validated the binding interaction patterns and structural behaviors of screened flavonoid compounds within the active region of the Ewing sarcoma protein (EWS). Furthermore, pharmacogenomics analysis was used to investigate potential drug interactions with Ewing sarcoma-associated genes. Finally, molecular dynamics simulations were used to investigate the stability of the best selected docked complexes. Taken together, daidzein, kaempferol, and genistein exhibited a result comparable to ifosfamide in the proposed in silico study and can be further analyzed as possible candidate compounds in biological in vitro studies against ES.
Collapse
Affiliation(s)
- Muhammad Yasir
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Jinyoung Park
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Won Sun Park
- Department of Physiology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Yong-Soo Kwon
- College of Pharmacy, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Hee-Jae Lee
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Mubashir Hassan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Wanjoo Chun
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
- Correspondence: ; Tel.: +82-33-250-8853
| |
Collapse
|
23
|
Kitagawa T, Kobayashi D, Baron B, Okita H, Miyamoto T, Takai R, Paudel D, Ohta T, Asaoka Y, Tokunaga M, Nakagawa K, Furutani-Seiki M, Araki N, Kuramitsu Y, Kobayashi M. AT-hook DNA-binding motif-containing protein one knockdown downregulates EWS-FLI1 transcriptional activity in Ewing's sarcoma cells. PLoS One 2022; 17:e0269077. [PMID: 36194562 PMCID: PMC9531837 DOI: 10.1371/journal.pone.0269077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/06/2022] [Indexed: 11/18/2022] Open
Abstract
Ewing's sarcoma is the second most common bone malignancy in children or young adults and is caused by an oncogenic transcription factor by a chromosomal translocation between the EWSR1 gene and the ETS transcription factor family. However, the transcriptional mechanism of EWS-ETS fusion proteins is still unclear. To identify the transcriptional complexes of EWS-ETS fusion transcription factors, we applied a proximal labeling system called BioID in Ewing's sarcoma cells. We identified AHDC1 as a proximal protein of EWS-ETS fusion proteins. AHDC1 knockdown showed a reduced cell growth and transcriptional activity of EWS-FLI1. AHDC1 knockdown also reduced BRD4 and BRG1 protein levels, both known as interacting proteins of EWS-FLI1. Our results suggest that AHDC1 supports cell growth through EWS-FLI1.
Collapse
Affiliation(s)
- Takao Kitagawa
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
- * E-mail:
| | - Daiki Kobayashi
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Department of Tumor Genetics and Biology, Faculty of Life Sciences, Kumamoto University, Kumamoto-Shi, Kumamoto, Japan
| | - Byron Baron
- Center for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Hajime Okita
- Division of Diagnostic Pathology, Keio University School of Medicine, Shinano, Shinjuku-ku, Tokyo, Japan
| | - Tatsuo Miyamoto
- Department of Molecular and Cellular Physiology, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Rie Takai
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| | - Durga Paudel
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| | - Tohru Ohta
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| | - Yoichi Asaoka
- Department of Systems Biochemistry in Pathology and Regeneration, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Masayuki Tokunaga
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Koji Nakagawa
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| | - Makoto Furutani-Seiki
- Department of Systems Biochemistry in Pathology and Regeneration, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Norie Araki
- Department of Tumor Genetics and Biology, Faculty of Life Sciences, Kumamoto University, Kumamoto-Shi, Kumamoto, Japan
| | - Yasuhiro Kuramitsu
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| | - Masanobu Kobayashi
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| |
Collapse
|
24
|
Li BX, David LL, Davis LE, Xiao X. Protein arginine methyltransferase 5 is essential for oncogene product EWSR1-ATF1-mediated gene transcription in clear cell sarcoma. J Biol Chem 2022; 298:102434. [PMID: 36041632 PMCID: PMC9513783 DOI: 10.1016/j.jbc.2022.102434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription dysregulation is common in sarcomas driven by oncogenic transcription factors. Clear cell sarcoma of soft tissue (CCSST) is a rare sarcoma with poor prognosis presently with no therapy. It is characterized by a balanced t(12;22) (q13;q12) chromosomal translocation, resulting in a fusion of the Ewing's sarcoma gene EWSR1 with activating transcription factor 1 (ATF1) to give an oncogene EWSR1-ATF1. Unlike normal ATF1, whose transcription activity is dependent on phosphorylation, EWSR1-ATF1 is constitutively active to drive ATF1-dependent gene transcription to cause tumorigenesis. No EWSR1-ATF1-targeted therapies have been identified due to the challenges in targeting intracellular transcription factors. Through proteomics screening to identify potential druggable targets for CCSST, we discovered protein arginine methyltransferase 5 (PRMT5) as a novel protein to interact with EWSR1-ATF1. PRMT5 is a type II protein arginine methyltransferase to symmetrically dimethylate arginine residues in substrate proteins to regulate a diverse range of activities including gene transcription, RNA splicing, and DNA repair. We found that PRMT5 enhances EWSR1-ATF1-mediated gene transcription to sustain CCSST cell proliferation. Genetic silencing of PRMT5 in CCSST cells resulted in severely impaired cell proliferation and EWSR1-ATF1-driven transcription. Furthermore, we demonstrate that the clinical-stage PRMT5 inhibitor JNJ-64619178 potently and efficaciously inhibited CCSST cell growth in vitro and in vivo. These results provide new insights into PRMT5 as a transcription regulator and warrant JNJ-64619178 for further clinical development to treat CCSST patients.
Collapse
Affiliation(s)
- Bingbing X Li
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, USA.
| | - Larry L David
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, USA
| | - Lara E Davis
- Knight Cancer Institute, Oregon Health & Science University, Portland, USA; Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, USA
| | - Xiangshu Xiao
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, USA.
| |
Collapse
|
25
|
Gedminas JM, Kaufman R, Boguslawski EA, Gross AC, Adams M, Beddows I, Kitchen-Goosen SM, Roberts RD, Grohar PJ. Lurbinectedin Inhibits the EWS-WT1 Transcription Factor in Desmoplastic Small Round Cell Tumor. Mol Cancer Ther 2022; 21:1296-1305. [PMID: 35657345 DOI: 10.1158/1535-7163.mct-21-1003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/17/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022]
Abstract
Desmoplastic small round cell tumor (DSRCT) is a rare pediatric sarcoma with poor overall survival. This tumor is absolutely dependent on the continued expression and activity of its defining molecular lesion, the EWS-WT1 transcription factor. Unfortunately, the therapeutic targeting of transcription factors is challenging, and there is a critical need to identify compounds that inhibit EWS-WT1. Here we show that the compound lurbinectedin inhibits EWS-WT1 by redistributing the protein within the nucleus to the nucleolus. This nucleolar redistribution interferes with the activity of EWS-WT1 to reverse the expression of over 70% of the transcriptome. In addition, the compound blocks the expression of the EWS-WT1 fusion protein to inhibit cell proliferation at the lowest GI50 ever reported for this compound in any cell type. The effects occur at concentrations that are easily achievable in the clinic and translate to the in vivo setting to cause tumor regressions in multiple mice in a xenograft and PDX model of DSRCT. Importantly, this mechanism of nucleolar redistribution is also seen with wild-type EWSR1 and the related fusion protein EWS-FLI1. This provides evidence for a "class effect" for the more than 18 tumors driven by EWSR1 fusion proteins. More importantly, the data establish lurbinectedin as a promising clinical candidate for DSRCT.
Collapse
Affiliation(s)
- Jenna M Gedminas
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rebecca Kaufman
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elissa A Boguslawski
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Amy C Gross
- Center for Childhood Cancer, Nationwide Children's Hospital, The Ohio State University James Comprehensive Cancer Center, Columbus, Ohio
| | - Marie Adams
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Ian Beddows
- Van Andel Research Institute, Grand Rapids, Michigan
| | | | - Ryan D Roberts
- Center for Childhood Cancer, Nationwide Children's Hospital, The Ohio State University James Comprehensive Cancer Center, Columbus, Ohio
| | - Patrick J Grohar
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| |
Collapse
|
26
|
Pedot G, Marques JG, Ambühl PP, Wachtel M, Kasper S, Ngo QA, Niggli FK, Schäfer BW. Inhibition of HDACs reduces Ewing sarcoma tumor growth through EWS-FLI1 protein destabilization. Neoplasia 2022; 27:100784. [PMID: 35366465 PMCID: PMC8971315 DOI: 10.1016/j.neo.2022.100784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/26/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022]
Abstract
Oncogenic transcription factors lacking enzymatic activity or targetable binding pockets are typically considered "undruggable". An example is provided by the EWS-FLI1 oncoprotein, whose continuous expression and activity as transcription factor are critically required for Ewing sarcoma tumor formation, maintenance, and proliferation. Because neither upstream nor downstream targets have so far disabled its oncogenic potential, we performed a high-throughput drug screen (HTS), enriched for FDA-approved drugs, coupled to a Global Protein Stability (GPS) approach to identify novel compounds capable to destabilize EWS-FLI1 protein by enhancing its degradation through the ubiquitin-proteasome system. The protein stability screen revealed the dual histone deacetylase (HDAC) and phosphatidylinositol-3-kinase (PI3K) inhibitor called fimepinostat (CUDC-907) as top candidate to modulate EWS-FLI1 stability. Fimepinostat strongly reduced EWS-FLI1 protein abundance, reduced viability of several Ewing sarcoma cell lines and PDX-derived primary cells and delayed tumor growth in a xenograft mouse model, whereas it did not significantly affect healthy cells. Mechanistically, we demonstrated that EWS-FLI1 protein levels were mainly regulated by fimepinostat's HDAC activity. Our study demonstrates that HTS combined to GPS is a reliable approach to identify drug candidates able to modulate stability of EWS-FLI1 and lays new ground for the development of novel therapeutic strategies aimed to reduce Ewing sarcoma tumor progression.
Collapse
Affiliation(s)
- Gloria Pedot
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Joana Graça Marques
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Philip P Ambühl
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Stephanie Kasper
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Quy A Ngo
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Felix K Niggli
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland.
| |
Collapse
|
27
|
Sun N, Tran BV, Peng Z, Wang J, Zhang C, Yang P, Zhang TX, Widjaja J, Zhang RY, Xia W, Keir A, She J, Yu H, Shyue J, Zhu H, Agopian VG, Pei R, Tomlinson JS, Toretsky JA, Jonas SJ, Federman N, Lu S, Tseng H, Zhu Y. Coupling Lipid Labeling and Click Chemistry Enables Isolation of Extracellular Vesicles for Noninvasive Detection of Oncogenic Gene Alterations. Adv Sci (Weinh) 2022; 9:e2105853. [PMID: 35486030 PMCID: PMC9108594 DOI: 10.1002/advs.202105853] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/13/2022] [Indexed: 05/06/2023]
Abstract
Well-preserved molecular cargo in circulating extracellular vesicles (EVs) offers an ideal material for detecting oncogenic gene alterations in cancer patients, providing a noninvasive diagnostic solution for detection of disease status and monitoring treatment response. Therefore, technologies that conveniently isolate EVs with sufficient efficiency are desperately needed. Here, a lipid labeling and click chemistry-based EV capture platform ("Click Beads"), which is ideal for EV message ribonucleic acid (mRNA) assays due to its efficient, convenient, and rapid purification of EVs, enabling downstream molecular quantification using reverse transcription digital polymerase chain reaction (RT-dPCR) is described and demonstrated. Ewing sarcoma protein (EWS) gene rearrangements and kirsten rat sarcoma viral oncogene homolog (KRAS) gene mutation status are detected and quantified using EVs isolated by Click Beads and matched with those identified in biopsy specimens from Ewing sarcoma or pancreatic cancer patients. Moreover, the quantification of gene alterations can be used for monitoring treatment responses and disease progression.
Collapse
Affiliation(s)
- Na Sun
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
- Key Laboratory for Nano‐Bio InterfaceSuzhou Institute of Nano‐Tech and Nano‐BionicsUniversity of Chinese Academy of SciencesChinese Academy of SciencesSuzhou215123P. R. China
| | - Benjamin V. Tran
- Department of SurgeryUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Zishan Peng
- Department of PathologyZhongshan HospitalFudan UniversityShanghai200032P. R. China
| | - Jing Wang
- Department of PathologyShanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Ceng Zhang
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Peng Yang
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Tiffany X. Zhang
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Josephine Widjaja
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Ryan Y. Zhang
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Wenxi Xia
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Alexandra Keir
- Department of PediatricsDavid Geffen School of MedicineEli and Edythe Broad Center of Regenerative Medicine and Stem Cell Researchand Children's Discovery and Innovation InstituteUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Jia‐Wei She
- Smart Organic Materials LaboratoryInstitute of ChemistryAcademia SinicaNankangTaipei115Taiwan
| | - Hsiao‐hua Yu
- Smart Organic Materials LaboratoryInstitute of ChemistryAcademia SinicaNankangTaipei115Taiwan
| | - Jing‐Jong Shyue
- Research Center for Applied SciencesAcademia SinicaNankangTaipei115Taiwan
| | - Hongguang Zhu
- Department of PathologyShanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Vatche G. Agopian
- Department of SurgeryUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Renjun Pei
- Key Laboratory for Nano‐Bio InterfaceSuzhou Institute of Nano‐Tech and Nano‐BionicsUniversity of Chinese Academy of SciencesChinese Academy of SciencesSuzhou215123P. R. China
| | - James S. Tomlinson
- Department of SurgeryUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Jeffrey A Toretsky
- Departments of Oncology and PediatricsGeorgetown UniversityWashingtonDC20057USA
| | - Steven J. Jonas
- Department of PediatricsDavid Geffen School of MedicineEli and Edythe Broad Center of Regenerative Medicine and Stem Cell Researchand Children's Discovery and Innovation InstituteUniversity of California, Los AngelesLos AngelesCA90095USA
- California NanoSystems InstituteDepartments of Chemistry and Biochemistry and of Materials Science and EngineeringUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Noah Federman
- Department of PediatricsDavid Geffen School of MedicineEli and Edythe Broad Center of Regenerative Medicine and Stem Cell Researchand Children's Discovery and Innovation InstituteUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Shaohua Lu
- Department of PathologyZhongshan HospitalFudan UniversityShanghai200032P. R. China
| | - Hsian‐Rong Tseng
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| | - Yazhen Zhu
- California NanoSystems InstituteCrump Institute for Molecular ImagingDepartment of Molecular and Medical PharmacologyUniversity of California, Los AngelesLos AngelesCA90095USA
| |
Collapse
|
28
|
Johnson CN, Xu X, Holloway SP, Libich DS. The 1H, 15N and 13C resonance assignments of the low-complexity domain from the oncogenic fusion protein EWS-FLI1. Biomol NMR Assign 2022; 16:67-73. [PMID: 34994941 PMCID: PMC9081151 DOI: 10.1007/s12104-021-10061-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The RNA-binding protein EWS is a multifunctional protein with roles in the regulation of transcription and RNA splicing. It is one of the FET (FUS, EWS and TAF15) family of RNA binding proteins that contain an intrinsically disordered, low-complexity N-terminal domain. The FET family proteins are prone to chromosomal translocations, often fusing their low-complexity domain with a transcription factor derived DNA-binding domain, that are oncogenic drivers in several leukemias and sarcomas. The fusion protein disrupts the normal function of cells through non-canonical DNA binding and alteration of normal transcriptional programs. However, the exact mechanism for how the intrinsically disordered domain contributes to aberrant DNA binding and abnormal transcription is unknown. The purification and 1H, 13C, and 15N backbone resonance assignments of the amino terminal domain comprising 264 residues of EWS is described. This segment is common to all known EWS-fusions that are the hallmark of the pediatric cancer Ewing sarcoma. This domain is intrinsically disordered and features significant sequence degeneracy resulting in spectra with poor chemical shift dispersion. To alleviate this problem, the domain was divided into three overlapping fragments, reducing the complexity of the spectra and enabling almost complete backbone resonance assignment of the full domain. These solution NMR chemical shift assignments represent the first steps towards understanding, at atomic resolution, how the low-complexity domain of EWS contributes to the aberrant functions of its oncogenic fusion proteins.
Collapse
Affiliation(s)
- Courtney N Johnson
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - Xiaoping Xu
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - Stephen P Holloway
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - David S Libich
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA.
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA.
| |
Collapse
|
29
|
Khoogar R, Li F, Chen Y, Ignatius M, Lawlor ER, Kitagawa K, Huang THM, Phelps DA, Houghton PJ. Single-cell RNA profiling identifies diverse cellular responses to EWSR1/FLI1 downregulation in Ewing sarcoma cells. Cell Oncol (Dordr) 2022; 45:19-40. [PMID: 34997546 PMCID: PMC10959445 DOI: 10.1007/s13402-021-00640-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The EWSR1/FLI1 gene fusion is the most common rearrangement leading to cell transformation in Ewing sarcoma (ES). Previous studies have indicated that expression at the cellular level is heterogeneous, and that levels of expression may oscillate, conferring different cellular characteristics. In ES the role of EWSR1/FLI1 in regulating subpopulation dynamics is currently unknown. METHODS We used siRNA to transiently suppress EWSR1/FLI1 expression and followed population dynamics using both single cell expression profiling, CyTOF and functional assays to define characteristics of exponentially growing ES cells and of ES cells in which EWSR1/FLI1 had been downregulated. Novel transcriptional states with distinct features were assigned using random forest feature selection in combination with machine learning. Cells isolated from ES xenografts in immune-deficient mice were interrogated to determine whether characteristics of specific subpopulations of cells in vitro could be identified. Stem-like characteristics were assessed by primary and secondary spheroid formation in vitro, and invasion/motility was determined for each identified subpopulation. Autophagy was determined by expression profiling, cell sorting and immunohistochemical staining. RESULTS We defined a workflow to study EWSR1/FLI1 driven transcriptional states and phenotypes. We tracked EWSR1/FLI1 dependent proliferative activity over time to discover sources of intra-tumoral diversity. Single-cell RNA profiling was used to compare expression profiles in exponentially growing populations (si-Control) or in two dormant populations (D1, D2) in which EWSR1/FLI1 had been suppressed. Three distinct transcriptional states were uncovered contributing to ES intra-heterogeneity. Our predictive model identified ~1% cells in a dormant-like state and ~ 2-4% cells with stem-like and neural stem-like features in an exponentially proliferating ES cell line and in ES xenografts. Following EWSR1/FLI1 knockdown, cells re-entering the proliferative cycle exhibited greater stem-like properties, whereas for those cells remaining quiescent, FAM134B-dependent dormancy may provide a survival mechanism. CONCLUSIONS We show that time-dependent changes induced by suppression of oncogenic EWSR1/FLI1 expression induces dormancy, with different subpopulation dynamics. Cells re-entering the proliferative cycle show enhanced stem-like characteristics, whereas those remaining dormant for prolonged periods appear to survive through autophagy. Cells with these characteristics identified in exponentially growing cell populations and in tumor xenografts may confer drug resistance and could potentially contribute to metastasis.
Collapse
Affiliation(s)
- Roxane Khoogar
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - Fuyang Li
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Myron Ignatius
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - Elizabeth R Lawlor
- Seattle Children's Research Institute, University of Washington Medical School, Washington, DC, USA
| | - Katsumi Kitagawa
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Doris A Phelps
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - Peter J Houghton
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA.
| |
Collapse
|
30
|
Balestra T, Manara MC, Laginestra MA, Pasello M, De Feo A, Bassi C, Guerzoni C, Landuzzi L, Lollini PL, Donati DM, Negrini M, Magnani M, Scotlandi K. Targeting CD99 Compromises the Oncogenic Effects of the Chimera EWS-FLI1 by Inducing Reexpression of Zyxin and Inhibition of GLI1 Activity. Mol Cancer Ther 2022; 21:58-69. [PMID: 34667115 DOI: 10.1158/1535-7163.mct-21-0189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/30/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022]
Abstract
Ewing sarcoma, a highly aggressive pediatric tumor, is driven by EWS-FLI1, an oncogenic transcription factor that remodels the tumor genetic landscape. Epigenetic mechanisms play a pivotal role in Ewing sarcoma pathogenesis, and the therapeutic value of compounds targeting epigenetic pathways is being identified in preclinical models. Here, we showed that modulation of CD99, a cell surface molecule highly expressed in Ewing sarcoma cells, may alter transcriptional dysregulation in Ewing sarcoma through control of the zyxin-GLI1 axis. Zyxin is transcriptionally repressed, but GLI1 expression is maintained by EWS-FLI1. We demonstrated that targeting CD99 with antibodies, including the human diabody C7, or genetically inhibiting CD99 is sufficient to increase zyxin expression and induce its dynamic nuclear accumulation. Nuclear zyxin functionally affects GLI1, inhibiting targets such as NKX2-2, cyclin D1, and PTCH1 and upregulating GAS1, a tumor suppressor protein negatively regulated by SHH/GLI1 signaling. We used a battery of functional assays to demonstrate (i) the relationship between CD99/zyxin and tumor cell growth/migration and (ii) how CD99 deprivation from the Ewing sarcoma cell surface is sufficient to specifically affect the expression of some crucial EWS-FLI1 targets, both in vitro and in vivo, even in the presence of EWS-FLI1. This article reveals that the CD99/zyxin/GLI1 axis is promising therapeutic target for reducing Ewing sarcoma malignancy.
Collapse
Affiliation(s)
- Tommaso Balestra
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Cristina Manara
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | | | - Michela Pasello
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alessandra De Feo
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Cristian Bassi
- Department of Translational Medicine and for Romagna, and "Laboratorio per le Tecnologie delle Terapie Avanzate" (LTTA), University of Ferrara, Ferrara, Italy
| | - Clara Guerzoni
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Lorena Landuzzi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Pier-Luigi Lollini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Davide Maria Donati
- Clinica Ortopedica III, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Massimo Negrini
- Department of Translational Medicine and for Romagna, and "Laboratorio per le Tecnologie delle Terapie Avanzate" (LTTA), University of Ferrara, Ferrara, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino, Fano, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
| |
Collapse
|
31
|
Seong BKA, Dharia NV, Lin S, Donovan KA, Chong S, Robichaud A, Conway A, Hamze A, Ross L, Alexe G, Adane B, Nabet B, Ferguson FM, Stolte B, Wang EJ, Sun J, Darzacq X, Piccioni F, Gray NS, Fischer ES, Stegmaier K. TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma. Cancer Cell 2021; 39:1262-1278.e7. [PMID: 34329586 PMCID: PMC8443273 DOI: 10.1016/j.ccell.2021.07.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/24/2021] [Accepted: 07/01/2021] [Indexed: 12/26/2022]
Abstract
Fusion-transcription factors (fusion-TFs) represent a class of driver oncoproteins that are difficult to therapeutically target. Recently, protein degradation has emerged as a strategy to target these challenging oncoproteins. The mechanisms that regulate fusion-TF stability, however, are generally unknown. Using CRISPR-Cas9 screening, we discovered tripartite motif-containing 8 (TRIM8) as an E3 ubiquitin ligase that ubiquitinates and degrades EWS/FLI, a driver fusion-TF in Ewing sarcoma. Moreover, we identified TRIM8 as a selective dependency in Ewing sarcoma compared with >700 other cancer cell lines. Mechanistically, TRIM8 knockout led to an increase in EWS/FLI protein levels that was not tolerated. EWS/FLI acts as a neomorphic substrate for TRIM8, defining the selective nature of the dependency. Our results demonstrate that fusion-TF protein stability is tightly regulated and highlight fusion oncoprotein-specific regulators as selective therapeutic targets. This study provides a tractable strategy to therapeutically exploit oncogene overdose in Ewing sarcoma and potentially other fusion-TF-driven cancers.
Collapse
Affiliation(s)
- Bo Kyung A Seong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shasha Chong
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Amanda Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amanda Hamze
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Linda Ross
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Biniam Adane
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Björn Stolte
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Dr.von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
| | - Emily Jue Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jialin Sun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; CIRM Center of Excellence, University of California, Berkeley, CA, 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
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
| |
Collapse
|
32
|
Jayabal P, Zhou F, Lei X, Ma X, Blackman B, Weintraub ST, Houghton PJ, Shiio Y. NELL2-cdc42 signaling regulates BAF complexes and Ewing sarcoma cell growth. Cell Rep 2021; 36:109254. [PMID: 34233189 PMCID: PMC8312579 DOI: 10.1016/j.celrep.2021.109254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/07/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022] Open
Abstract
BAF chromatin remodeling complexes play important roles in chromatin regulation and cancer. Here, we report that Ewing sarcoma cells are dependent on the autocrine signaling mediated by NELL2, a secreted glycoprotein that has been characterized as an axon guidance molecule. NELL2 uses Robo3 as the receptor to transmit critical growth signaling. NELL2 signaling inhibits cdc42 and upregulates BAF complexes and EWS-FLI1 transcriptional output. We demonstrate that cdc42 is a negative regulator of BAF complexes, inducing actin polymerization and complex disassembly. Furthermore, we identify NELL2highCD133highEWS-FLI1high and NELL2lowCD133lowEWS-FLI1low populations in Ewing sarcoma, which display phenotypes consistent with high and low NELL2 signaling, respectively. We show that NELL2, CD133, and EWS-FLI1 positively regulate each other and upregulate BAF complexes and cell proliferation in Ewing sarcoma. These results reveal a signaling pathway regulating critical chromatin remodeling complexes and cancer cell proliferation.
Collapse
Affiliation(s)
- Panneerselvam Jayabal
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Fuchun Zhou
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xiufen Lei
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xiuye Ma
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Barron Blackman
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Molecular Medicine, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yuzuru Shiio
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA.
| |
Collapse
|
33
|
Slotkin EK, Bowman AS, Levine MF, Dela Cruz F, Coutinho DF, Sanchez GI, Rosales N, Modak S, Tap WD, Gounder MM, Thornton KA, Bouvier N, You D, Gundem G, Gerstle JT, Heaton TE, LaQuaglia MP, Wexler LH, Meyers PA, Kung AL, Papaemmanuil E, Zehir A, Ladanyi M, Shukla N. Comprehensive Molecular Profiling of Desmoplastic Small Round Cell Tumor. Mol Cancer Res 2021; 19:1146-1155. [PMID: 33753552 PMCID: PMC8293793 DOI: 10.1158/1541-7786.mcr-20-0722] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/27/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022]
Abstract
Desmoplastic small round cell tumor (DSRCT) is characterized by the EWSR1-WT1 t(11;22) (p13:q12) translocation. Few additional putative drivers have been identified, and research has suffered from a lack of model systems. Next-generation sequencing (NGS) data from 68 matched tumor-normal samples, whole-genome sequencing data from 10 samples, transcriptomic and affymetrix array data, and a bank of DSRCT patient-derived xenograft (PDX) are presented. EWSR1-WT1 fusions were noted to be simple, balanced events. Recurrent mutations were uncommon, but were noted in TERT (3%), ARID1A (6%), HRAS (5%), and TP53 (3%), and recurrent loss of heterozygosity (LOH) at 11p, 11q, and 16q was identified in 18%, 22%, and 34% of samples, respectively. Comparison of tumor-normal matched versus unmatched analysis suggests overcalling of somatic mutations in prior publications of DSRCT NGS data. Alterations in fibroblast growth factor receptor 4 (FGFR4) were identified in 5 of 68 (7%) of tumor samples, whereas differential overexpression of FGFR4 was confirmed orthogonally using 2 platforms. PDX models harbored the pathognomic EWSR1-WT1 fusion and were highly representative of corresponding tumors. Our analyses confirm DSRCT as a genomically quiet cancer defined by the balanced translocation, t(11;22)(p13:q12), characterized by a paucity of secondary mutations but a significant number of copy number alterations. Against this genomically quiet background, recurrent activating alterations of FGFR4 stood out, and suggest that this receptor tyrosine kinase, also noted to be highly expressed in DSRCT, should be further investigated. Future studies of DSRCT biology and preclinical therapeutic strategies should benefit from the PDX models characterized in this study. IMPLICATIONS: These data describe the general quiescence of the desmoplastic small round cell tumor (DSRCT) genome, present the first available bank of DSRCT model systems, and nominate FGFR4 as a key receptor tyrosine kinase in DSRCT, based on high expression, recurrent amplification, and recurrent activating mutations.
Collapse
Affiliation(s)
- Emily K Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Max F Levine
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Filemon Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Diego F Coutinho
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Glorymar I Sanchez
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nestor Rosales
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shakeel Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mrinal M Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katherine A Thornton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gunes Gundem
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justin T Gerstle
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Todd E Heaton
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael P LaQuaglia
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard H Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
34
|
Jiménez JA, Apfelbaum AA, Hawkins AG, Svoboda LK, Kumar A, Ruiz RO, Garcia AX, Haarer E, Nwosu ZC, Bradin J, Purohit T, Chen D, Cierpicki T, Grembecka J, Lyssiotis CA, Lawlor ER. EWS-FLI1 and Menin Converge to Regulate ATF4 Activity in Ewing Sarcoma. Mol Cancer Res 2021; 19:1182-1195. [PMID: 33741715 PMCID: PMC8462528 DOI: 10.1158/1541-7786.mcr-20-0679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 01/15/2021] [Accepted: 03/11/2021] [Indexed: 11/16/2022]
Abstract
Ewing sarcomas are driven by EWS-ETS fusions, most commonly EWS-FLI1, which promotes widespread metabolic reprogramming, including activation of serine biosynthesis. We previously reported that serine biosynthesis is also activated in Ewing sarcoma by the scaffolding protein menin through as yet undefined mechanisms. Here, we investigated whether EWS-FLI1 and/or menin orchestrate serine biosynthesis via modulation of ATF4, a stress-response gene that acts as a master transcriptional regulator of serine biosynthesis in other tumors. Our results show that in Ewing sarcoma, ATF4 levels are high and that ATF4 modulates transcription of core serine synthesis pathway (SSP) genes. Inhibition of either EWS-FLI1 or menin leads to loss of ATF4, and this is associated with diminished expression of SSP transcripts and proteins. We identified and validated an EWS-FLI1 binding site at the ATF4 promoter, indicating that the fusion can directly activate ATF4 transcription. In contrast, our results suggest that menin-dependent regulation of ATF4 is mediated by transcriptional and post-transcriptional mechanisms. Importantly, our data also reveal that the downregulation of SSP genes that occurs in the context of EWS-FLI1 or menin loss is indicative of broader inhibition of ATF4-dependent transcription. Moreover, we find that menin inhibition similarly leads to loss of ATF4 and the ATF4-dependent transcriptional signature in MLL-rearranged B-cell acute lymphoblastic leukemia, extending our findings to another cancer in which menin serves an oncogenic role. IMPLICATIONS: These studies provide new insights into metabolic reprogramming in Ewing sarcoma and also uncover a previously undescribed role for menin in the regulation of ATF4.
Collapse
Affiliation(s)
- Jennifer A Jiménez
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - April A Apfelbaum
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Pediatrics, University of Washington, Seattle, Washington
- Seattle Children's Research Institute, Seattle, Washington
| | - Allegra G Hawkins
- New York Genome Center, New York, New York
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | | | - Abhijay Kumar
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Ramon Ocadiz Ruiz
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Alessandra X Garcia
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Elena Haarer
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Zeribe C Nwosu
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joshua Bradin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Trupta Purohit
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Dong Chen
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Elizabeth R Lawlor
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan.
- Department of Pediatrics, University of Washington, Seattle, Washington
- Seattle Children's Research Institute, Seattle, Washington
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| |
Collapse
|
35
|
Dong XH, Lu ZF, Kang CM, Li XH, Haworth KE, Ma X, Lu JB, Liu XH, Fang FC, Wang CS, Ye JH, Zheng L, Wang Q, Ye S, Hu YW. The Long Noncoding RNA RP11-728F11.4 Promotes Atherosclerosis. Arterioscler Thromb Vasc Biol 2021; 41:1191-1204. [PMID: 33406853 DOI: 10.1161/atvbaha.120.315114] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Noncoding RNAs are emerging as important players in gene regulation and cardiovascular diseases. Their roles in the pathogenesis of atherosclerosis are not fully understood. The purpose of this study was to determine the role played by a previously uncharacterized long noncoding RNA, RP11-728F11.4, in the development of atherosclerosis and the mechanisms by which it acts. Approach and Results: Expression microarray analysis revealed that atherosclerotic plaques had increased expression of RP11-728F11.4 as well as the cognate gene FXYD6 (FXYD domain containing ion transport regulator 6), which encodes a modulator of Na+/K+-ATPase. In vitro experiments showed that RP11-728F11.4 interacted with the RNA-binding protein EWSR1 (Ewings sarcoma RNA binding protein-1) and upregulated FXYD6 expression. Lentivirus-induced overexpression of RP11-728F11.4 in cultured monocytes-derived macrophages resulted in higher Na+/K+-ATPase activity, intracellular cholesterol accumulation, and increased proinflammatory cytokine production. The effects of RP11-728F11.4 were enhanced by siRNA-mediated knockdown of EWSR1 and reduced by downregulation of FXYD domain containing ion transport regulator 6. In vivo experiments in apoE knockout mice fed a Western diet demonstrated that RP11-728F11.4 increased proinflammatory cytokine production and augmented atherosclerotic lesions. CONCLUSIONS RP11-728F11.4 promotes atherosclerosis, with an influence on cholesterol homeostasis and proinflammatory molecule production, thus representing a potential therapeutic target. Graphic Abstract: A graphic abstract is available for this article.
Collapse
MESH Headings
- Animals
- Atherosclerosis/etiology
- Atherosclerosis/genetics
- Atherosclerosis/metabolism
- Cells, Cultured
- Cholesterol/metabolism
- Cytokines/metabolism
- Disease Models, Animal
- Endothelial Cells/metabolism
- Female
- Gene Knockdown Techniques
- Humans
- Ion Channels/genetics
- Ion Channels/metabolism
- Lipid Metabolism
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout, ApoE
- Middle Aged
- Plaque, Atherosclerotic/etiology
- Plaque, Atherosclerotic/genetics
- Plaque, Atherosclerotic/pathology
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA-Binding Protein EWS/antagonists & inhibitors
- RNA-Binding Protein EWS/genetics
- RNA-Binding Protein EWS/metabolism
- Sodium-Potassium-Exchanging ATPase/metabolism
- Up-Regulation
Collapse
Affiliation(s)
- Xian-Hui Dong
- Department of Clinical Laboratory, Guangzhou Women and Children Medical Center, Guangzhou Medical University, China (X.-H.D., Y.-W.H.)
| | - Zhi-Feng Lu
- Laboratory Medicine Center (Z.-F.L., C.-M.K., X.-H. Li, X.-H. Liu, L.Z., Q.W., Y.-W.H.), Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chun-Min Kang
- Laboratory Medicine Center (Z.-F.L., C.-M.K., X.-H. Li, X.-H. Liu, L.Z., Q.W., Y.-W.H.), Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xue-Heng Li
- Laboratory Medicine Center (Z.-F.L., C.-M.K., X.-H. Li, X.-H. Liu, L.Z., Q.W., Y.-W.H.), Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kim E Haworth
- Department of Cardiovascular Sciences and NIHR (National Institute for Health Research) Leicester Biomedical Research Centre, University of Leicester, United Kingdom (K.E.H., S.Y.)
| | - Xin Ma
- Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jing-Bo Lu
- Department of Vascular Surgery (J.-B.L.), Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Vascular Surgery, Shenzhen Sun Yat-Sen Cardiovascular Hospital, China (J.-B.L.)
| | - Xue-Hui Liu
- Laboratory Medicine Center (Z.-F.L., C.-M.K., X.-H. Li, X.-H. Liu, L.Z., Q.W., Y.-W.H.), Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fu-Chun Fang
- Department of Stomatology (F.-C.F.), Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Claire S Wang
- Gonville and Caius College, University of Cambridge, United Kindgom (C.S.W.)
| | - John H Ye
- University Hospitals of Leicester NHS Trust, United Kingdom (J.H.Y.)
| | - Lei Zheng
- Laboratory Medicine Center (Z.-F.L., C.-M.K., X.-H. Li, X.-H. Liu, L.Z., Q.W., Y.-W.H.), Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qian Wang
- Laboratory Medicine Center (Z.-F.L., C.-M.K., X.-H. Li, X.-H. Liu, L.Z., Q.W., Y.-W.H.), Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shu Ye
- Department of Cardiovascular Sciences and NIHR (National Institute for Health Research) Leicester Biomedical Research Centre, University of Leicester, United Kingdom (K.E.H., S.Y.)
- Shantou University Medical College, China (S.Y.)
| | - Yan-Wei Hu
- Department of Clinical Laboratory, Guangzhou Women and Children Medical Center, Guangzhou Medical University, China (X.-H.D., Y.-W.H.)
- Laboratory Medicine Center (Z.-F.L., C.-M.K., X.-H. Li, X.-H. Liu, L.Z., Q.W., Y.-W.H.), Nanfang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
36
|
Koustas E, Sarantis P, Karamouzis MV, Vielh P, Theocharis S. The Controversial Role of Autophagy in Ewing Sarcoma Pathogenesis-Current Treatment Options. Biomolecules 2021; 11:biom11030355. [PMID: 33652741 PMCID: PMC7996923 DOI: 10.3390/biom11030355] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/10/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Ewing Sarcoma (ES) is a rare, aggressive, and highly metastasizing cancer in children and young adults. Most ES cases carry the fusion of the Ewing Sarcoma Breakpoint Region 1 (EWSR1) and FLI1 (Friend leukemia virus integration site 1) genes, leading to an EWS-FLI1 fused protein, which is associated with autophagy, a homeostatic and catabolic mechanism under normal and pathological conditions. Following such interesting and controversial data regarding autophagy in ES, many clinical trials using modulators of autophagy are now underway in this field. In the present review, we summarize current data and clinical trials that associate autophagy with ES. In vitro studies highlight the controversial role of autophagy as a tumor promoter or a tumor suppressor mechanism in ES. Clinical and in vitro studies on ES, together with the autophagy modulators, suggest that caution should be adopted in the application of autophagy as a therapeutic target. Monitoring and targeting autophagy in every ES patient could eliminate the need for targeting multiple pathways in order to achieve the maximum beneficial effect. Future studies are required to focus on which ES patients are affected by autophagy modulators in order to provide novel and more efficient therapeutic protocols for patients with ES based on the current autophagy status of the tumors.
Collapse
Affiliation(s)
- Evangelos Koustas
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.K.); (P.S.)
- Molecular Oncology Unit, Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Panagiotis Sarantis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.K.); (P.S.)
- Molecular Oncology Unit, Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Michalis V. Karamouzis
- Molecular Oncology Unit, Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Philippe Vielh
- Medipath & American Hospital of Paris, 17 rue Gazan, 75014 Paris, France;
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.K.); (P.S.)
- Correspondence: or ; Tel.: +30-210-7462267; Fax: +30-2107462157
| |
Collapse
|
37
|
Affiliation(s)
- Nicolò Riggi
- From the Institute of Pathology, Faculty of Biology and Medicine, University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland (N.R., I.S.); and the Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, and the Broad Institute of Harvard University and the Massachusetts Institute of Technology, Cambridge - both in Massachusetts (M.L.S.)
| | - Mario L Suvà
- From the Institute of Pathology, Faculty of Biology and Medicine, University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland (N.R., I.S.); and the Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, and the Broad Institute of Harvard University and the Massachusetts Institute of Technology, Cambridge - both in Massachusetts (M.L.S.)
| | - Ivan Stamenkovic
- From the Institute of Pathology, Faculty of Biology and Medicine, University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland (N.R., I.S.); and the Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, and the Broad Institute of Harvard University and the Massachusetts Institute of Technology, Cambridge - both in Massachusetts (M.L.S.)
| |
Collapse
|
38
|
Tian H, Billings T, Petkov PM. EWSR1 affects PRDM9-dependent histone 3 methylation and provides a link between recombination hotspots and the chromosome axis protein REC8. Mol Biol Cell 2021; 32:1-14. [PMID: 33175657 PMCID: PMC8098819 DOI: 10.1091/mbc.e20-09-0604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022] Open
Abstract
Meiotic recombination in most mammals requires recombination hotspot activation through the action of the histone 3 Lys-4 and Lys-36 methyltransferase PRDM9 to ensure successful double-strand-break initiation and repair. Here we show that EWSR1, a protein whose role in meiosis was not previously clarified in detail, binds to both PRDM9 and pREC8, a phosphorylated meiosis-specific cohesin, in male meiotic cells. We created a Ewsr1 conditional knockout mouse model to deplete EWSR1 before the onset of meiosis and found that absence of EWSR1 causes meiotic arrest with decreased histone trimethylation at meiotic hotspots, impaired DNA double-strand-break repair, and reduced crossover number. Our results demonstrate that EWSR1 is essential for promoting PRDM9-dependent histone methylation and normal meiotic progress, possibly by facilitating the linking between PRDM9-bound hotspots and the nascent chromosome axis through its component cohesin pREC8.
Collapse
Affiliation(s)
- Hui Tian
- The Jackson Laboratory, Bar Harbor, ME 04609
| | | | | |
Collapse
|
39
|
Srivastava A, Giangiobbe S, Skopelitou D, Miao B, Paramasivam N, Diquigiovanni C, Bonora E, Hemminki K, Försti A, Bandapalli OR. Whole Genome Sequencing Prioritizes CHEK2, EWSR1, and TIAM1 as Possible Predisposition Genes for Familial Non-Medullary Thyroid Cancer. Front Endocrinol (Lausanne) 2021; 12:600682. [PMID: 33692755 PMCID: PMC7937922 DOI: 10.3389/fendo.2021.600682] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/04/2021] [Indexed: 01/08/2023] Open
Abstract
Familial inheritance in non-medullary thyroid cancer (NMTC) is an area that has yet to be adequately explored. Despite evidence suggesting strong familial clustering of non-syndromic NMTC, known variants still account for a very small percentage of the genetic burden. In a recent whole genome sequencing (WGS) study of five families with several NMTCs, we shortlisted promising variants with the help of our in-house developed Familial Cancer Variant Prioritization Pipeline (FCVPPv2). Here, we report potentially disease-causing variants in checkpoint kinase 2 (CHEK2), Ewing sarcoma breakpoint region 1 (EWSR1) and T-lymphoma invasion and metastasis-inducing protein 1 (TIAM1) in one family. Performing WGS on three cases, one probable case and one healthy individual in a family with familial NMTC left us with 112254 variants with a minor allele frequency of less than 0.1%, which was reduced by pedigree-based filtering to 6368. Application of the pipeline led to the prioritization of seven coding and nine non-coding variants from this family. The variant identified in CHEK2, a known tumor suppressor gene involved in DNA damage-induced DNA repair, cell cycle arrest, and apoptosis, has been previously identified as a germline variant in breast and prostate cancer and has been functionally validated by Roeb et al. in a yeast-based assay to have an intermediate effect on protein function. We thus hypothesized that this family may harbor additional disease-causing variants in other functionally related genes. We evaluated two further variants in EWSR1 and TIAM1 with promising in silico results and reported interaction in the DNA-damage repair pathway. Hence, we propose a polygenic mode of inheritance in this family. As familial NMTC is considered to be more aggressive than its sporadic counterpart, it is important to identify such susceptibility genes and their associated pathways. In this way, the advancement of personalized medicine in NMTC patients can be fostered. We also wish to reopen the discussion on monogenic vs polygenic inheritance in NMTC and instigate further development in this area of research.
Collapse
Affiliation(s)
- Aayushi Srivastava
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Preclinical Pediatric Oncology, Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Sara Giangiobbe
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Diamanto Skopelitou
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Preclinical Pediatric Oncology, Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Beiping Miao
- Preclinical Pediatric Oncology, Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Nagarajan Paramasivam
- Computational Oncology, National Center for Tumor Diseases (NCT), Molecular Diagnostics Program, Heidelberg, Germany
| | - Chiara Diquigiovanni
- Unit of Medical Genetics, Department of Medical and Surgical Sciences, S. Orsola-Malphigi Hospital, University of Bologna, Bologna, Italy
| | - Elena Bonora
- Unit of Medical Genetics, Department of Medical and Surgical Sciences, S. Orsola-Malphigi Hospital, University of Bologna, Bologna, Italy
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czechia
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Preclinical Pediatric Oncology, Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Obul Reddy Bandapalli
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Preclinical Pediatric Oncology, Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Medical Faculty, Heidelberg University, Heidelberg, Germany
- *Correspondence: Obul Reddy Bandapalli,
| |
Collapse
|
40
|
Shi X, Zheng Y, Jiang L, Zhou B, Yang W, Li L, Ding L, Huang M, Gery S, Lin DC, Koeffler HP. EWS-FLI1 regulates and cooperates with core regulatory circuitry in Ewing sarcoma. Nucleic Acids Res 2020; 48:11434-11451. [PMID: 33080033 PMCID: PMC7672457 DOI: 10.1093/nar/gkaa901] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/22/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Core regulatory circuitry (CRC)-dependent transcriptional network is critical for developmental tumors in children and adolescents carrying few gene mutations. However, whether and how CRC contributes to transcription regulation in Ewing sarcoma is unknown. Here, we identify and functionally validate a CRC 'trio' constituted by three transcription factors (TFs): KLF15, TCF4 and NKX2-2, in Ewing sarcoma cells. Epigenomic analyses demonstrate that EWS-FLI1, the primary fusion driver for this cancer, directly establishes super-enhancers of each of these three TFs to activate their transcription. In turn, KLF15, TCF4 and NKX2-2 co-bind to their own and each other's super-enhancers and promoters, forming an inter-connected auto-regulatory loop. Functionally, CRC factors contribute significantly to cell proliferation of Ewing sarcoma both in vitro and in vivo. Mechanistically, CRC factors exhibit prominent capacity of co-regulating the epigenome in cooperation with EWS-FLI1, occupying 77.2% of promoters and 55.6% of enhancers genome-wide. Downstream, CRC TFs coordinately regulate gene expression networks in Ewing sarcoma, controlling important signaling pathways for cancer, such as lipid metabolism pathway, PI3K/AKT and MAPK signaling pathways. Together, molecular characterization of the oncogenic CRC model advances our understanding of the biology of Ewing sarcoma. Moreover, CRC-downstream genes and signaling pathways may contain potential therapeutic targets for this malignancy.
Collapse
Affiliation(s)
- Xianping Shi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation; State Key Laboratory of Respiratory Disease; Affiliated Cancer Hospital of Guangzhou Medical University; Sino-French Hoffmann institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 510120, P.R. China
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Liling Jiang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation; State Key Laboratory of Respiratory Disease; Affiliated Cancer Hospital of Guangzhou Medical University; Sino-French Hoffmann institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 510120, P.R. China
| | - Bo Zhou
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Liyan Li
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Lingwen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117600, Singapore
| | - Moli Huang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, P.R. China
| | - Sigal Gery
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117600, Singapore
- National University Cancer Institute, National University Hospital Singapore, Singapore 119074, Singapore
| |
Collapse
|
41
|
Nicholas TR, Meng J, Greulich BM, Morris TS, Hollenhorst PC. --A high-throughput screen identifies inhibitors of the interaction between the oncogenic transcription factor ERG and the cofactor EWS. PLoS One 2020; 15:e0238999. [PMID: 32915889 PMCID: PMC7485968 DOI: 10.1371/journal.pone.0238999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Aberrant expression of the transcription factor ERG is a key driving event in approximately one-half of all of prostate cancers. Lacking an enzymatic pocket and mainly disordered, the structure of ERG is difficult to exploit for therapeutic design. We recently identified EWS as a specific interacting partner of ERG that is required for oncogenic function. In this study, we aimed to target this specific protein-protein interaction with small molecules. A high-throughput screening (HTS) strategy was implemented to identify potential protein-protein interaction inhibitors. Secondary assays verified the function of several hit compounds, and one lead compound inhibited ERG-mediated phenotypes in prostate cells. This is the first study aimed at targeting the ERG-EWS protein-protein interaction for the development of a small molecule-based prostate cancer therapy.
Collapse
Affiliation(s)
- Taylor R. Nicholas
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Jingwei Meng
- Chemical Genomics Core Facility, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Benjamin M. Greulich
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Teresa Stevie Morris
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Peter C. Hollenhorst
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, United States of America
- * E-mail:
| |
Collapse
|
42
|
Tran TAN. "Primary cutaneous biphasic sarcomatoid basal cell carcinoma with myoepithelial carcinoma differentiation": Is it a new variant of sarcomatoid basal cell carcinoma or a collision tumor composed of a myoepithelial carcinoma and an incidental basal cell carcinoma? J Cutan Pathol 2020; 47:576-578. [PMID: 31995232 DOI: 10.1111/cup.13651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/08/2020] [Accepted: 01/21/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Tien Anh N Tran
- Department of Pathology, Advent Health Orlando, Orlando, Florida
| |
Collapse
|
43
|
Mestre-Alagarda C, Monteagudo C. Reply to "Primary cutaneous biphasic sarcomatoid basal cell carcinoma with myoepithelial carcinoma differentiation. Is it a new variant of sarcomatoid basal cell carcinoma or a collision tumor composed of a myoepithelial carcinoma and an incidental basal cell carcinoma?". J Cutan Pathol 2020; 47:578-580. [PMID: 32181509 DOI: 10.1111/cup.13685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/13/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Claudia Mestre-Alagarda
- Department of Anatomic Pathology, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | | |
Collapse
|
44
|
Le Moigne R, Subra F, Karam M, Auclair C. The β-Carboline Harmine Induces Actin Dynamic Remodeling and Abrogates the Malignant Phenotype in Tumorigenic Cells. Cells 2020; 9:cells9051168. [PMID: 32397195 PMCID: PMC7290983 DOI: 10.3390/cells9051168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
Numerous studies have shown that alteration of actin remodeling plays a pivotal role in the regulation of morphologic and phenotypic changes leading to malignancy. In the present study, we searched for drugs that can regulate actin polymerization and reverse the malignant phenotype in cancer cells. We developed a cell-free high-throughput screening assay for the identification of compounds that induce the actin polymerization in vitro, by fluorescence anisotropy. Then, the potential of the hit compound to restore the actin cytoskeleton and reverse the malignant phenotype was checked in EWS-Fli1-transformed fibroblasts and in B16-F10 melanoma cells. A β-carboline extracted from Peganum harmala (i.e., harmine) is identified as a stimulator of actin polymerization through a mechanism independent of actin binding and requiring intracellular factors involved in a process that regulates actin kinetics. Treatment of malignant cells with non-cytotoxic concentrations of harmine induces the recovery of a non-malignant cell morphology accompanied by reorganization of the actin cytoskeleton, rescued cell–cell adhesion, inhibition of cell motility and loss of anchorage-independent growth. In conclusion, harmine induces the reversion of the malignant phenotype by a process involving the modulation of actin dynamics and is a potential anti-tumor agent acting principally through a non-cytotoxic process.
Collapse
Affiliation(s)
- Ronan Le Moigne
- Centre National de la Recherche Scientifique, CNRS UMR 8113, Laboratoire de Biologie et Pharmacologie Appliquée, 94230 Cachan, France; (R.L.M.); (F.S.)
| | - Frédéric Subra
- Centre National de la Recherche Scientifique, CNRS UMR 8113, Laboratoire de Biologie et Pharmacologie Appliquée, 94230 Cachan, France; (R.L.M.); (F.S.)
| | - Manale Karam
- AC Bioscience, Innovation Park, Ecole Polytechnique Fédérale de Lausanne, CH-1024 Ecublens, Switzerland;
| | - Christian Auclair
- AC Bioscience, Innovation Park, Ecole Polytechnique Fédérale de Lausanne, CH-1024 Ecublens, Switzerland;
- Département de Biologie, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 94230 Cachan, France
- Correspondence:
| |
Collapse
|
45
|
Chen Z, Yang Y, Chen R, Ng CS, Shi H. Primary pulmonary myxoid sarcoma with EWSR1-CREB1 fusion: a case report and review of the literature. Diagn Pathol 2020; 15:15. [PMID: 32039736 PMCID: PMC7008573 DOI: 10.1186/s13000-020-00930-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Primary pulmonary myxoid sarcoma (PPMS) is an extremely rare lung sarcoma that is characterized in most cases by recurrent balanced chromosomal translocation t(2;22)(q33;q12) leading to the oncogenic fusion gene EWSR1-CREB1. CASE PRESENTATION We report a case of PPMS with molecular confirmation using fluorescence in situ hybridization (FISH) and DNA sequencing in a 45-year-old female patient. Computer tomography (CT) scanning revealed a peripheral circumscribed solid mass of 2.1 × 2 cm in the right lung superior lobe. Histologically, the tumor cells ranged from stellate, polygonal to chondrocyte-like or physaliferous-like, forming reticular network of delicate lace-like cellular strands and cords in abundant myxoid stroma. The tumor cell immunophenotype was positive for vimentin, EMA and negative for CK-pan, TTF-1, CAM5.2, S-100, calponin, SMA, desmin, ALK, CD31 and CD34. Molecular analysis demonstrated EWSR1-CREB1 gene fusion in this tumor. During 38 months of follow-up, the patient was alive with no clinical or radiological evidence of recurrence or metastasis. CONCLUSION PPMS is a rare low-grade sarcoma with distinct histological and genetic features. We add another case to the literature of this rare tumor and report for the first time occurrence of chondrocyte-like and physaliferous-like tumor cells in this tumor, thus enriching its morphologic and cytologic spectrum.
Collapse
Affiliation(s)
- Zhenwei Chen
- Department of Pathology, Jinhua Municipal Central Hospital, 351 Mingyue Road, Jinhua, 321000 Zhejiang Province People’s Republic of China
| | - Yihui Yang
- Department of Pathology, Jinhua Municipal Central Hospital, 351 Mingyue Road, Jinhua, 321000 Zhejiang Province People’s Republic of China
| | - Rongming Chen
- Department of Pathology, the People’s Hospital of Changfeng County, Changfeng County, Anhui Province People’s Republic of China
| | - Chi Sing Ng
- Department of Pathology, St. Teresa’s Hospital, Kowloon, Hong Kong
| | - Hongqi Shi
- Department of Pathology, Jinhua Municipal Central Hospital, 351 Mingyue Road, Jinhua, 321000 Zhejiang Province People’s Republic of China
| |
Collapse
|
46
|
Palombo R, Verdile V, Paronetto MP. Poison-Exon Inclusion in DHX9 Reduces Its Expression and Sensitizes Ewing Sarcoma Cells to Chemotherapeutic Treatment. Cells 2020; 9:cells9020328. [PMID: 32023846 PMCID: PMC7072589 DOI: 10.3390/cells9020328] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing is a combinatorial mechanism by which exons are joined to produce multiple mRNA variants, thus expanding the coding potential and plasticity of eukaryotic genomes. Defects in alternative splicing regulation are associated with several human diseases, including cancer. Ewing sarcoma is an aggressive tumor of bone and soft tissue, mainly affecting adolescents and young adults. DHX9 is a key player in Ewing sarcoma malignancy, and its expression correlates with worse prognosis in patients. In this study, by screening a library of siRNAs, we have identified splicing factors that regulate the alternative inclusion of a poison exon in DHX9 mRNA, leading to its downregulation. In particular, we found that hnRNPM and SRSF3 bind in vivo to this poison exon and suppress its inclusion. Notably, DHX9 expression correlates with that of SRSF3 and hnRNPM in Ewing sarcoma patients. Furthermore, downregulation of SRSF3 or hnRNPM inhibited DHX9 expression and Ewing sarcoma cell proliferation, while sensitizing cells to chemotherapeutic treatment. Hence, our study suggests that inhibition of hnRNPM and SRSF3 expression or activity could be exploited as a therapeutic tool to enhance the efficacy of chemotherapy in Ewing sarcoma.
Collapse
Affiliation(s)
- Ramona Palombo
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
| | - Veronica Verdile
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
- Correspondence: ; Tel.:+39-0636733576
| |
Collapse
|
47
|
Sen N, Cross AM, Lorenzi PL, Khan J, Gryder BE, Kim S, Caplen NJ. EWS-FLI1 reprograms the metabolism of Ewing sarcoma cells via positive regulation of glutamine import and serine-glycine biosynthesis. Mol Carcinog 2018; 57:1342-1357. [PMID: 29873416 PMCID: PMC6175245 DOI: 10.1002/mc.22849] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 05/22/2018] [Accepted: 06/01/2018] [Indexed: 12/12/2022]
Abstract
Ewing sarcoma (EWS) is a soft tissue and bone tumor that occurs primarily in adolescents and young adults. In most cases of EWS, the chimeric transcription factor, EWS-FLI1 is the primary oncogenic driver. The epigenome of EWS cells reflects EWS-FLI1 binding and activation or repression of transcription. Here, we demonstrate that EWS-FLI1 positively regulates the expression of proteins required for serine-glycine biosynthesis and uptake of the alternative nutrient source glutamine. Specifically, we show that EWS-FLI1 activates expression of PHGDH, PSAT1, PSPH, and SHMT2. Using cell-based studies, we also establish that EWS cells are dependent on glutamine for cell survival and that EWS-FLI1 positively regulates expression of the glutamine transporter, SLC1A5 and two enzymes involved in the one-carbon cycle, MTHFD2 and MTHFD1L. Inhibition of serine-glycine biosynthesis in EWS cells impacts their redox state leading to an accumulation of reactive oxygen species, DNA damage, and apoptosis. Importantly, analysis of EWS primary tumor transcriptome data confirmed that the aforementioned genes we identified as regulated by EWS-FLI1 exhibit increased expression compared with normal tissues. Furthermore, retrospective analysis of an independent data set generated a significant stratification of the overall survival of EWS patients into low- and high-risk groups based on the expression of PHGDH, PSAT1, PSPH, SHMT2, SLC1A5, MTHFD2, and MTHFD1L. In summary, our study demonstrates that EWS-FLI1 reprograms the metabolism of EWS cells and that serine-glycine metabolism or glutamine uptake are potential targetable vulnerabilities in this tumor type.
Collapse
Affiliation(s)
- Nirmalya Sen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research (CCR)National Cancer Institute (NCI)BethesdaMaryland
| | - Allison M. Cross
- Functional Genetics Section, Genetics Branch, Center for Cancer Research (CCR)National Cancer Institute (NCI)BethesdaMaryland
| | - Philip L. Lorenzi
- Proteomic and Metabolomics Core Facility, Department of Bioinformatics and Computational BiologyThe University of Texas MD Anderson Cancer CenterHoustonTexas
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research (CCR)National Cancer Institute (NCI)BethesdaMaryland
| | - Berkley E. Gryder
- Oncogenomics Section, Genetics Branch, Center for Cancer Research (CCR)National Cancer Institute (NCI)BethesdaMaryland
| | - Suntae Kim
- Functional Genetics Section, Genetics Branch, Center for Cancer Research (CCR)National Cancer Institute (NCI)BethesdaMaryland
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research (CCR)National Cancer Institute (NCI)BethesdaMaryland
| |
Collapse
|
48
|
Urbini M, Indio V, Astolfi A, Tarantino G, Renne SL, Pilotti S, Dei Tos AP, Maestro R, Collini P, Nannini M, Saponara M, Murrone L, Dagrada GP, Colombo C, Gronchi A, Pession A, Casali PG, Stacchiotti S, Pantaleo MA. Identification of an Actionable Mutation of KIT in a Case of Extraskeletal Myxoid Chondrosarcoma. Int J Mol Sci 2018; 19:ijms19071855. [PMID: 29937513 PMCID: PMC6073125 DOI: 10.3390/ijms19071855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 01/03/2023] Open
Abstract
Extraskeletal myxoid chondrosarcoma (EMC) is an extremely rare soft tissue sarcoma, marked by a translocation involving the NR4A3 gene. EMC is usually indolent and moderately sensitive to anthracycline-based chemotherapy. Recently, we reported on the therapeutic activity of sunitinib in a series of EMC cases, however the molecular target of sunitinib in EMC is unknown. Moreover, there is still the need to identify alternative therapeutic strategies. To better characterize this disease, we performed whole transcriptome sequencing in five EMC cases. Peculiarly, in one sample, an in-frame deletion (c.1735_1737delGAT p.D579del) was identified in exon 11 of KIT. The deletion was somatic and heterozygous and was validated both at DNA and mRNA level. This sample showed a marked high expression of KIT at the mRNA level and a mild phosphorylation of the receptor. Sanger sequencing of KIT in additional 15 Formalin Fixed Paraffin Embedded (FFPE) EMC did not show any other mutated cases. In conclusion, exon 11 KIT mutation was detected only in one out of 20 EMC cases analyzed, indicating that KIT alteration is not a recurrent event in these tumors and cannot explain the EMC sensitivity to sunitinib, although it is an actionable mutation in the individual case in which it has been identified.
Collapse
MESH Headings
- Base Sequence
- Chondrosarcoma/diagnosis
- Chondrosarcoma/genetics
- Chondrosarcoma/metabolism
- Chondrosarcoma/pathology
- Computational Biology
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Exons
- Gene Expression Regulation, Neoplastic
- Humans
- Neoplasms, Connective and Soft Tissue/diagnosis
- Neoplasms, Connective and Soft Tissue/genetics
- Neoplasms, Connective and Soft Tissue/metabolism
- Neoplasms, Connective and Soft Tissue/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Proto-Oncogene Proteins c-kit/genetics
- Proto-Oncogene Proteins c-kit/metabolism
- RNA-Binding Protein EWS/genetics
- RNA-Binding Protein EWS/metabolism
- Receptors, Steroid/genetics
- Receptors, Steroid/metabolism
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/metabolism
- Sequence Deletion
- Transcriptome
- Exome Sequencing
Collapse
Affiliation(s)
- Milena Urbini
- "Giorgio Prodi" Cancer Research Center, University of Bologna, 40138 Bologna, Italy.
| | - Valentina Indio
- "Giorgio Prodi" Cancer Research Center, University of Bologna, 40138 Bologna, Italy.
| | - Annalisa Astolfi
- "Giorgio Prodi" Cancer Research Center, University of Bologna, 40138 Bologna, Italy.
| | - Giuseppe Tarantino
- "Giorgio Prodi" Cancer Research Center, University of Bologna, 40138 Bologna, Italy.
| | - Salvatore Lorenzo Renne
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Silvana Pilotti
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | | | - Roberta Maestro
- Unit of Experimental Oncology 1, CRO Aviano National Cancer Institute, 33081 Aviano, Italy.
| | - Paola Collini
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Margherita Nannini
- Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy.
| | - Maristella Saponara
- Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy.
| | - Ludovica Murrone
- "Giorgio Prodi" Cancer Research Center, University of Bologna, 40138 Bologna, Italy.
| | - Gian Paolo Dagrada
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Chiara Colombo
- Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133Milan, Italy.
| | - Alessandro Gronchi
- Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133Milan, Italy.
| | - Andrea Pession
- "Giorgio Prodi" Cancer Research Center, University of Bologna, 40138 Bologna, Italy.
| | - Paolo Giovanni Casali
- Department of Cancer Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133Milan, Italy.
| | - Silvia Stacchiotti
- Department of Cancer Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133Milan, Italy.
| | - Maria Abbondanza Pantaleo
- Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy.
| |
Collapse
|
49
|
Tanner JM, Bensard C, Wei P, Krah NM, Schell JC, Gardiner J, Schiffman J, Lessnick SL, Rutter J. EWS/FLI is a Master Regulator of Metabolic Reprogramming in Ewing Sarcoma. Mol Cancer Res 2017; 15:1517-1530. [PMID: 28720588 PMCID: PMC5668171 DOI: 10.1158/1541-7786.mcr-17-0182] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/06/2017] [Accepted: 07/14/2017] [Indexed: 12/28/2022]
Abstract
Ewing sarcoma is a bone malignancy driven by a translocation event resulting in the fusion protein EWS/FLI1 (EF). EF functions as an aberrant and oncogenic transcription factor that misregulates the expression of thousands of genes. Previous work has focused principally on determining important transcriptional targets of EF, as well as characterizing important regulatory partnerships in EF-dependent transcriptional programs. Less is known, however, about EF-dependent metabolic changes or their role in Ewing sarcoma biology. Therefore, the metabolic effects of silencing EF in Ewing sarcoma cells were determined. Metabolomic analyses revealed distinct separation of metabolic profiles in EF-knockdown versus control-knockdown cells. Mitochondrial stress tests demonstrated that knockdown of EF increased respiratory as well as glycolytic functions. Enzymes and metabolites in several metabolic pathways were altered, including de novo serine synthesis and elements of one-carbon metabolism. Furthermore, phosphoglycerate dehydrogenase (PHGDH) was found to be highly expressed in Ewing sarcoma and correlated with worse patient survival. PHGDH knockdown or pharmacologic inhibition in vitro caused impaired proliferation and cell death. Interestingly, PHGDH modulation also led to elevated histone expression and methylation. These studies demonstrate that the translocation-derived fusion protein EF is a master regulator of metabolic reprogramming in Ewing sarcoma, diverting metabolites toward biosynthesis. As such, these data suggest that the metabolic aberrations induced by EF are important contributors to the oncogenic biology of these tumors.Implications: This previously unexplored role of EWS/FLI1-driven metabolic changes expands the understanding of Ewing sarcoma biology, and has potential to significantly inform development of therapeutic strategies. Mol Cancer Res; 15(11); 1517-30. ©2017 AACR.
Collapse
Affiliation(s)
- Jason M Tanner
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah
| | - Claire Bensard
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah
| | - Peng Wei
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah
| | - Nathan M Krah
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - John C Schell
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah
| | - Jamie Gardiner
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Joshua Schiffman
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Stephen L Lessnick
- Center for Childhood Cancer & Blood Diseases, Nationwide Children's Hospital, Columbus, Ohio
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah.
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah
| |
Collapse
|
50
|
Grünewald TGP. [Functional genomics of Ewing sarcoma]. Pathologe 2017; 38:198-201. [PMID: 28849372 DOI: 10.1007/s00292-017-0332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ewing sarcoma is a highly aggressive bone or soft-tissue tumor mostly occurring in children and adolescents. Conventional multi-modal therapies are associated with considerable acute and chronic toxicity. Thus, more effective and in particular less toxic therapeutic strategies are urgently required. Despite the fact that Ewing sarcoma is characterized by specific EWSR1-ETS gene fusions, the resulting fusion oncoproteins are not suitable for targeted therapy due to their low immunogenicity and the ubiquitous expression of their constituents. However, functional genomics revealed several EWSR1-ETS target genes, which are only minimally expressed in normal tissues, and which could serve as surrogate-targets for (immuno-)therapeutic approaches. Moreover, functional genomic analyses yielded first mechanistic explanations for the relatively high incidence of Ewing sarcoma in Europeans, and first studies are exploring the value of circulating free DNA and/or exosomal mRNA of EWSR1-ETS fusion oncogenes as minimal-residual-disease markers in Ewing sarcoma. This review summarizes key contributions to these aspects and gives a perspective on their medical relevance.
Collapse
Affiliation(s)
- T G P Grünewald
- Max-Eder Nachwuchsgruppe für Pädiatrische Sarkombiologie, Pathologisches Institut, Medizinische Fakultät, LMU München, Thalkirchner Str. 36, 80337, München, Deutschland.
| |
Collapse
|