51
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Hughes CJ, Fields KM, Danis EP, Hsu JY, Neelakantan D, Vincent MY, Gustafson AL, Oliphant MJ, Sreekanth V, Zaberezhnyy V, Costello JC, Jedlicka P, Ford HL. SIX1 and EWS/FLI1 co-regulate an anti-metastatic gene network in Ewing Sarcoma. Nat Commun 2023; 14:4357. [PMID: 37468459 DOI: 10.1038/s41467-023-39945-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 07/05/2023] [Indexed: 07/21/2023] Open
Abstract
Ewing sarcoma (ES), which is characterized by the presence of oncogenic fusion proteins such as EWS/FLI1, is an aggressive pediatric malignancy with a high rate of early dissemination and poor outcome after distant spread. Here we demonstrate that the SIX1 homeoprotein, which enhances metastasis in most tumor types, suppresses ES metastasis by co-regulating EWS/FLI1 target genes. Like EWS/FLI1, SIX1 promotes cell growth/transformation, yet dramatically inhibits migration and invasion, as well as metastasis in vivo. We show that EWS/FLI1 promotes SIX1 protein expression, and that the two proteins share genome-wide binding profiles and transcriptional regulatory targets, including many metastasis-associated genes such as integrins, which they co-regulate. We further show that SIX1 downregulation of integrins is critical to its ability to inhibit invasion, a key characteristic of metastatic cells. These data demonstrate an unexpected anti-metastatic function for SIX1, through coordinate gene regulation with the key oncoprotein in ES, EWS/FLI1.
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Affiliation(s)
- Connor J Hughes
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Pharmacology Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Kaiah M Fields
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
- Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Etienne P Danis
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Jessica Y Hsu
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Deepika Neelakantan
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
- Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- OU Health Stephenson Cancer Center, Oklahoma City, OK, 73104, USA
| | - Melanie Y Vincent
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
- Vigeo Therapeutics, 85 Bolton St, Cambridge, MA, 02140, USA
| | - Annika L Gustafson
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
- Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Michael J Oliphant
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
- Integrative Physiology Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Varsha Sreekanth
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Vadym Zaberezhnyy
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - James C Costello
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Pharmacology Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Paul Jedlicka
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Heide L Ford
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Pharmacology Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA.
- Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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52
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Li M, Yang L, Chan AKN, Pokharel SP, Liu Q, Mattson N, Xu X, Chang W, Miyashita K, Singh P, Zhang L, Li M, Wu J, Wang J, Chen B, Chan LN, Lee J, Zhang XH, Rosen ST, Müschen M, Qi J, Chen J, Hiom K, Bishop AJR, Chen C. Epigenetic Control of Translation Checkpoint and Tumor Progression via RUVBL1-EEF1A1 Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206584. [PMID: 37075745 PMCID: PMC10265057 DOI: 10.1002/advs.202206584] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/23/2023] [Indexed: 05/03/2023]
Abstract
Epigenetic dysregulation is reported in multiple cancers including Ewing sarcoma (EwS). However, the epigenetic networks underlying the maintenance of oncogenic signaling and therapeutic response remain unclear. Using a series of epigenetics- and complex-focused CRISPR screens, RUVBL1, the ATPase component of NuA4 histone acetyltransferase complex, is identified to be essential for EwS tumor progression. Suppression of RUVBL1 leads to attenuated tumor growth, loss of histone H4 acetylation, and ablated MYC signaling. Mechanistically, RUVBL1 controls MYC chromatin binding and modulates the MYC-driven EEF1A1 expression and thus protein synthesis. High-density CRISPR gene body scan pinpoints the critical MYC interacting residue in RUVBL1. Finally, this study reveals the synergism between RUVBL1 suppression and pharmacological inhibition of MYC in EwS xenografts and patient-derived samples. These results indicate that the dynamic interplay between chromatin remodelers, oncogenic transcription factors, and protein translation machinery can provide novel opportunities for combination cancer therapy.
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Affiliation(s)
- Mingli Li
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Lu Yang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Anthony K. N. Chan
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Sheela Pangeni Pokharel
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Qiao Liu
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Nicole Mattson
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Xiaobao Xu
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Wen‐Han Chang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Kazuya Miyashita
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Priyanka Singh
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Leisi Zhang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Maggie Li
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Jun Wu
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Jinhui Wang
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Bryan Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Lai N. Chan
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOH44195USA
| | - Jaewoong Lee
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
- School of Biosystems and Biomedical SciencesCollege of Health ScienceKorea UniversitySeoul02841South Korea
- Interdisciplinary Program in Precision Public HealthKorea UniversitySeoul02841South Korea
| | | | | | - Markus Müschen
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
| | - Jun Qi
- Department of Cancer BiologyDana‐Farber Cancer InstituteHarvard Medical SchoolBostonMA02215USA
| | - Jianjun Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Kevin Hiom
- Division of Cellular MedicineSchool of MedicineUniversity of DundeeNethergateDundeeDD1 4HNUK
| | - Alexander J. R. Bishop
- Department of Cellular Systems and AnatomyUniversity of Texas Health Science Center at San AntonioSan AntonioTX78229USA
- Greehey Children's Cancer Research InstituteUniversity of Texas Health Science Center at San AntonioSan AntonioTX78229USA
| | - Chun‐Wei Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
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53
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Menon S, Breese MR, Lin YP, Allegakoen H, Perati S, Heslin A, Horlbeck MA, Weissman J, Sweet-Cordero EA, Bivona TG, Tulpule A. FET fusion oncoproteins disrupt physiologic DNA repair networks in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.30.538578. [PMID: 37205599 PMCID: PMC10187251 DOI: 10.1101/2023.04.30.538578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
While oncogenes promote cancer cell growth, unrestrained proliferation represents a significant stressor to cellular homeostasis networks such as the DNA damage response (DDR). To enable oncogene tolerance, many cancers disable tumor suppressive DDR signaling through genetic loss of DDR pathways and downstream effectors (e.g., ATM or p53 tumor suppressor mutations). Whether and how oncogenes can help "self-tolerize" by creating analogous functional deficiencies in physiologic DDR networks is not known. Here we focus on Ewing sarcoma, a FET fusion oncoprotein (EWS-FLI1) driven pediatric bone tumor, as a model for the class of FET rearranged cancers. Native FET protein family members are among the earliest factors recruited to DNA double-strand breaks (DSBs) during the DDR, though the function of both native FET proteins and FET fusion oncoproteins in DNA repair remains to be defined. Using preclinical mechanistic studies of the DDR and clinical genomic datasets from patient tumors, we discover that the EWS-FLI1 fusion oncoprotein is recruited to DNA DSBs and interferes with native FET (EWS) protein function in activating the DNA damage sensor ATM. As a consequence of FET fusion-mediated interference with the DDR, we establish functional ATM deficiency as the principal DNA repair defect in Ewing sarcoma and the compensatory ATR signaling axis as a collateral dependency and therapeutic target in multiple FET rearranged cancers. More generally, we find that aberrant recruitment of a fusion oncoprotein to sites of DNA damage can disrupt physiologic DSB repair, revealing a mechanism for how growth-promoting oncogenes can also create a functional deficiency within tumor suppressive DDR networks.
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Affiliation(s)
- Shruti Menon
- Tow Center for Developmental Oncology and Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10021
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 444 East 68th Street, 9th Floor, New York, NY 10065
| | - Marcus R. Breese
- Division of Pediatric Oncology, University of California, San Francisco, San Francisco, CA 94143
| | - Yone Phar Lin
- Division of Pediatric Oncology, University of California, San Francisco, San Francisco, CA 94143
| | - Hannah Allegakoen
- Division of Pediatric Oncology, University of California, San Francisco, San Francisco, CA 94143
| | - Shruthi Perati
- Division of Pediatric Oncology, University of California, San Francisco, San Francisco, CA 94143
| | - Ann Heslin
- Division of Pediatric Oncology, University of California, San Francisco, San Francisco, CA 94143
| | - Max A. Horlbeck
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, 02115
| | - Jonathan Weissman
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave, 68-132, Cambridge, MA 02139
| | | | - Trever G. Bivona
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94143
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Asmin Tulpule
- Tow Center for Developmental Oncology and Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10021
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 444 East 68th Street, 9th Floor, New York, NY 10065
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54
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Stefan K, Barski A. Cis-regulatory atlas of primary human CD4+ T cells. BMC Genomics 2023; 24:253. [PMID: 37170195 PMCID: PMC10173520 DOI: 10.1186/s12864-023-09288-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/31/2023] [Indexed: 05/13/2023] Open
Abstract
Cis-regulatory elements (CRE) are critical for coordinating gene expression programs that dictate cell-specific differentiation and homeostasis. Recently developed self-transcribing active regulatory region sequencing (STARR-Seq) has allowed for genome-wide annotation of functional CREs. Despite this, STARR-Seq assays are only employed in cell lines, in part, due to difficulties in delivering reporter constructs. Herein, we implemented and validated a STARR-Seq-based screen in human CD4+ T cells using a non-integrating lentiviral transduction system. Lenti-STARR-Seq is the first example of a genome-wide assay of CRE function in human primary cells, identifying thousands of functional enhancers and negative regulatory elements (NREs) in human CD4+ T cells. We find an unexpected difference in nucleosome organization between enhancers and NRE: enhancers are located between nucleosomes, whereas NRE are occupied by nucleosomes in their endogenous locations. We also describe chromatin modification, eRNA production, and transcription factor binding at both enhancers and NREs. Our findings support the idea of silencer repurposing as enhancers in alternate cell types. Collectively, these data suggest that Lenti-STARR-Seq is a successful approach for CRE screening in primary human cell types, and provides an atlas of functional CREs in human CD4+ T cells.
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Affiliation(s)
- Kurtis Stefan
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7028, Cincinnati, OH, 45229-3026, USA
- Medical Scientist Training Program (MSTP), University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7028, Cincinnati, OH, 45229-3026, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229-3026, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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55
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Sanalkumar R, Dong R, Lee L, Xing YH, Iyer S, Letovanec I, La Rosa S, Finzi G, Musolino E, Papait R, Chebib I, Nielsen GP, Renella R, Cote GM, Choy E, Aryee M, Stegmaier K, Stamenkovic I, Rivera MN, Riggi N. Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity. SCIENCE ADVANCES 2023; 9:eabo3789. [PMID: 37000878 DOI: 10.1126/sciadv.abo3789] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 01/18/2023] [Indexed: 06/19/2023]
Abstract
Cell fate transitions observed in embryonic development involve changes in three-dimensional genomic organization that provide proper lineage specification. Whether similar events occur within tumor cells and contribute to cancer evolution remains largely unexplored. We modeled this process in the pediatric cancer Ewing sarcoma and investigated high-resolution looping and large-scale nuclear conformation changes associated with the oncogenic fusion protein EWS-FLI1. We show that chromatin interactions in tumor cells are dominated by highly connected looping hubs centered on EWS-FLI1 binding sites, which directly control the activity of linked enhancers and promoters to establish oncogenic expression programs. Conversely, EWS-FLI1 depletion led to the disassembly of these looping networks and a widespread nuclear reorganization through the establishment of new looping patterns and large-scale compartment configuration matching those observed in mesenchymal stem cells, a candidate Ewing sarcoma progenitor. Our data demonstrate that major architectural features of nuclear organization in cancer cells can depend on single oncogenes and are readily reversed to reestablish latent differentiation programs.
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Affiliation(s)
- Rajendran Sanalkumar
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Rui Dong
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Lukuo Lee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Yu-Hang Xing
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sowmya Iyer
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Igor Letovanec
- Department of Histopathology, Central Institute, Valais Hospital, Sion, Switzerland
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stefano La Rosa
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Giovanna Finzi
- Department of Pathology, ASST Sette Laghi, Varese, Italy
| | - Elettra Musolino
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Roberto Papait
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- IRCSS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Ivan Chebib
- Department of Pathology and Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - G Petur Nielsen
- Department of Pathology and Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raffaele Renella
- Department Woman-Mother-Child, Division of Pediatrics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gregory M Cote
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Edwin Choy
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Martin Aryee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Kimberly Stegmaier
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Ivan Stamenkovic
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Miguel N Rivera
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Nicolò Riggi
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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56
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Shifting from a Biological-Agnostic Approach to a Molecular-Driven Strategy in Rare Cancers: Ewing Sarcoma Archetype. Biomedicines 2023; 11:biomedicines11030874. [PMID: 36979853 PMCID: PMC10045500 DOI: 10.3390/biomedicines11030874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Sarcomas of the thoracic cavity are rare entities that predominantly affect children and young adults. They can be very heterogeneous encompassing several different histological entities. Ewing Sarcoma (ES) can potentially arise from every bone, soft tissue, or visceral site in the body. However, it represents an extremely rare finding when it affects the thoracic cavity. It represents the second most frequent type of thoracic sarcoma, after chondrosarcoma. ES arises more frequently in sites that differ from the thoracic cavity, but it displays the same biological features and behavior of extra-thoracic ones. Current management of ES often requires a multidisciplinary treatment approach including surgery, radiotherapy, and systemic therapy, as it can guarantee local and distant disease control, at least transiently, although the long-term outcome remains poor. Unfortunately, due to the paucity of clinical trials purposely designed for this rare malignancy, there are no optimal strategies that can be used for disease recurrence. As a result of its complex biological features, ES might be suitable for emerging biology-based therapeutic strategies. However, a deeper understanding of the molecular mechanisms driving tumor growth and treatment resistance, including those related to oncogenic pathways, epigenetic landscape, and immune microenvironment, is necessary in order to develop new valid therapeutic opportunities. Here, we provide an overview of the most recent therapeutic advances for ES in both the preclinical and clinical settings. We performed a review of the current available literature and of the ongoing clinical trials focusing on new treatment strategies, after failure of conventional multimodal treatments.
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57
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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] [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.
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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.
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Chen E, Huang J, Chen M, Wu J, Ouyang P, Wang X, Shi D, Liu Z, Zhu W, Sun H, Yang S, Zhang B, Deng W, Qiu H, Xie F. FLI1 regulates radiotherapy resistance in nasopharyngeal carcinoma through TIE1-mediated PI3K/AKT signaling pathway. J Transl Med 2023; 21:134. [PMID: 36814284 PMCID: PMC9945741 DOI: 10.1186/s12967-023-03986-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Radiotherapy resistance is the main cause of treatment failure in nasopharyngeal carcinoma (NPC), which leads to poor prognosis. It is urgent to elucidate the molecular mechanisms underlying radiotherapy resistance. METHODS RNA-seq analysis was applied to five paired progressive disease (PD) and complete response (CR) NPC tissues. Loss-and gain-of-function assays were used for oncogenic function of FLI1 both in vitro and in vivo. RNA-seq analysis, ChIP assays and dual luciferase reporter assays were performed to explore the interaction between FLI1 and TIE1. Gene expression with clinical information from tissue microarray of NPC were analyzed for associations between FLI1/TIE1 expression and NPC prognosis. RESULTS FLI1 is a potential radiosensitivity regulator which was dramatically overexpressed in the patients with PD to radiotherapy compared to those with CR. FLI1 induced radiotherapy resistance and enhanced the ability of DNA damage repair in vitro, and promoted radiotherapy resistance in vivo. Mechanistic investigations showed that FLI1 upregulated the transcription of TIE1 by binding to its promoter, thus activated the PI3K/AKT signaling pathway. A decrease in TIE1 expression restored radiosensitivity of NPC cells. Furthermore, NPC patients with high levels of FLI1 and TIE1 were correlated with poor prognosis. CONCLUSION Our study has revealed that FLI1 regulates radiotherapy resistance of NPC through TIE1-mediated PI3K/AKT signaling pathway, suggesting that targeting the FLI1/TIE1 signaling pathway could be a potential therapeutic strategy to enhance the efficacy of radiotherapy in NPC.
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Affiliation(s)
- Enni Chen
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Jiajia Huang
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Miao Chen
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Jiawei Wu
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Puyun Ouyang
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Xiaonan Wang
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Dingbo Shi
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Zhiqiao Liu
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Wancui Zhu
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Haohui Sun
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Shanshan Yang
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Baoyu Zhang
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 China
| | - Wuguo Deng
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - Huijuan Qiu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - Fangyun Xie
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
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Lu DY, Ellegast JM, Ross KN, Malone CF, Lin S, Mabe NW, Dharia NV, Meyer A, Conway A, Su AH, Selich-Anderson J, Taslim C, Byrum AK, Seong BKA, Adane B, Gray NS, Rivera MN, Lessnick SL, Stegmaier K. The ETS transcription factor ETV6 constrains the transcriptional activity of EWS-FLI to promote Ewing sarcoma. Nat Cell Biol 2023; 25:285-297. [PMID: 36658220 PMCID: PMC9928584 DOI: 10.1038/s41556-022-01059-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 11/24/2022] [Indexed: 01/21/2023]
Abstract
Transcription factors (TFs) are frequently mutated in cancer. Paediatric cancers exhibit few mutations genome-wide but frequently harbour sentinel mutations that affect TFs, which provides a context to precisely study the transcriptional circuits that support mutant TF-driven oncogenesis. A broadly relevant mechanism that has garnered intense focus involves the ability of mutant TFs to hijack wild-type lineage-specific TFs in self-reinforcing transcriptional circuits. However, it is not known whether this specific type of circuitry is equally crucial in all mutant TF-driven cancers. Here we describe an alternative yet central transcriptional mechanism that promotes Ewing sarcoma, wherein constraint, rather than reinforcement, of the activity of the fusion TF EWS-FLI supports cancer growth. We discover that ETV6 is a crucial TF dependency that is specific to this disease because it, counter-intuitively, represses the transcriptional output of EWS-FLI. This work discovers a previously undescribed transcriptional mechanism that promotes cancer.
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Affiliation(s)
- Diana Y Lu
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jana M Ellegast
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth N Ross
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashleigh Meyer
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Conway
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Angela H Su
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Andrea K Byrum
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Bo Kyung A Seong
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Biniam Adane
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Miguel N Rivera
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Division of Pediatric Hematology, Oncology and BMT, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nat Cell Biol 2023; 25:298-308. [PMID: 36658219 PMCID: PMC10101761 DOI: 10.1038/s41556-022-01060-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/24/2022] [Indexed: 01/21/2023]
Abstract
The EWS-FLI1 fusion oncoprotein deregulates transcription to initiate the paediatric cancer Ewing sarcoma. Here we used a domain-focused CRISPR screen to implicate the transcriptional repressor ETV6 as a unique dependency in this tumour. Using biochemical assays and epigenomics, we show that ETV6 competes with EWS-FLI1 for binding to select DNA elements enriched for short GGAA repeat sequences. Upon inactivating ETV6, EWS-FLI1 overtakes and hyper-activates these cis-elements to promote mesenchymal differentiation, with SOX11 being a key downstream target. We show that squelching of ETV6 with a dominant-interfering peptide phenocopies these effects and suppresses Ewing sarcoma growth in vivo. These findings reveal targeting of ETV6 as a strategy for neutralizing the EWS-FLI1 oncoprotein by reprogramming of genomic occupancy.
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61
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Apfelbaum AA, Lawlor ER. Oncogenic role for an EWS-FLI1 suppressor. Nat Cell Biol 2023; 25:214-216. [PMID: 36658218 DOI: 10.1038/s41556-022-01067-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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62
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Verbiest M, Maksimov M, Jin Y, Anisimova M, Gymrek M, Bilgin Sonay T. Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species. J Evol Biol 2023; 36:321-336. [PMID: 36289560 PMCID: PMC9990875 DOI: 10.1111/jeb.14106] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/29/2022] [Accepted: 08/01/2022] [Indexed: 02/03/2023]
Abstract
Short tandem repeats (STRs) are units of 1-6 bp that repeat in a tandem fashion in DNA. Along with single nucleotide polymorphisms and large structural variations, they are among the major genomic variants underlying genetic, and likely phenotypic, divergence. STRs experience mutation rates that are orders of magnitude higher than other well-studied genotypic variants. Frequent copy number changes result in a wide range of alleles, and provide unique opportunities for modulating complex phenotypes through variation in repeat length. While classical studies have identified key roles of individual STR loci, the advent of improved sequencing technology, high-quality genome assemblies for diverse species, and bioinformatics methods for genome-wide STR analysis now enable more systematic study of STR variation across wide evolutionary ranges. In this review, we explore mutation and selection processes that affect STR copy number evolution, and how these processes give rise to varying STR patterns both within and across species. Finally, we review recent examples of functional and adaptive changes linked to STRs.
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Affiliation(s)
- Max Verbiest
- Institute of Computational Life Sciences, School of Life Sciences and Facility ManagementZürich University of Applied SciencesWädenswilSwitzerland
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Mikhail Maksimov
- Department of Computer Science & EngineeringUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Ye Jin
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of BioengineeringUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Maria Anisimova
- Institute of Computational Life Sciences, School of Life Sciences and Facility ManagementZürich University of Applied SciencesWädenswilSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Melissa Gymrek
- Department of Computer Science & EngineeringUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Tugce Bilgin Sonay
- Institute of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNew YorkUSA
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63
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Vital T, Wali A, Butler KV, Xiong Y, Foster JP, Marcel SS, McFadden AW, Nguyen VU, Bailey BM, Lamb KN, James LI, Frye SV, Mosely AL, Jin J, Pattenden SG, Davis IJ. MS0621, a novel small-molecule modulator of Ewing sarcoma chromatin accessibility, interacts with an RNA-associated macromolecular complex and influences RNA splicing. Front Oncol 2023; 13:1099550. [PMID: 36793594 PMCID: PMC9924231 DOI: 10.3389/fonc.2023.1099550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Ewing sarcoma is a cancer of children and young adults characterized by the critical translocation-associated fusion oncoprotein EWSR1::FLI1. EWSR1::FLI1 targets characteristic genetic loci where it mediates aberrant chromatin and the establishment of de novo enhancers. Ewing sarcoma thus provides a model to interrogate mechanisms underlying chromatin dysregulation in tumorigenesis. Previously, we developed a high-throughput chromatin-based screening platform based on the de novo enhancers and demonstrated its utility in identifying small molecules capable of altering chromatin accessibility. Here, we report the identification of MS0621, a molecule with previously uncharacterized mechanism of action, as a small molecule modulator of chromatin state at sites of aberrant chromatin accessibility at EWSR1::FLI1-bound loci. MS0621 suppresses cellular proliferation of Ewing sarcoma cell lines by cell cycle arrest. Proteomic studies demonstrate that MS0621 associates with EWSR1::FLI1, RNA binding and splicing proteins, as well as chromatin regulatory proteins. Surprisingly, interactions with chromatin and many RNA-binding proteins, including EWSR1::FLI1 and its known interactors, were RNA-independent. Our findings suggest that MS0621 affects EWSR1::FLI1-mediated chromatin activity by interacting with and altering the activity of RNA splicing machinery and chromatin modulating factors. Genetic modulation of these proteins similarly inhibits proliferation and alters chromatin in Ewing sarcoma cells. The use of an oncogene-associated chromatin signature as a target allows for a direct approach to screen for unrecognized modulators of epigenetic machinery and provides a framework for using chromatin-based assays for future therapeutic discovery efforts.
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Affiliation(s)
- Tamara Vital
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Aminah Wali
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kyle V. Butler
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Joseph P. Foster
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shelsa S. Marcel
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Andrew W. McFadden
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Valerie U. Nguyen
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benton M. Bailey
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lindsey I. James
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stephen V. Frye
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amber L. Mosely
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Samantha G. Pattenden
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ian J. Davis
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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64
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Mikhailova EV, Romanova IV, Bagrov AY, Agalakova NI. Fli1 and Tissue Fibrosis in Various Diseases. Int J Mol Sci 2023; 24:ijms24031881. [PMID: 36768203 PMCID: PMC9915382 DOI: 10.3390/ijms24031881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/02/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
Being initially described as a factor of virally-induced leukemias, Fli1 (Friend leukemia integration 1) has attracted considerable interest lately due to its role in both healthy physiology and a variety of pathological conditions. Over the past few years, Fli1 has been found to be one of the crucial regulators of normal hematopoiesis, vasculogenesis, and immune response. However, abnormal expression of Fli1 due to genetic predisposition, epigenetic reprogramming (modifications), or environmental factors is associated with a few diseases of different etiology. Fli1 hyperexpression leads to malignant transformation of cells and progression of cancers such as Ewing's sarcoma. Deficiency in Fli1 is implicated in the development of systemic sclerosis and hypertensive disorders, which are often accompanied by pronounced fibrosis in different organs. This review summarizes the initial findings and the most recent advances in defining the role of Fli1 in diseases of different origin with emphasis on its pro-fibrotic potential.
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Affiliation(s)
- Elena V. Mikhailova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Thorez Avenue, 194223 Saint-Petersburg, Russia
| | - Irina V. Romanova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Thorez Avenue, 194223 Saint-Petersburg, Russia
| | | | - Natalia I. Agalakova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Thorez Avenue, 194223 Saint-Petersburg, Russia
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65
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Yu L, Davis IJ, Liu P. Regulation of EWSR1-FLI1 Function by Post-Transcriptional and Post-Translational Modifications. Cancers (Basel) 2023; 15:382. [PMID: 36672331 PMCID: PMC9857208 DOI: 10.3390/cancers15020382] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Ewing sarcoma is the second most common bone tumor in childhood and adolescence. Currently, first-line therapy includes multidrug chemotherapy with surgery and/or radiation. Although most patients initially respond to chemotherapy, recurrent tumors become treatment refractory. Pathologically, Ewing sarcoma consists of small round basophilic cells with prominent nuclei marked by expression of surface protein CD99. Genetically, Ewing sarcoma is driven by a fusion oncoprotein that results from one of a small number of chromosomal translocations composed of a FET gene and a gene encoding an ETS family transcription factor, with ~85% of tumors expressing the EWSR1::FLI1 fusion. EWSR1::FLI1 regulates transcription, splicing, genome instability and other cellular functions. Although a tumor-specific target, EWSR1::FLI1-targeted therapy has yet to be developed, largely due to insufficient understanding of EWSR1::FLI1 upstream and downstream signaling, and the challenges in targeting transcription factors with small molecules. In this review, we summarize the contemporary molecular understanding of Ewing sarcoma, and the post-transcriptional and post-translational regulatory mechanisms that control EWSR1::FLI1 function.
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Affiliation(s)
- Le Yu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian J. Davis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pediatrics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pengda Liu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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66
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Kodgule R, Goldman JW, Monovich AC, Saari T, Aguilar AR, Hall CN, Rajesh N, Gupta J, Chu SCA, Ye L, Gurumurthy A, Iyer A, Brown NA, Chiang MY, Cieslik MP, Ryan RJ. ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia. Blood Cancer Discov 2023; 4:34-53. [PMID: 36350827 PMCID: PMC9820540 DOI: 10.1158/2643-3230.bcd-21-0224] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/30/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
Distal enhancers play critical roles in sustaining oncogenic gene-expression programs. We identify aberrant enhancer-like activation of GGAA tandem repeats as a characteristic feature of B-cell acute lymphoblastic leukemia (B-ALL) with genetic defects of the ETV6 transcriptional repressor, including ETV6-RUNX1+ and ETV6-null B-ALL. We show that GGAA repeat enhancers are direct activators of previously identified ETV6-RUNX1+/- like B-ALL "signature" genes, including the likely leukemogenic driver EPOR. When restored to ETV6-deficient B-ALL cells, ETV6 directly binds to GGAA repeat enhancers, represses their acetylation, downregulates adjacent genes, and inhibits B-ALL growth. In ETV6-deficient B-ALL cells, we find that the ETS transcription factor ERG directly binds to GGAA microsatellite enhancers and is required for sustained activation of repeat enhancer-activated genes. Together, our findings reveal an epigenetic gatekeeper function of the ETV6 tumor suppressor gene and establish microsatellite enhancers as a key mechanism underlying the unique gene-expression program of ETV6-RUNX1+/- like B-ALL. SIGNIFICANCE We find a unifying mechanism underlying a leukemia subtype-defining gene-expression signature that relies on repetitive elements with poor conservation between humans and rodents. The ability of ETV6 to antagonize promiscuous, nonphysiologic ERG activity may shed light on other roles of these key regulators in hematolymphoid development and human disease. See related commentary by Mercher, p. 2. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Rohan Kodgule
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joshua W. Goldman
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | | | - Travis Saari
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Athalee R. Aguilar
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Cody N. Hall
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Niharika Rajesh
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Juhi Gupta
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Shih-Chun A. Chu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Li Ye
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Aishwarya Gurumurthy
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Ashwin Iyer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Noah A. Brown
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mark Y. Chiang
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Marcin P. Cieslik
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Russell J.H. Ryan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
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67
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Mo J, Tan K, Dong Y, Lu W, Liu F, Mei Y, Huang H, Zhao K, Lv Z, Ye Y, Tang Y. Therapeutic targeting the oncogenic driver EWSR1::FLI1 in Ewing sarcoma through inhibition of the FACT complex. Oncogene 2023; 42:11-25. [PMID: 36357572 DOI: 10.1038/s41388-022-02533-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/12/2022]
Abstract
EWS/ETS fusion transcription factors, most commonly EWSR1::FLI1, drives initiation and progression of Ewing sarcoma (EwS). Even though direct targeting EWSR1::FLI1 is a formidable challenge, epigenetic/transcriptional modulators have been proved to be promising therapeutic targets for indirectly disrupting its expression and/or function. Here, we identified structure-specific recognition protein 1 (SSRP1), a subunit of the Facilitates Chromatin Transcription (FACT) complex, to be an essential tumor-dependent gene directly induced by EWSR1::FLI1 in EwS. The FACT-targeted drug CBL0137 exhibits potent therapeutic efficacy against multiple EwS preclinical models both in vitro and in vivo. Mechanistically, SSRP1 and EWSR1::FLI1 form oncogenic positive feedback loop via mutual transcriptional regulation and activation, and cooperatively promote cell cycle/DNA replication process and IGF1R-PI3K-AKT-mTOR pathway to drive EwS oncogenesis. The FACT inhibitor drug CBL0137 effectively targets the EWSR1::FLI1-FACT circuit, resulting in transcriptional disruption of EWSR1::FLI1, SSRP1 and their downstream effector oncogenic signatures. Our study illustrates a crucial role of the FACT complex in facilitating the expression and function of EWSR1::FLI1 and demonstrates FACT inhibition as a novel and effective epigenetic/transcriptional-targeted therapeutic strategy against EwS, providing preclinical support for adding EwS to CBL0137's future clinical trials.
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Affiliation(s)
- Jialin Mo
- Research Center of Translational medicine, Shanghai children's hospital, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
- Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Kezhe Tan
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062, Shanghai, China
| | - Yu Dong
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenjie Lu
- Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Fang Liu
- Research Center of Translational medicine, Shanghai children's hospital, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Yanqing Mei
- Research Center of Translational medicine, Shanghai children's hospital, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Hongting Huang
- Department of Hepatic Surgery and Liver Transplantation Center, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200127, Shanghai, China
| | - Kewen Zhao
- Research Center of Translational medicine, Shanghai children's hospital, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Zhibao Lv
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062, Shanghai, China.
| | - Youqiong Ye
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yujie Tang
- Research Center of Translational medicine, Shanghai children's hospital, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
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68
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Wang S, Huo X, Yang Y, Mo Y, Kollipara RK, Kittler R. Ablation of EWS-FLI1 by USP9X inhibition suppresses cancer cell growth in Ewing sarcoma. Cancer Lett 2023; 552:215984. [PMID: 36330954 DOI: 10.1016/j.canlet.2022.215984] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/11/2022] [Accepted: 10/24/2022] [Indexed: 11/26/2022]
Abstract
The neomorphic transcription factor EWS-FLI1 is a key driver of Ewing sarcoma. Ablation of EWS-FLI1 may present a promising therapeutic strategy for this malignancy. Here we found that the deubiquitinase, ubiquitin specific peptidase 9 X-linked (USP9X) stabilizes EWS-FLI1 protein expression in Ewing sarcoma. We show that USP9X binds the ETS domain of EWS-FLI1 in Ewing sarcoma cells and deubiquitinates EWS-FLI1 and that USP9X and EWS-FLI1 protein expression is correlated in clinical Ewing sarcoma specimens. We found that treatment of Ewing sarcoma cells with the USP9X inhibitor WP1130 mediates rapid EWS-FLI1 degradation in vitro and in vivo which coincides with reduced growth of Ewing sarcoma cells and tumors. Our results suggest that USP9X might be a potential therapeutic target to mediate EWS-FLI1 depletion in Ewing sarcoma.
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Affiliation(s)
- Shan Wang
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, China; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofang Huo
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yiping Yang
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Yingxi Mo
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ralf Kittler
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA; Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA; Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA.
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69
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Suvarna K, Jayabal P, Ma X, Shiio Y. Slit2 signaling stimulates Ewing sarcoma growth. Genes Cancer 2022; 13:88-99. [PMID: 36533189 PMCID: PMC9753566 DOI: 10.18632/genesandcancer.227] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
Ewing sarcoma is a cancer of bone and soft tissue in children driven by EWS::ETS fusion, most commonly EWS::FLI1. Because current cytotoxic chemotherapies are not improving the survival of those with metastatic or recurrent Ewing sarcoma cases, there is a need for novel and more effective targeted therapies. While EWS::FLI1 is the major driver of Ewing sarcoma, EWS::FLI1 has been difficult to target. A promising alternative approach is to identify and target the molecular vulnerabilities created by EWS::FLI1. Here we report that EWS::FLI1 induces the expression of Slit2, the ligand of Roundabout (Robo) receptors implicated in axon guidance and multiple other developmental processes. EWS::FLI1 binds to the Slit2 gene promoter and stimulates the expression of Slit2. Slit2 inactivates cdc42 and stabilizes the BAF chromatin remodeling complexes, enhancing EWS::FLI1 transcriptional output. Silencing of Slit2 strongly inhibited anchorage-dependent and anchorage-independent growth of Ewing sarcoma cells. Silencing of Slit2 receptors, Robo1 and Robo2, inhibited Ewing sarcoma growth as well. These results uncover a new role for Slit2 signaling in stimulating Ewing sarcoma growth and suggest that this pathway can be targeted therapeutically.
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Affiliation(s)
- Kruthi Suvarna
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Panneerselvam Jayabal
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Xiuye Ma
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Yuzuru Shiio
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA,2Cancer Therapy and Research Center, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA,3Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA,Correspondence to:Yuzuru Shiio, email:
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70
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Orth MF, Surdez D, Faehling T, Ehlers AC, Marchetto A, Grossetête S, Volckmann R, Zwijnenburg DA, Gerke JS, Zaidi S, Alonso J, Sastre A, Baulande S, Sill M, Cidre-Aranaz F, Ohmura S, Kirchner T, Hauck SM, Reischl E, Gymrek M, Pfister SM, Strauch K, Koster J, Delattre O, Grünewald TGP. Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation. Cell Rep 2022; 41:111761. [PMID: 36476851 DOI: 10.1016/j.celrep.2022.111761] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/25/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Ewing sarcoma (EwS) is characterized by EWSR1-ETS fusion transcription factors converting polymorphic GGAA microsatellites (mSats) into potent neo-enhancers. Although the paucity of additional mutations makes EwS a genuine model to study principles of cooperation between dominant fusion oncogenes and neo-enhancers, this is impeded by the limited number of well-characterized models. Here we present the Ewing Sarcoma Cell Line Atlas (ESCLA), comprising whole-genome, DNA methylation, transcriptome, proteome, and chromatin immunoprecipitation sequencing (ChIP-seq) data of 18 cell lines with inducible EWSR1-ETS knockdown. The ESCLA shows hundreds of EWSR1-ETS-targets, the nature of EWSR1-ETS-preferred GGAA mSats, and putative indirect modes of EWSR1-ETS-mediated gene regulation, converging in the duality of a specific but plastic EwS signature. We identify heterogeneously regulated EWSR1-ETS-targets as potential prognostic EwS biomarkers. Our freely available ESCLA (http://r2platform.com/escla/) is a rich resource for EwS research and highlights the power of comprehensive datasets to unravel principles of heterogeneous gene regulation by chimeric transcription factors.
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Affiliation(s)
- Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Didier Surdez
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zürich, 8008 Zürich, Switzerland
| | - Tobias Faehling
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Anna C Ehlers
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Sandrine Grossetête
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Richard Volckmann
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Danny A Zwijnenburg
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Julia S Gerke
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Sakina Zaidi
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CB06/07/1009, CIBERER-ISCIII), 28029 Madrid, Spain
| | - Ana Sastre
- Unidad Hemato-oncología Pediátrica, Hospital Infantil Universitario La Paz, 28029 Madrid, Spain
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, 75005 Paris, France
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Florencia Cidre-Aranaz
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Shunya Ohmura
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, 80337 Munich, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Eva Reischl
- Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Melissa Gymrek
- Division of Genetics, Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Department of Pediatric Hematology & Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Konstantin Strauch
- Institute of Medical Biometry, Epidemiology, and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, LMU Munich, 81377 Munich, Germany
| | - Jan Koster
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Olivier Delattre
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany; Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
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71
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Apfelbaum AA, Wrenn ED, Lawlor ER. The importance of fusion protein activity in Ewing sarcoma and the cell intrinsic and extrinsic factors that regulate it: A review. Front Oncol 2022; 12:1044707. [PMID: 36505823 PMCID: PMC9727305 DOI: 10.3389/fonc.2022.1044707] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidence shows that despite clonal origins tumors eventually become complex communities comprised of phenotypically distinct cell subpopulations. This heterogeneity arises from both tumor cell intrinsic programs and signals from spatially and temporally dynamic microenvironments. While pediatric cancers usually lack the mutational burden of adult cancers, they still exhibit high levels of cellular heterogeneity that are largely mediated by epigenetic mechanisms. Ewing sarcomas are aggressive bone and soft tissue malignancies with peak incidence in adolescence and the prognosis for patients with relapsed and metastatic disease is dismal. Ewing sarcomas are driven by a single pathognomonic fusion between a FET protein and an ETS family transcription factor, the most common of which is EWS::FLI1. Despite sharing a single driver mutation, Ewing sarcoma cells demonstrate a high degree of transcriptional heterogeneity both between and within tumors. Recent studies have identified differential fusion protein activity as a key source of this heterogeneity which leads to profoundly different cellular phenotypes. Paradoxically, increased invasive and metastatic potential is associated with lower EWS::FLI1 activity. Here, we review what is currently understood about EWS::FLI1 activity, the cell autonomous and tumor microenvironmental factors that regulate it, and the downstream consequences of these activity states on tumor progression. We specifically highlight how transcription factor regulation, signaling pathway modulation, and the extracellular matrix intersect to create a complex network of tumor cell phenotypes. We propose that elucidation of the mechanisms by which these essential elements interact will enable the development of novel therapeutic approaches that are designed to target this complexity and ultimately improve patient outcomes.
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Affiliation(s)
| | | | - Elizabeth R. Lawlor
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute and Department of Pediatrics, University of Washington, Seattle, WA, United States
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Albarrán V, Villamayor ML, Chamorro J, Rosero DI, Pozas J, San Román M, Calvo JC, Pérez de Aguado P, Moreno J, Guerrero P, González C, García de Quevedo C, Álvarez-Ballesteros P, Vaz MÁ. Receptor Tyrosine Kinase Inhibitors for the Treatment of Recurrent and Unresectable Bone Sarcomas. Int J Mol Sci 2022; 23:13784. [PMID: 36430263 PMCID: PMC9697271 DOI: 10.3390/ijms232213784] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Bone sarcomas are a heterogeneous group of rare tumors with a predominance in the young population. Few options of systemic treatment are available once they become unresectable and resistant to conventional chemotherapy. A better knowledge of the key role that tyrosine kinase receptors (VEGFR, RET, MET, AXL, PDGFR, KIT, FGFR, IGF-1R) may play in the pathogenesis of these tumors has led to the development of multi-target inhibitors (TKIs) that are progressively being incorporated into our therapeutic arsenal. Osteosarcoma (OS) is the most frequent primary bone tumor and several TKIs have demonstrated clinical benefit in phase II clinical trials (cabozantinib, regorafenib, apatinib, sorafenib, and lenvatinib). Although the development of TKIs for other primary bone tumors is less advanced, preclinical data and early trials have begun to show their potential benefit in advanced Ewing sarcoma (ES) and rarer bone tumors (chondrosarcoma, chordoma, giant cell tumor of bone, and undifferentiated pleomorphic sarcoma). Previous reviews have mainly provided information on TKIs for OS and ES. We aim to summarize the existing knowledge regarding the use of TKIs in all bone sarcomas including the most recent studies as well as the potential synergistic effects of their combination with other systemic therapies.
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Affiliation(s)
- Víctor Albarrán
- Department of Medical Oncology, Ramon y Cajal University Hospital, 28034 Madrid, Spain
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Sánchez-Molina S, Figuerola-Bou E, Sánchez-Margalet V, de la Cruz-Merino L, Mora J, de Álava Casado E, García-Domínguez DJ, Hontecillas-Prieto L. Ewing Sarcoma Meets Epigenetics, Immunology and Nanomedicine: Moving Forward into Novel Therapeutic Strategies. Cancers (Basel) 2022; 14:5473. [PMID: 36358891 PMCID: PMC9658520 DOI: 10.3390/cancers14215473] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Ewing Sarcoma (EWS) is an aggressive bone and soft tissue tumor that mainly affects children, adolescents, and young adults. The standard therapy, including chemotherapy, surgery, and radiotherapy, has substantially improved the survival of EWS patients with localized disease. Unfortunately, this multimodal treatment remains elusive in clinics for those patients with recurrent or metastatic disease who have an unfavorable prognosis. Consistently, there is an urgent need to find new strategies for patients that fail to respond to standard therapies. In this regard, in the last decade, treatments targeting epigenetic dependencies in tumor cells and the immune system have emerged into the clinical scenario. Additionally, recent advances in nanomedicine provide novel delivery drug systems, which may address challenges such as side effects and toxicity. Therefore, therapeutic strategies stemming from epigenetics, immunology, and nanomedicine yield promising alternatives for treating these patients. In this review, we highlight the most relevant EWS preclinical and clinical studies in epigenetics, immunotherapy, and nanotherapy conducted in the last five years.
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Affiliation(s)
- Sara Sánchez-Molina
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
- Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Elisabet Figuerola-Bou
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
- Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Víctor Sánchez-Margalet
- Clinical Laboratory, Department of Medical Biochemistry and Molecular Biology, School of Medicine, Virgen Macarena University Hospital, University of Seville, 41009 Seville, Spain
| | - Luis de la Cruz-Merino
- Oncology Service, Department of Medicines, School of Medicine, Virgen Macarena University Hospital, University of Seville, 41009 Seville, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
- Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Enrique de Álava Casado
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío/CSIC/University of Seville/CIBERONC, 41013 Seville, Spain
- Pathology Unit, Hospital Universitario Virgen del Rocío/CSIC/University of Seville/CIBERONC, 41013 Seville, Spain
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, 41009 Seville, Spain
| | - Daniel José García-Domínguez
- Clinical Laboratory, Department of Medical Biochemistry and Molecular Biology, School of Medicine, Virgen Macarena University Hospital, University of Seville, 41009 Seville, Spain
- Oncology Service, Department of Medicines, School of Medicine, Virgen Macarena University Hospital, University of Seville, 41009 Seville, Spain
| | - Lourdes Hontecillas-Prieto
- Clinical Laboratory, Department of Medical Biochemistry and Molecular Biology, School of Medicine, Virgen Macarena University Hospital, University of Seville, 41009 Seville, Spain
- Oncology Service, Department of Medicines, School of Medicine, Virgen Macarena University Hospital, University of Seville, 41009 Seville, Spain
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Apfelbaum AA, Wu F, Hawkins AG, Magnuson B, Jiménez JA, Taylor SD, Wrenn ED, Waltner O, Pfaltzgraff ER, Song JY, Hall C, Wellik DM, Ljungman M, Furlan SN, Ryan RJ, Sarthy JF, Lawlor ER. EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma. Clin Cancer Res 2022; 28:4466-4478. [PMID: 35653119 PMCID: PMC9588607 DOI: 10.1158/1078-0432.ccr-22-0384] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/05/2022] [Accepted: 05/25/2022] [Indexed: 01/28/2023]
Abstract
PURPOSE Propagation of Ewing sarcoma requires precise regulation of EWS::FLI1 transcriptional activity. Determining the mechanisms of fusion regulation will advance our understanding of tumor progression. Here we investigated whether HOXD13, a developmental transcription factor that promotes Ewing sarcoma metastatic phenotypes, influences EWS::FLI1 transcriptional activity. EXPERIMENTAL DESIGN Existing tumor and cell line datasets were used to define EWS::FLI1 binding sites and transcriptional targets. Chromatin immunoprecipitation and CRISPR interference were employed to identify enhancers. CUT&RUN and RNA sequencing defined binding sites and transcriptional targets of HOXD13. Transcriptional states were investigated using bulk and single-cell transcriptomic data from cell lines, patient-derived xenografts, and patient tumors. Mesenchymal phenotypes were assessed by gene set enrichment, flow cytometry, and migration assays. RESULTS We found that EWS::FLI1 creates a de novo GGAA microsatellite enhancer in a developmentally conserved regulatory region of the HOXD locus. Knockdown of HOXD13 led to widespread changes in expression of developmental gene programs and EWS::FLI1 targets. HOXD13 binding was enriched at established EWS::FLI1 binding sites where it influenced expression of EWS::FLI1-activated genes. More strikingly, HOXD13 bound and activated EWS::FLI1-repressed genes, leading to adoption of mesenchymal and migratory cell states that are normally suppressed by the fusion. Single-cell analysis confirmed that direct transcriptional antagonism between HOXD13-mediated gene activation and EWS::FLI1-dependent gene repression defines the state of Ewing sarcoma cells along a mesenchymal axis. CONCLUSIONS Ewing sarcoma tumors are comprised of tumor cells that exist along a mesenchymal transcriptional continuum. The identity of cells along this continuum is, in large part, determined by the competing activities of EWS::FLI1 and HOXD13. See related commentary by Weiss and Bailey, p. 4360.
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Affiliation(s)
- April A. Apfelbaum
- Cancer Biology PhD Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Seattle Children’s Research Institute, Seattle, WA, 98101, USA
| | - Feinan Wu
- Genomics and Bioinformatics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Allegra G. Hawkins
- Childhood Cancer Data Lab Alex’s Lemonade Stand Foundation, Philadelphia, PA, USA
| | - Brian Magnuson
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jennifer A. Jiménez
- Cancer Biology PhD Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sean D. Taylor
- Seattle Children’s Research Institute, Seattle, WA, 98101, USA
| | - Emma D. Wrenn
- Seattle Children’s Research Institute, Seattle, WA, 98101, USA
| | - Olivia Waltner
- Fred Hutch Cancer Research Center, Seattle, WA, 98109, USA
| | | | - Jane Y. Song
- Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cody Hall
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, 53705
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Scott N. Furlan
- Fred Hutch Cancer Research Center, Seattle, WA, 98109, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98105, USA
| | - Russell J.H. Ryan
- Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jay F. Sarthy
- Fred Hutch Cancer Research Center, Seattle, WA, 98109, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98105, USA
| | - Elizabeth R. Lawlor
- Seattle Children’s Research Institute, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98105, USA
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75
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Neomorphic DNA-binding enables tumor-specific therapeutic gene expression in fusion-addicted childhood sarcoma. Mol Cancer 2022; 21:199. [PMID: 36229873 PMCID: PMC9558418 DOI: 10.1186/s12943-022-01641-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
Chimeric fusion transcription factors are oncogenic hallmarks of several devastating cancer entities including pediatric sarcomas, such as Ewing sarcoma (EwS) and alveolar rhabdomyosarcoma (ARMS). Despite their exquisite specificity, these driver oncogenes have been considered largely undruggable due to their lack of enzymatic activity. Here, we show in the EwS model that – capitalizing on neomorphic DNA-binding preferences – the addiction to the respective fusion transcription factor EWSR1-FLI1 can be leveraged to express therapeutic genes. We genetically engineered a de novo enhancer-based, synthetic and highly potent expression cassette that can elicit EWSR1-FLI1-dependent expression of a therapeutic payload as evidenced by episomal and CRISPR-edited genomic reporter assays. Combining in silico screens and immunohistochemistry, we identified GPR64 as a highly specific cell surface antigen for targeted transduction strategies in EwS. Functional experiments demonstrated that anti-GPR64-pseudotyped lentivirus harboring our expression cassette can specifically transduce EwS cells to promote the expression of viral thymidine kinase sensitizing EwS for treatment to otherwise relatively non-toxic (Val)ganciclovir and leading to strong anti-tumorigenic, but no adverse effects in vivo. Further, we prove that similar vector designs can be applied in PAX3-FOXO1-driven ARMS, and to express immunomodulatory cytokines, such as IL-15 and XCL1, in tumor entities typically considered to be immunologically ‘cold’. Collectively, these results generated in pediatric sarcomas indicate that exploiting, rather than suppressing, the neomorphic functions of chimeric transcription factors may open inroads to innovative and personalized therapies, and that our highly versatile approach may be translatable to other cancers addicted to oncogenic transcription factors with unique DNA-binding properties.
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76
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Regulation of Metastasis in Ewing Sarcoma. Cancers (Basel) 2022; 14:cancers14194902. [PMID: 36230825 PMCID: PMC9563756 DOI: 10.3390/cancers14194902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022] Open
Abstract
Ewing sarcoma (EwS) is a type of bone and soft tissue tumor in children and adolescents. Over 85% of cases are caused by the expression of fusion protein EWSR1-FLI1 generated by chromosome translocation. Acting as a potent chimeric oncoprotein, EWSR1-FLI1 binds to chromatin, changes the epigenetic states, and thus alters the expression of a large set of genes. Several studies have revealed that the expression level of EWSR1-FLI1 is variable and dynamic within and across different EwS cell lines and primary tumors, leading to tumoral heterogeneity. Cells with high EWSR1-FLI1 expression (EWSR1-FLI1-high) proliferate in an exponential manner, whereas cells with low EWSR1-FLI1 expression (EWSR1-FLI1-low) tend to have a strong propensity to migrate, invade, and metastasize. Metastasis is the leading cause of cancer-related deaths. The continuous evolution of EwS research has revealed some of the molecular underpinnings of this dissemination process. In this review, we discuss the molecular signatures that contribute to metastasis.
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Molnar C, Reina J, Herrero A, Heinen JP, Méndiz V, Bonnal S, Irimia M, Sánchez-Jiménez M, Sánchez-Molina S, Mora J, Gonzalez C. Human EWS-FLI protein recapitulates in Drosophila the neomorphic functions that induce Ewing sarcoma tumorigenesis. PNAS NEXUS 2022; 1:pgac222. [PMID: 36714878 PMCID: PMC9802468 DOI: 10.1093/pnasnexus/pgac222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Ewing sarcoma (EwS) is a human malignant tumor typically driven by the Ewing sarcoma-Friend leukemia integration (EWS-FLI) fusion protein. A paucity of genetically modified animal models, partially owed to the high toxicity of EWS-FLI, hinders research on EwS. Here, we report a spontaneous mutant variant, EWS-FLI1FS, that circumvents the toxicity issue in Drosophila. Through proteomic and genomic analyses, we show that human EWS-FLI1FS interacts with the Drosophila homologues of EWS-FLI human protein partners, including core subunits of chromatin remodeling complexes, the transcription machinery, and the spliceosome; brings about a massive dysregulation of transcription that affects a significant fraction of known targets of EWS-FLI in human cells; and modulates splicing. We also show that EWS-FLI1FS performs in Drosophila the two major neomorphic activities that it is known to have in human cells: activation of transcription from GGAA microsatellites and out competition of ETS transcription factors. We conclude that EWS-FLI1FS reproduces in Drosophila the known oncogenic activities of EWS-FLI that drive EwS tumorigenesis in humans. These results open up an unprecedented opportunity to investigate EWS-FLI's oncogenic pathways in vivo in a genetically tractable organism.
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Affiliation(s)
- Cristina Molnar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Jose Reina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Anastasia Herrero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac 10, 08028 Barcelona, Spain,Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat 08950 Barcelona, Spain
| | - Jan Peter Heinen
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Victoria Méndiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Pg Lluis Companys 23, 08010 Barcelona, Spain
| | - María Sánchez-Jiménez
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat 08950 Barcelona, Spain,Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Sara Sánchez-Molina
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat 08950 Barcelona, Spain,Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Jaume Mora
- To whom correspondence should be addressed:
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78
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Jiménez JA, Lawlor ER, Lyssiotis CA. Amino acid metabolism in primary bone sarcomas. Front Oncol 2022; 12:1001318. [PMID: 36276057 PMCID: PMC9581121 DOI: 10.3389/fonc.2022.1001318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/19/2022] [Indexed: 12/30/2022] Open
Abstract
Primary bone sarcomas, including osteosarcoma (OS) and Ewing sarcoma (ES), are aggressive tumors with peak incidence in childhood and adolescence. The intense standard treatment for these patients consists of combined surgery and/or radiation and maximal doses of chemotherapy; a regimen that has not seen improvement in decades. Like other tumor types, ES and OS are characterized by dysregulated cellular metabolism and a rewiring of metabolic pathways to support the biosynthetic demands of malignant growth. Not only are cancer cells characterized by Warburg metabolism, or aerobic glycolysis, but emerging work has revealed a dependence on amino acid metabolism. Aside from incorporation into proteins, amino acids serve critical functions in redox balance, energy homeostasis, and epigenetic maintenance. In this review, we summarize current studies describing the amino acid metabolic requirements of primary bone sarcomas, focusing on OS and ES, and compare these dependencies in the normal bone and malignant tumor contexts. We also examine insights that can be gleaned from other cancers to better understand differential metabolic susceptibilities between primary and metastatic tumor microenvironments. Lastly, we discuss potential metabolic vulnerabilities that may be exploited therapeutically and provide better-targeted treatments to improve the current standard of care.
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Affiliation(s)
- Jennifer A. Jiménez
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, United States,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Elizabeth R. Lawlor
- Department of Pediatrics, University of Washington, Seattle, WA, United States,Seattle Children’s Research Institute, Seattle, WA, United States,*Correspondence: Elizabeth R. Lawlor, ; Costas A. Lyssiotis,
| | - Costas A. Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, United States,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States,Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI, United States,*Correspondence: Elizabeth R. Lawlor, ; Costas A. Lyssiotis,
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79
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Kloeber JA, Lou Z. Critical DNA damaging pathways in tumorigenesis. Semin Cancer Biol 2022; 85:164-184. [PMID: 33905873 PMCID: PMC8542061 DOI: 10.1016/j.semcancer.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022]
Abstract
The acquisition of DNA damage is an early driving event in tumorigenesis. Premalignant lesions show activated DNA damage responses and inactivation of DNA damage checkpoints promotes malignant transformation. However, DNA damage is also a targetable vulnerability in cancer cells. This requires a detailed understanding of the cellular and molecular mechanisms governing DNA integrity. Here, we review current work on DNA damage in tumorigenesis. We discuss DNA double strand break repair, how repair pathways contribute to tumorigenesis, and how double strand breaks are linked to the tumor microenvironment. Next, we discuss the role of oncogenes in promoting DNA damage through replication stress. Finally, we discuss our current understanding on DNA damage in micronuclei and discuss therapies targeting these DNA damage pathways.
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Affiliation(s)
- Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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80
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Fuest S, Post C, Balbach ST, Jabar S, Neumann I, Schimmelpfennig S, Sargin S, Nass E, Budde T, Kailayangiri S, Altvater B, Ranft A, Hartmann W, Dirksen U, Rössig C, Schwab A, Pethő Z. Relevance of Abnormal KCNN1 Expression and Osmotic Hypersensitivity in Ewing Sarcoma. Cancers (Basel) 2022; 14:4819. [PMID: 36230742 PMCID: PMC9564116 DOI: 10.3390/cancers14194819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 12/02/2022] Open
Abstract
Ewing sarcoma (EwS) is a rare and highly malignant bone tumor occurring mainly in childhood and adolescence. Physiologically, the bone is a central hub for Ca2+ homeostasis, which is severely disturbed by osteolytic processes in EwS. Therefore, we aimed to investigate how ion transport proteins involved in Ca2+ homeostasis affect EwS pathophysiology. We characterized the expression of 22 candidate genes of Ca2+-permeable or Ca2+-regulated ion channels in three EwS cell lines and found the Ca2+-activated K+ channel KCa2.1 (KCNN1) to be exceptionally highly expressed. We revealed that KCNN1 expression is directly regulated by the disease-driving oncoprotein EWSR1-FL1. Due to its consistent overexpression in EwS, KCNN1 mRNA could be a prognostic marker in EwS. In a large cohort of EwS patients, however, KCNN1 mRNA quantity does not correlate with clinical parameters. Several functional studies including patch clamp electrophysiology revealed no evidence for KCa2.1 function in EwS cells. Thus, elevated KCNN1 expression is not translated to KCa2.1 channel activity in EwS cells. However, we found that the low K+ conductance of EwS cells renders them susceptible to hypoosmotic solutions. The absence of a relevant K+ conductance in EwS thereby provides an opportunity for hypoosmotic therapy that can be exploited during tumor surgery.
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Affiliation(s)
- Sebastian Fuest
- Institute of Physiology II, University Münster, 48149 Münster, Germany
| | - Christoph Post
- Institute of Physiology II, University Münster, 48149 Münster, Germany
| | - Sebastian T Balbach
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149 Münster, Germany
| | - Susanne Jabar
- Pediatrics III, University Hospital Essen, 45147 Essen, Germany
| | - Ilka Neumann
- Institute of Physiology II, University Münster, 48149 Münster, Germany
| | | | - Sarah Sargin
- Institute of Physiology II, University Münster, 48149 Münster, Germany
| | - Elke Nass
- Institute of Physiology I, University Münster, 48149 Münster, Germany
| | - Thomas Budde
- Institute of Physiology I, University Münster, 48149 Münster, Germany
| | - Sareetha Kailayangiri
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149 Münster, Germany
| | - Bianca Altvater
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149 Münster, Germany
| | - Andreas Ranft
- Pediatrics III, University Hospital Essen, 45147 Essen, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, University Münster, 48149 Münster, Germany
| | - Uta Dirksen
- Pediatrics III, University Hospital Essen, 45147 Essen, Germany
| | - Claudia Rössig
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149 Münster, Germany
| | - Albrecht Schwab
- Institute of Physiology II, University Münster, 48149 Münster, Germany
| | - Zoltán Pethő
- Institute of Physiology II, University Münster, 48149 Münster, Germany
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81
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Showpnil IA, Selich-Anderson J, Taslim C, Boone MA, Crow JC, Theisen ER, Lessnick SL. EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma. Nucleic Acids Res 2022; 50:9814-9837. [PMID: 36124657 PMCID: PMC9508825 DOI: 10.1093/nar/gkac747] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 08/10/2022] [Accepted: 08/23/2022] [Indexed: 12/13/2022] Open
Abstract
Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or a highly related FET/ETS chimera. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma cells using a well-validated ‘knock-down/rescue’ model of EWS/FLI function in combination with next generation sequencing assays to evaluate how the chromatin landscape changes with loss, and recovery, of EWS/FLI expression. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. This EWS/FLI binding signature is associated with establishment of topologically-associated domain (TAD) boundaries, compartment activation, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. In addition, EWS/FLI co-localizes with the loop-extrusion factor cohesin to promote chromatin loops and TAD boundaries. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators of three-dimensional reprogramming of chromatin.
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Affiliation(s)
- Iftekhar A Showpnil
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.,Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Megann A Boone
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Jesse C Crow
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Emily R Theisen
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.,Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.,Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA.,Division of Pediatric Heme/Onc/BMT, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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82
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Huang R, Huang D, Wang S, Xian S, Liu Y, Jin M, Zhang X, Chen S, Yue X, Zhang W, Lu J, Liu H, Huang Z, Zhang H, Yin H. Repression of enhancer RNA PHLDA1 promotes tumorigenesis and progression of Ewing sarcoma via decreasing infiltrating T‐lymphocytes: A bioinformatic analysis. Front Genet 2022; 13:952162. [PMID: 36092920 PMCID: PMC9453160 DOI: 10.3389/fgene.2022.952162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The molecular mechanisms of EWS-FLI-mediating target genes and downstream pathways may provide a new way in the targeted therapy of Ewing sarcoma. Meanwhile, enhancers transcript non-coding RNAs, known as enhancer RNAs (eRNAs), which may serve as potential diagnosis markers and therapeutic targets in Ewing sarcoma. Materials and methods: Differentially expressed genes (DEGs) were identified between 85 Ewing sarcoma samples downloaded from the Treehouse database and 3 normal bone samples downloaded from the Sequence Read Archive database. Included in DEGs, differentially expressed eRNAs (DEeRNAs) and target genes corresponding to DEeRNAs (DETGs), as well as the differentially expressed TFs, were annotated. Then, cell type identification by estimating relative subsets of known RNA transcripts (CIBERSORT) was used to infer portions of infiltrating immune cells in Ewing sarcoma and normal bone samples. To evaluate the prognostic value of DEeRNAs and immune function, cross validation, independent prognosis analysis, and Kaplan–Meier survival analysis were implemented using sarcoma samples from the Cancer Genome Atlas database. Next, hallmarks of cancer by gene set variation analysis (GSVA) and immune gene sets by single-sample gene set enrichment analysis (ssGSEA) were identified to be significantly associated with Ewing sarcoma. After screening by co-expression analysis, most significant DEeRNAs, DETGs and DETFs, immune cells, immune gene sets, and hallmarks of cancer were merged to construct a co-expression regulatory network to eventually identify the key DEeRNAs in tumorigenesis of Ewing sarcoma. Moreover, Connectivity Map Analysis was utilized to identify small molecules targeting Ewing sarcoma. External validation based on multidimensional online databases and scRNA-seq analysis were used to verify our key findings. Results: A six-different-dimension regulatory network was constructed based on 17 DEeRNAs, 29 DETFs, 9 DETGs, 5 immune cells, 24 immune gene sets, and 8 hallmarks of cancer. Four key DEeRNAs (CCR1, CD3D, PHLDA1, and RASD1) showed significant co-expression relationships in the network. Connectivity Map Analysis screened two candidate compounds, MS-275 and pyrvinium, that might target Ewing sarcoma. PHLDA1 (key DEeRNA) was extensively expressed in cancer stem cells of Ewing sarcoma, which might play a critical role in the tumorigenesis of Ewing sarcoma. Conclusion: PHLDA1 is a key regulator in the tumorigenesis and progression of Ewing sarcoma. PHLDA1 is directly repressed by EWS/FLI1 protein and low expression of FOSL2, resulting in the deregulation of FOX proteins and CC chemokine receptors. The decrease of infiltrating T‐lymphocytes and TNFA signaling may promote tumorigenesis and progression of Ewing sarcoma.
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Affiliation(s)
- Runzhi Huang
- Department of Orthopedics, School of Medicine, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai, China
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Tongji University School of Medicine, Shanghai, China
| | - Dan Huang
- Tongji University School of Medicine, Shanghai, China
| | - Siqiao Wang
- Tongji University School of Medicine, Shanghai, China
| | - Shuyuan Xian
- Tongji University School of Medicine, Shanghai, China
| | - Yifan Liu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minghao Jin
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinkun Zhang
- Tongji University School of Medicine, Shanghai, China
| | - Shaofeng Chen
- Department of Orthopedics, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Xi Yue
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Zhang
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Jianyu Lu
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Huizhen Liu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Tongji University School of Medicine, Shanghai, China
- *Correspondence: Zongqiang Huang, ; Hao Zhang, ; Huabin Yin,
| | - Hao Zhang
- Department of Orthopedics, Naval Medical Center of PLA, Second Military Medical University, Shanghai, China
- *Correspondence: Zongqiang Huang, ; Hao Zhang, ; Huabin Yin,
| | - Huabin Yin
- Department of Orthopedics, School of Medicine, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai, China
- *Correspondence: Zongqiang Huang, ; Hao Zhang, ; Huabin Yin,
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83
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The efficacy of selinexor (KPT-330), an XPO1 inhibitor, on non-hematologic cancers: a comprehensive review. J Cancer Res Clin Oncol 2022; 149:2139-2155. [PMID: 35941226 DOI: 10.1007/s00432-022-04247-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/01/2022] [Indexed: 10/15/2022]
Abstract
PURPOSE Selinexor is a novel XPO1 inhibitor which inhibits the export of tumor suppressor proteins and oncoprotein mRNAs, leading to cell-cycle arrest and apoptosis in cancer cells. While selinexor is currently FDA approved to treat multiple myeloma, compelling preclinical and early clinical studies reveal selinexor's efficacy in treating hematologic and non-hematologic malignancies, including sarcoma, gastric, bladder, prostate, breast, ovarian, skin, lung, and brain cancers. Current reviews of selinexor primarily highlight its use in hematologic malignancies; however, this review seeks to summarize the recent evidence of selinexor treatment in solid tumors. METHODS Pertinent literature searches in PubMed and the Karyopharm Therapeutics website for selinexor and non-hematologic malignancies preclinical and clinical trials. RESULTS This review provides evidence that selinexor is a promising agent used alone or in combination with other anticancer medications in non-hematologic malignancies. CONCLUSION Further clinical investigation of selinexor treatment for solid malignancies is warranted.
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Sardar D, Chen HC, Reyes A, Varadharajan S, Jain A, Mohila C, Curry R, Lozzi B, Rajendran K, Cervantes A, Yu K, Jalali A, Rao G, Mack SC, Deneen B. Sox9 directs divergent epigenomic states in brain tumor subtypes. Proc Natl Acad Sci U S A 2022; 119:e2202015119. [PMID: 35858326 PMCID: PMC9303974 DOI: 10.1073/pnas.2202015119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/31/2022] [Indexed: 01/17/2023] Open
Abstract
Epigenetic dysregulation is a universal feature of cancer that results in altered patterns of gene expression that drive malignancy. Brain tumors exhibit subtype-specific epigenetic alterations; however, the molecular mechanisms responsible for these diverse epigenetic states remain unclear. Here, we show that the developmental transcription factor Sox9 differentially regulates epigenomic states in high-grade glioma (HGG) and ependymoma (EPN). Using our autochthonous mouse models, we found that Sox9 suppresses HGG growth and expands associated H3K27ac states, while promoting ZFTA-RELA (ZRFUS) EPN growth and diminishing H3K27ac states. These contrasting roles for Sox9 correspond with protein interactions with histone deacetylating complexes in HGG and an association with the ZRFUS oncofusion in EPN. Mechanistic studies revealed extensive Sox9 and ZRFUS promoter co-occupancy, indicating functional synergy in promoting EPN tumorigenesis. Together, our studies demonstrate how epigenomic states are differentially regulated in distinct subtypes of brain tumors, while revealing divergent roles for Sox9 in HGG and EPN tumorigenesis.
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Affiliation(s)
- Debosmita Sardar
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030
| | - Hsiao-Chi Chen
- Cancer Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030
| | - Amanda Reyes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030
- Department of Biomedical Engineering, University of Houston, Houston, TX 77004
| | - Srinidhi Varadharajan
- Department of Developmental Neurobiology, Neurobiology and Brain Tumor Program, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Antrix Jain
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX 77030
| | - Carrie Mohila
- Department of Pathology, Texas Children’s Hospital, Houston, TX 77030
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
| | - Rachel Curry
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030
- Cancer Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030
| | - Brittney Lozzi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030
- Genetics and Genomics Program, Baylor College of Medicine, Houston, TX 77030
| | - Kavitha Rajendran
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030
| | - Alexis Cervantes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030
| | - Kwanha Yu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030
| | - Ganesh Rao
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030
| | - Stephen C. Mack
- Department of Developmental Neurobiology, Neurobiology and Brain Tumor Program, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030
- Cancer Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030
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85
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Tokarsky EJ, Crow JC, Guenther LM, Sherman J, Taslim C, Alexe G, Pishas KI, Rask G, Justis BS, Kasumova A, Stegmaier K, Lessnick SL, Theisen ER. Mitochondrial Dysfunction Is a Driver of SP-2509 Drug Resistance in Ewing Sarcoma. Mol Cancer Res 2022; 20:1035-1046. [PMID: 35298000 PMCID: PMC9284474 DOI: 10.1158/1541-7786.mcr-22-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 01/07/2023]
Abstract
Expression of the fusion oncoprotein EWS/FLI causes Ewing sarcoma, an aggressive pediatric tumor characterized by widespread epigenetic deregulation. These epigenetic changes are targeted by novel lysine-specific demethylase-1 (LSD1) inhibitors, which are currently in early-phase clinical trials. Single-agent-targeted therapy often induces resistance, and successful clinical development requires knowledge of resistance mechanisms, enabling the design of effective combination strategies. Here, we used a genome-scale CRISPR-Cas9 loss-of-function screen to identify genes whose knockout (KO) conferred resistance to the LSD1 inhibitor SP-2509 in Ewing sarcoma cell lines. Multiple genes required for mitochondrial electron transport chain (ETC) complexes III and IV function were hits in our screen. We validated this finding using genetic and chemical approaches, including CRISPR KO, ETC inhibitors, and mitochondrial depletion. Further global transcriptional profiling revealed that altered complex III/IV function disrupted the oncogenic program mediated by EWS/FLI and LSD1 and blunted the transcriptomic response to SP-2509. IMPLICATIONS These findings demonstrate that mitochondrial dysfunction modulates SP-2509 efficacy and suggest that new therapeutic strategies combining LSD1 with agents that prevent mitochondrial dysfunction may benefit patients with this aggressive malignancy.
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Affiliation(s)
- E. John Tokarsky
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Jesse C. Crow
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Lillian M. Guenther
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - John Sherman
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Galen Rask
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Blake S. Justis
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Ana Kasumova
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stephen L. Lessnick
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Emily R. Theisen
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio.,Corresponding Author: Emily R. Theisen, Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205. Phone: 614-355-2927; E-mail:
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86
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Karlina I, Schroeder BA, Kirgizov K, Romantsova O, Istranov AL, Nedorubov A, Timashev P, Ulasov I. Latest developments in the pathobiology of Ewing sarcoma. J Bone Oncol 2022; 35:100440. [PMID: 35855933 PMCID: PMC9287185 DOI: 10.1016/j.jbo.2022.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Irina Karlina
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Brett A. Schroeder
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Kirill Kirgizov
- Research Institute of Pediatric Oncology and Hematology at N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia Moscow, 115478, Russia
| | - Olga Romantsova
- Research Institute of Pediatric Oncology and Hematology at N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia Moscow, 115478, Russia
| | - Andrey L. Istranov
- Department of Oncology, radiation therapy and plastic surgery, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Andrey Nedorubov
- Center for Preclinical Research, Institute of Translational Medicine and Biotechnology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Peter Timashev
- World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Ilya Ulasov
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Corresponding author at: Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia.
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87
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Saratov V, Ngo QA, Pedot G, Sidorov S, Wachtel M, Niggli FK, Schäfer BW. CRISPR activation screen identifies TGFβ-associated PEG10 as a crucial tumor suppressor in Ewing sarcoma. Sci Rep 2022; 12:10671. [PMID: 35739280 PMCID: PMC9225990 DOI: 10.1038/s41598-022-12659-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/19/2022] [Indexed: 11/10/2022] Open
Abstract
As the second most common pediatric bone and soft tissue tumor, Ewing sarcoma (ES) is an aggressive disease with a pathognomonic chromosomal translocation t(11;22) resulting in expression of EWS-FLI1, an "undruggable" fusion protein acting as transcriptional modulator. EWS-FLI1 rewires the protein expression in cancer cells by activating and repressing a multitude of genes. The role and contribution of most repressed genes remains unknown to date. To address this, we established a CRISPR activation system in clonal SKNMC cell lines and interrogated a custom focused library covering 871 genes repressed by EWS-FLI1. Among the hits several members of the TGFβ pathway were identified, where PEG10 emerged as prime candidate due to its strong antiproliferative effect. Mechanistic investigations revealed that PEG10 overexpression caused cellular dropout via induction of cell death. Furthermore, non-canonical TGFβ pathways such as RAF/MEK/ERK, MKK/JNK, MKK/P38, known to lead to apoptosis or autophagy, were highly activated upon PEG10 overexpression. Our study sheds new light onto the contribution of TGFβ signalling pathway repression to ES tumorigenesis and suggest that its re-activation might constitute a novel therapeutic strategy.
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Affiliation(s)
- Vadim Saratov
- 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
| | - Gloria Pedot
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Semjon Sidorov
- Experimental Infectious Diseases and Cancer Research, Children's Research Center, University Children's Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Felix K Niggli
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland.
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88
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Deng Q, Natesan R, Cidre-Aranaz F, Arif S, Liu Y, Rasool RU, Wang P, Mitchell-Velasquez E, Das CK, Vinca E, Cramer Z, Grohar PJ, Chou M, Kumar-Sinha C, Weber K, Eisinger-Mathason TK, Grillet N, Grünewald T, Asangani IA. Oncofusion-driven de novo enhancer assembly promotes malignancy in Ewing sarcoma via aberrant expression of the stereociliary protein LOXHD1. Cell Rep 2022; 39:110971. [PMID: 35705030 PMCID: PMC9716578 DOI: 10.1016/j.celrep.2022.110971] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/05/2022] [Accepted: 05/24/2022] [Indexed: 01/16/2023] Open
Abstract
Ewing sarcoma (EwS) is a highly aggressive tumor of bone and soft tissues that mostly affects children and adolescents. The pathognomonic oncofusion EWSR1::FLI1 transcription factor drives EwS by orchestrating an oncogenic transcription program through de novo enhancers. By integrative analysis of thousands of transcriptomes representing pan-cancer cell lines, primary cancers, metastasis, and normal tissues, we identify a 32-gene signature (ESS32 [Ewing Sarcoma Specific 32]) that stratifies EwS from pan-cancer. Among the ESS32, LOXHD1, encoding a stereociliary protein, is the most highly expressed gene through an alternative transcription start site. Deletion or silencing of EWSR1::FLI1 bound upstream de novo enhancer results in loss of the LOXHD1 short isoform, altering EWSR1::FLI1 and HIF1α pathway genes and resulting in decreased proliferation/invasion of EwS cells. These observations implicate LOXHD1 as a biomarker and a determinant of EwS metastasis and suggest new avenues for developing LOXHD1-targeted drugs or cellular therapies for this deadly disease.
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Affiliation(s)
- Qu Deng
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA 19104, USA,These authors contributed equally
| | - Ramakrishnan Natesan
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA 19104, USA,These authors contributed equally
| | - Florencia Cidre-Aranaz
- Max-Eder Research Group of Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany,Hopp Children’s Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany
| | - Shehbeel Arif
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA 19104, USA
| | - Ying Liu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, BRBII/III, Philadelphia, PA, USA
| | - Reyaz ur Rasool
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA 19104, USA
| | - Pei Wang
- Department of Otolaryngology-Head & Neck Surgery, School of Medicine, Stanford University, Stanford, CA, USA
| | - Erick Mitchell-Velasquez
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA 19104, USA
| | - Chandan Kanta Das
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA 19104, USA
| | - Endrit Vinca
- Hopp Children’s Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany,Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Hopp Children’s Cancer Center (KiTZ), Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Zvi Cramer
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA 19104, USA
| | | | - Margaret Chou
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, BRBII/III, Philadelphia, PA, USA
| | - Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kristy Weber
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - T.S. Karin Eisinger-Mathason
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, BRBII/III, Philadelphia, PA, USA,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicolas Grillet
- Department of Otolaryngology-Head & Neck Surgery, School of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas Grünewald
- Max-Eder Research Group of Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany,Hopp Children’s Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany,Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Hopp Children’s Cancer Center (KiTZ), Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Irfan A. Asangani
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA 19104, USA,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,Lead contact,Correspondence:
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89
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Super-Enhancers, Phase-Separated Condensates, and 3D Genome Organization in Cancer. Cancers (Basel) 2022; 14:cancers14122866. [PMID: 35740532 PMCID: PMC9221043 DOI: 10.3390/cancers14122866] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 01/27/2023] Open
Abstract
3D chromatin organization plays an important role in transcription regulation and gene expression. The 3D genome is highly maintained by several architectural proteins, such as CTCF, Yin Yang 1, and cohesin complex. This structural organization brings regulatory DNA elements in close proximity to their target promoters. In this review, we discuss the 3D chromatin organization of super-enhancers and their relationship to phase-separated condensates. Super-enhancers are large clusters of DNA elements. They can physically contact with their target promoters by chromatin looping during transcription. Multiple transcription factors can bind to enhancer and promoter sequences and recruit a complex array of transcriptional co-activators and RNA polymerase II to effect transcriptional activation. Phase-separated condensates of transcription factors and transcriptional co-activators have been implicated in assembling the transcription machinery at particular enhancers. Cancer cells can hijack super-enhancers to drive oncogenic transcription to promote cell survival and proliferation. These dysregulated transcriptional programs can cause cancer cells to become highly dependent on transcriptional regulators, such as Mediator and BRD4. Moreover, the expression of oncogenes that are driven by super-enhancers is sensitive to transcriptional perturbation and often occurs in phase-separated condensates, supporting therapeutic rationales of targeting SE components, 3D genome organization, or dysregulated condensates in cancer.
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90
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Martin JC, Sims JR, Gupta A, Bakin AV, Ohm JE. WEE1 inhibition augments CDC7 (DDK) inhibitor-induced cell death in Ewing sarcoma by forcing premature mitotic entry and mitotic catastrophe. CANCER RESEARCH COMMUNICATIONS 2022; 2:471-482. [PMID: 36338546 PMCID: PMC9635308 DOI: 10.1158/2767-9764.crc-22-0130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/08/2022] [Accepted: 05/25/2022] [Indexed: 06/16/2023]
Abstract
Ewing sarcoma is an aggressive childhood cancer for which treatment options remain limited and toxic. There is an urgent need for the identification of novel therapeutic strategies. Our group has recently shown that Ewing cells rely on the S-phase kinase CDC7 (DDK) to maintain replication rates and cell viability and that DDK inhibition causes an increase in the phosphorylation of CDK1 and a significant delay in mitotic entry. Here, we expand on our previous findings and show that DDK inhibitor-induced mitotic entry delay is dependent upon WEE1 kinase. Specifically, WEE1 phosphorylates CDK1 and prevents mitotic entry upon DDK inhibition due to the presence of under-replicated DNA, potentially limiting the cytotoxic effects of DDK inhibition. To overcome this, we combined the inhibition of DDK with the inhibition of WEE1 and found that this results in elevated levels of premature mitotic entry, mitotic catastrophe, and apoptosis. Importantly, we have found that DDK and WEE1 inhibitors display a synergistic relationship with regards to reducing cell viability of Ewing sarcoma cells. Interestingly, the cytotoxic nature of this combination can be suppressed by the inhibition of CDK1 or microtubule polymerization, indicating that mitotic progression is required to elicit the cytotoxic effects. This is the first study to display the potential of utilizing the combined inhibition of DDK and WEE1 for the treatment of cancer. We believe this will offer a potential therapeutic strategy for the treatment of Ewing sarcoma as well as other tumor types that display sensitivity to DDK inhibitors.
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Affiliation(s)
- Jeffrey C. Martin
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Jennie R. Sims
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Ajay Gupta
- Division of Pediatric Oncology, Roswell Park Comprehensive Cancer Center, Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York
| | - Andrei V. Bakin
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Joyce Ellen Ohm
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
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91
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Kang B, Kang B, Roh TY, Seong RH, Kim W. The Chromatin Accessibility Landscape of Nonalcoholic Fatty Liver Disease Progression. Mol Cells 2022; 45:343-352. [PMID: 35422452 PMCID: PMC9095509 DOI: 10.14348/molcells.2022.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/03/2022] Open
Abstract
The advent of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) has shown great potential as a leading method for analyzing the genome-wide profiling of chromatin accessibility. A comprehensive reference to the ATAC-seq dataset for disease progression is important for understanding the regulatory specificity caused by genetic or epigenetic changes. In this study, we present a genome-wide chromatin accessibility profile of 44 liver samples spanning the full histological spectrum of nonalcoholic fatty liver disease (NAFLD). We analyzed the ATAC-seq signal enrichment, fragment size distribution, and correlation coefficients according to the histological severity of NAFLD (healthy control vs steatosis vs fibrotic nonalcoholic steatohepatitis), demonstrating the high quality of the dataset. Consequently, 112,303 merged regions (genomic regions containing one or multiple overlapping peak regions) were identified. Additionally, we found differentially accessible regions (DARs) and performed transcription factor binding motif enrichment analysis and de novo motif analysis to determine new biomarker candidates. These data revealed the generegulatory interactions and noncoding factors that can affect NAFLD progression. In summary, our study provides a valuable resource for the human epigenome by applying an advanced approach to facilitate diagnosis and treatment by understanding the non-coding genome of NAFLD.
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Affiliation(s)
- Byeonggeun Kang
- Department of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul 08826, Korea
| | - Byunghee Kang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Rho Hyun Seong
- Department of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul 08826, Korea
| | - Won Kim
- Department of Internal Medicine, SMG-SNU Boramae Medical Center, Seoul National University College of Medicine, Seoul 07061, Korea
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92
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Zullow HJ, Sankar A, Ingram DR, Guerra DDS, D’Avino AR, Collings CK, Segura RNL, Yang WL, Liang Y, Qi J, Lazar A, Kadoch C. The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma. Mol Cell 2022; 82:1737-1750.e8. [PMID: 35390276 PMCID: PMC9465545 DOI: 10.1016/j.molcel.2022.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/30/2021] [Accepted: 03/11/2022] [Indexed: 12/13/2022]
Abstract
Mammalian SWI/SNF (mSWI/SNF or BAF) ATP-dependent chromatin remodeling complexes play critical roles in governing genomic architecture and gene expression and are frequently perturbed in human cancers. Transcription factors (TFs), including fusion oncoproteins, can bind to BAF complex surfaces to direct chromatin targeting and accessibility, often activating oncogenic gene loci. Here, we demonstrate that the FUS::DDIT3 fusion oncoprotein hallmark to myxoid liposarcoma (MLPS) inhibits BAF complex-mediated remodeling of adipogenic enhancer sites via sequestration of the adipogenic TF, CEBPB, from the genome. In mesenchymal stem cells, small-molecule inhibition of BAF complex ATPase activity attenuates adipogenesis via failure of BAF-mediated DNA accessibility and gene activation at CEBPB target sites. BAF chromatin occupancy and gene expression profiles of FUS::DDIT3-expressing cell lines and primary tumors exhibit similarity to SMARCB1-deficient tumor types. These data present a mechanism by which a fusion oncoprotein generates a BAF complex loss-of-function phenotype, independent of deleterious subunit mutations.
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Affiliation(s)
- Hayley J. Zullow
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Medical Scientist Training Program, Harvard Medical School, Cambridge, MA USA
| | - Akshay Sankar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Davis R. Ingram
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel D. Same Guerra
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew R. D’Avino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clayton K. Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - We-Lien Yang
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander Lazar
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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93
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Vibert J, Saulnier O, Collin C, Petit F, Borgman KJE, Vigneau J, Gautier M, Zaidi S, Pierron G, Watson S, Gruel N, Hénon C, Postel-Vinay S, Deloger M, Raynal V, Baulande S, Laud-Duval K, Hill V, Grossetête S, Dingli F, Loew D, Torrejon J, Ayrault O, Orth MF, Grünewald TGP, Surdez D, Coulon A, Waterfall JJ, Delattre O. Oncogenic chimeric transcription factors drive tumor-specific transcription, processing, and translation of silent genomic regions. Mol Cell 2022; 82:2458-2471.e9. [PMID: 35550257 DOI: 10.1016/j.molcel.2022.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/20/2022] [Accepted: 04/14/2022] [Indexed: 12/11/2022]
Abstract
Many cancers are characterized by gene fusions encoding oncogenic chimeric transcription factors (TFs) such as EWS::FLI1 in Ewing sarcoma (EwS). Here, we find that EWS::FLI1 induces the robust expression of a specific set of novel spliced and polyadenylated transcripts within otherwise transcriptionally silent regions of the genome. These neogenes (NGs) are virtually undetectable in large collections of normal tissues or non-EwS tumors and can be silenced by CRISPR interference at regulatory EWS::FLI1-bound microsatellites. Ribosome profiling and proteomics further show that some NGs are translated into highly EwS-specific peptides. More generally, we show that hundreds of NGs can be detected in diverse cancers characterized by chimeric TFs. Altogether, this study identifies the transcription, processing, and translation of novel, specific, highly expressed multi-exonic transcripts from otherwise silent regions of the genome as a new activity of aberrant TFs in cancer.
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Affiliation(s)
- Julien Vibert
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Olivier Saulnier
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Céline Collin
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Floriane Petit
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Kyra J E Borgman
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR 3664, Laboratoire Dynamique du Noyau, 75005 Paris, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Jérômine Vigneau
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Maud Gautier
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Gaëlle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Sarah Watson
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Medical Oncology Department, PSL Research University, Institut Curie Hospital, Paris, France
| | - Nadège Gruel
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Clémence Hénon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Sophie Postel-Vinay
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France; Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
| | - Marc Deloger
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Virginie Raynal
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Institut Curie Research Center, Paris, France
| | - Karine Laud-Duval
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Véronique Hill
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Institut Curie Research Center, Paris, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Institut Curie Research Center, Paris, France
| | - Jacob Torrejon
- Institut Curie, CNRS UMR3347, INSERM, PSL Research University, Orsay, France; CNRS UMR 3347, INSERM U1021, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Olivier Ayrault
- Institut Curie, CNRS UMR3347, INSERM, PSL Research University, Orsay, France; CNRS UMR 3347, INSERM U1021, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thomas G P Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Antoine Coulon
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR 3664, Laboratoire Dynamique du Noyau, 75005 Paris, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Joshua J Waterfall
- INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France.
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR 3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.
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94
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Pedot G, Marques JG, Ambühl PP, Wachtel M, Kasper S, Ngo QA, Niggli FK, Schäfer BW. Inhibition of HDACs reduces Ewing sarcoma tumor growth through EWS-FLI1 protein destabilization. Neoplasia 2022; 27:100784. [PMID: 35366465 PMCID: PMC8971315 DOI: 10.1016/j.neo.2022.100784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/26/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022]
Abstract
Oncogenic transcription factors lacking enzymatic activity or targetable binding pockets are typically considered "undruggable". An example is provided by the EWS-FLI1 oncoprotein, whose continuous expression and activity as transcription factor are critically required for Ewing sarcoma tumor formation, maintenance, and proliferation. Because neither upstream nor downstream targets have so far disabled its oncogenic potential, we performed a high-throughput drug screen (HTS), enriched for FDA-approved drugs, coupled to a Global Protein Stability (GPS) approach to identify novel compounds capable to destabilize EWS-FLI1 protein by enhancing its degradation through the ubiquitin-proteasome system. The protein stability screen revealed the dual histone deacetylase (HDAC) and phosphatidylinositol-3-kinase (PI3K) inhibitor called fimepinostat (CUDC-907) as top candidate to modulate EWS-FLI1 stability. Fimepinostat strongly reduced EWS-FLI1 protein abundance, reduced viability of several Ewing sarcoma cell lines and PDX-derived primary cells and delayed tumor growth in a xenograft mouse model, whereas it did not significantly affect healthy cells. Mechanistically, we demonstrated that EWS-FLI1 protein levels were mainly regulated by fimepinostat's HDAC activity. Our study demonstrates that HTS combined to GPS is a reliable approach to identify drug candidates able to modulate stability of EWS-FLI1 and lays new ground for the development of novel therapeutic strategies aimed to reduce Ewing sarcoma tumor progression.
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Affiliation(s)
- Gloria Pedot
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Joana Graça Marques
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Philip P Ambühl
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Stephanie Kasper
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Quy A Ngo
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Felix K Niggli
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital, Steinwiesstrasse 32, 8032, Zurich, Switzerland.
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95
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Hu W, Yuan L, Zhang X, Ni Y, Hong D, Wang Z, Li X, Ling Y, Zhang C, Deng W, Tian M, Ding R, Song C, Li J, Zhang X. Development and validation of an RNA sequencing panel for gene fusions in soft tissue sarcoma. Cancer Sci 2022; 113:1843-1854. [PMID: 35238118 PMCID: PMC9128172 DOI: 10.1111/cas.15317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/08/2022] [Accepted: 02/24/2022] [Indexed: 11/29/2022] Open
Abstract
Gene fusions are one of the most common genomic alterations in soft tissue sarcomas (STS), which contain more than 70 subtypes. In this study, a custom-designed RNA sequencing panel including 67 genes was developed and validated to identify gene fusions in STS. In total, 92 STS samples were analyzed using the RNA panel and 95.7% (88/92) successfully passed all the quality control parameters. Fusion transcripts were detected in 60.2% (53/88) of samples, including three novel fusions (MEG3-PLAG1, SH3BP1-NTRK1, and RPSAP52-HMGA2). The panel demonstrated excellent analytic accuracy, with 93.9% sensitivity and 100% specificity. The intra-assay, inter-assay, and personnel consistencies were all 100.0% in four samples and three replicates. In addition, different variants of ESWR1-FLI, COL1A1-PDGFB, NAB2-STAT6, and SS18-SSX were also identified in the corresponding subtypes of STS. In combination with histological and molecular diagnosis, 14.8% (13/88) patients finally changed preliminary histology-based classification. Collectively, this RNA panel developed in our study shows excellent performance on RNA from formalin-fixed, paraffin-embedded samples and can complement DNA-based assay, thereby facilitating precise diagnosis and novel fusion detection.
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Affiliation(s)
- Wanming Hu
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineDepartment of PathologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Li Yuan
- Department of PathologyGuangzhou Women and Children's Medical CenterGuangzhouChina
| | - Xinke Zhang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineDepartment of PathologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Yang Ni
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
- Department of MedicineNanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
| | - Dongchun Hong
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineDepartment of Medical Melanoma and SarcomaSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Zhicai Wang
- Department of General SurgeryJiangsu Cancer Hospital & Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical UniversityNanjingChina
| | - Xiaomin Li
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Yuan Ling
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Chao Zhang
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Wanglong Deng
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Minqi Tian
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Ran Ding
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
- Department of MedicineNanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
| | - Jianmin Li
- Department of OrthopedicsQilu Hospital of Shandong UniversityJinanChina
| | - Xing Zhang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineDepartment of Medical Melanoma and SarcomaSun Yat‐sen University Cancer CenterGuangzhouChina
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96
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Koppenhafer SL, Goss KL, Voigt E, Croushore E, Terry WW, Ostergaard J, Gordon PM, Gordon DJ. Inhibitor of DNA binding 2 (ID2) regulates the expression of developmental genes and tumorigenesis in ewing sarcoma. Oncogene 2022; 41:2873-2884. [PMID: 35422476 PMCID: PMC9107507 DOI: 10.1038/s41388-022-02310-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 11/24/2022]
Abstract
Sarcomas are difficult to treat and the therapy, even when effective, is associated with long-term and life-threatening side effects. In addition, the treatment regimens for many sarcomas, including Ewing sarcoma, rhabdomyosarcoma, and osteosarcoma, are relatively unchanged over the past two decades, indicating a critical lack of progress. Although differentiation-based therapies are used for the treatment of some cancers, the application of this approach to sarcomas has proven challenging. Here, using a CRISPR-mediated gene knockout approach, we show that Inhibitor of DNA Binding 2 (ID2) is a critical regulator of developmental-related genes and tumor growth in vitro and in vivo in Ewing sarcoma tumors. We also identified that homoharringtonine, which is an inhibitor of protein translation and FDA-approved for the treatment of leukemia, decreases the level of the ID2 protein and significantly reduces tumor growth and prolongs mouse survival in an Ewing sarcoma xenograft model. Furthermore, in addition to targeting ID2, homoharringtonine also reduces the protein levels of ID1 and ID3, which are additional members of the ID family of proteins with well-described roles in tumorigenesis, in multiple types of cancer. Overall, these results provide insight into developmental regulation in Ewing sarcoma tumors and identify a novel, therapeutic approach to target the ID family of proteins using an FDA-approved drug.
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Affiliation(s)
- Stacia L Koppenhafer
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, Iowa City, IA, 52242, USA
| | - Kelli L Goss
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, Iowa City, IA, 52242, USA
| | - Ellen Voigt
- Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Emma Croushore
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, Iowa City, IA, 52242, USA
| | - William W Terry
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, Iowa City, IA, 52242, USA
| | - Jason Ostergaard
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Peter M Gordon
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - David J Gordon
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, Iowa City, IA, 52242, USA.
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97
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Affiliation(s)
- Chelsea Self
- Division of Hematology, Oncology, and Stem Cell Transplantation, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Kyle L MacQuarrie
- Division of Hematology, Oncology, and Stem Cell Transplantation, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Carrye R Cost
- Center for Cancer and Blood Disorders, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO
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98
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Möller E, Praz V, Rajendran S, Dong R, Cauderay A, Xing YH, Lee L, Fusco C, Broye LC, Cironi L, Iyer S, Rengarajan S, Awad ME, Naigles B, Letovanec I, Ormas N, Finzi G, La Rosa S, Sessa F, Chebib I, Petur Nielsen G, Digklia A, Spentzos D, Cote GM, Choy E, Aryee M, Stamenkovic I, Boulay G, Rivera MN, Riggi N. EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma. Nat Commun 2022; 13:2267. [PMID: 35477713 PMCID: PMC9046276 DOI: 10.1038/s41467-022-29910-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/07/2022] [Indexed: 11/26/2022] Open
Abstract
Oncogenic fusion proteins generated by chromosomal translocations play major roles in cancer. Among them, fusions between EWSR1 and transcription factors generate oncogenes with powerful chromatin regulatory activities, capable of establishing complex gene expression programs in permissive precursor cells. Here we define the epigenetic and 3D connectivity landscape of Clear Cell Sarcoma, an aggressive cancer driven by the EWSR1-ATF1 fusion gene. We find that EWSR1-ATF1 displays a distinct DNA binding pattern that requires the EWSR1 domain and promotes ATF1 retargeting to new distal sites, leading to chromatin activation and the establishment of a 3D network that controls oncogenic and differentiation signatures observed in primary CCS tumors. Conversely, EWSR1-ATF1 depletion results in a marked reconfiguration of 3D connectivity, including the emergence of regulatory circuits that promote neural crest-related developmental programs. Taken together, our study elucidates the epigenetic mechanisms utilized by EWSR1-ATF1 to establish regulatory networks in CCS, and points to precursor cells in the neural crest lineage as candidate cells of origin for these tumors. The relationship between cellular histogenesis and molecular phenotypes for the EWSR1- ATF1 fusion in clear cell sarcoma (CCS) requires further characterization. Here, the authors investigate the EWSR1-ATF1 gene regulation networks in CCS cell lines, primary tumors, and mesenchymal stem cells.
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Affiliation(s)
- Emely Möller
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Viviane Praz
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sanalkumar Rajendran
- 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
| | - Alexandra Cauderay
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,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
| | - Lukuo Lee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Carlo Fusco
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Liliane C Broye
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Luisa Cironi
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sowmya Iyer
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Shruthi Rengarajan
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Mary E Awad
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Beverly Naigles
- 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
| | - Nicola Ormas
- Department of Pathology, ASST Sette Laghi, Varese, Italy
| | - Giovanna Finzi
- Department of Pathology, ASST Sette Laghi, Varese, Italy
| | - 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
| | - Fausto Sessa
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Ivan Chebib
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - G Petur Nielsen
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Antonia Digklia
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dimitrios Spentzos
- Department of Orthopaedic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - 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.,Broad Institute, Cambridge, MA, USA
| | - Ivan Stamenkovic
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gaylor Boulay
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Miguel N Rivera
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA.,Broad Institute, Cambridge, MA, USA
| | - Nicolò Riggi
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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99
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Lemma RB, Fleischer T, Martinsen E, Ledsaak M, Kristensen V, Eskeland R, Gabrielsen OS, Mathelier A. Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics Chromatin 2022; 15:13. [PMID: 35440061 PMCID: PMC9016969 DOI: 10.1186/s13072-022-00444-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesised that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression-methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.
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Affiliation(s)
- Roza Berhanu Lemma
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Emily Martinsen
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marit Ledsaak
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vessela Kristensen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild Eskeland
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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100
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KDM5B promotes tumorigenesis of Ewing sarcoma via FBXW7/CCNE1 axis. Cell Death Dis 2022; 13:354. [PMID: 35428764 PMCID: PMC9012801 DOI: 10.1038/s41419-022-04800-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/26/2022]
Abstract
Ewing sarcoma (EwS) is an aggressive tumor that affects children and young adults. Patients with relapsed/refractory diseases have limited treatment options. Targeting the driver fusion oncoproteins of EwS remains a technical problem. Epigenetic mechanisms have been pointed out as key players and alternative therapeutic targets in EwS. Here, we reported that lysine demethylase 5B (KDM5B), a histone demethylase that specifically demethylates tri- and di-methylated H3 Lys-4 (H3K4), was upregulated in EwS and overexpressed KDM5B was correlated with poor outcomes of patients. KDM5B knockdown and KDM5B inhibitor AS-8351 suppressed EwS cell proliferation and induced cell cycle arrest. Bioinformatics analysis revealed that KDM5B mainly influenced the cell cycle pathways in EwS. In mechanistic studies, we found that overexpression of KDM5B resulted in increased CCNE1 protein level, but did not affect the mRNA level of CCNE1. KDM5B upregulation blocked the degradation pathway of CCNE1 by reducing the expression of FBXW7. KDM5B downregulated FBXW7 gene by demethylation of H3K4me3 at promoter region. Moreover, AS-8351 could inhibit tumor growth in nude mice models, indicating the antitumor effect of targeting KDM5B in EwS. Our study uncovered that KDM5B in EwS attenuated FBXW7 transcription and accumulated CCNE1 protein, leading to malignant proliferation of EwS. Epigenetic drug targeting KDM5B could be a potential treatment for EwS.
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