1
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Bayanjargal A, Taslim C, Showpnil IA, Selich-Anderson J, Crow JC, Lessnick SL, Theisen ER. DBD-α4 helix of EWSR1::FLI1 is required for GGAA microsatellite binding that underlies genome regulation in Ewing sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578127. [PMID: 38352344 PMCID: PMC10862889 DOI: 10.1101/2024.01.31.578127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ewing sarcoma is the second most common bone cancer in children and young adults. In 85% of patients, a translocation between chromosomes 11 and 22 results in a potent fusion oncoprotein, EWSR1::FLI1. EWSR1::FLI1 is the only genetic alteration in an otherwise unaltered genome of Ewing sarcoma tumors. The EWSR1 portion of the protein is an intrinsically disordered domain involved in transcriptional regulation by EWSR1::FLI1. The FLI portion of the fusion contains a DNA binding domain shown to bind core GGAA motifs and GGAA repeats. A small alpha-helix in the DNA binding domain of FLI1, DBD-𝛼4 helix, is critical for the transcription function of EWSR1::FLI1. In this study, we aimed to understand the mechanism by which the DBD-𝛼4 helix promotes transcription, and therefore oncogenic transformation. We utilized a multi-omics approach to assess chromatin organization, active chromatinmarks, genome binding, and gene expression in cells expressing EWSR1::FLI1 constructs with and without the DBD-𝛼4 helix. Our studies revealed DBD-𝛼4 helix is crucial for cooperative binding of EWSR1::FLI1 at GGAA microsatellites. This binding underlies many aspects of genome regulation by EWSR1::FLI1 such as formation of TADs, chromatin loops, enhancers and productive transcription hubs.
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2
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Rask GC, Taslim C, Bayanjargal A, Cannon MV, Selich-Anderson J, Crow JC, Duncan A, Theisen ER. Seclidemstat blocks the transcriptional function of multiple FET-fusion oncoproteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.19.594897. [PMID: 38826330 PMCID: PMC11142045 DOI: 10.1101/2024.05.19.594897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Genes encoding the RNA-binding proteins FUS, EWSR1, and TAF15 (FET proteins) are involved in chromosomal translocations in rare sarcomas. FET-rearranged sarcomas are often aggressive malignancies affecting patients of all ages. New therapies are needed. These translocations fuse the 5' portion of the FET gene with a 3' partner gene encoding a transcription factor (TF). The resulting fusion proteins are oncogenic TFs with a FET protein low complexity domain (LCD) and a DNA binding domain. FET fusion proteins have proven stubbornly difficult to target directly and promising strategies target critical co-regulators. One candidate is lysine specific demethylase 1 (LSD1). LSD1 is recruited by multiple FET fusions, including EWSR1::FLI1. LSD1 promotes EWSR1::FLI1 activity and treatment with the noncompetitive inhibitor SP-2509 blocks EWSR1::FLI1 transcriptional function. A similar molecule, seclidemstat (SP-2577), is currently in clinical trials for FET-rearranged sarcomas (NCT03600649). However, whether seclidemstat has pharmacological activity against FET fusions has not been demonstrated. Here, we evaluate the in vitro potency of seclidemstat against multiple FET-rearranged sarcoma cell lines, including Ewing sarcoma, desmoplastic small round cell tumor, clear cell sarcoma, and myxoid liposarcoma. We also define the transcriptomic effects of seclidemstat treatment and evaluated the activity of seclidemstat against FET fusion transcriptional regulation. Seclidemstat showed potent activity in cell viability assays across FET-rearranged sarcomas and disrupted the transcriptional function of all tested fusions. Though epigenetic and targeted inhibitors are unlikely to be effective as a single agents in the clinic, these data suggest seclidemstat remains a promising new treatment strategy for patients with FET-rearranged sarcomas.
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Affiliation(s)
- Galen C. Rask
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Cenny Taslim
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Ariunaa Bayanjargal
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
- Medical Scientist Training Program, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew V. Cannon
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Jesse C. Crow
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | | | - Emily R. Theisen
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
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3
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Yoon I, Kim U, Song Y, Park T, Lee DS. 3C methods in cancer research: recent advances and future prospects. Exp Mol Med 2024; 56:788-798. [PMID: 38658701 PMCID: PMC11059347 DOI: 10.1038/s12276-024-01236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
In recent years, Hi-C technology has revolutionized cancer research by elucidating the mystery of three-dimensional chromatin organization and its role in gene regulation. This paper explored the impact of Hi-C advancements on cancer research by delving into high-resolution techniques, such as chromatin loops, structural variants, haplotype phasing, and extrachromosomal DNA (ecDNA). Distant regulatory elements interact with their target genes through chromatin loops. Structural variants contribute to the development and progression of cancer. Haplotype phasing is crucial for understanding allele-specific genomic rearrangements and somatic clonal evolution in cancer. The role of ecDNA in driving oncogene amplification and drug resistance in cancer cells has also been revealed. These innovations offer a deeper understanding of cancer biology and the potential for personalized therapies. Despite these advancements, challenges, such as the accurate mapping of repetitive sequences and precise identification of structural variants, persist. Integrating Hi-C with multiomics data is key to overcoming these challenges and comprehensively understanding complex cancer genomes. Thus, Hi-C is a powerful tool for guiding precision medicine in cancer research and treatment.
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Affiliation(s)
- Insoo Yoon
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Uijin Kim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Yousuk Song
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Taesoo Park
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Dong-Sung Lee
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea.
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4
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Mallard HJ, Wan S, Nidhi P, Hanscom-Trofy YD, Mohapatra B, Woods NT, Lopez-Guerrero JA, Llombart-Bosch A, Machado I, Scotlandi K, Kreiling NF, Perry MC, Mirza S, Coulter DW, Band V, Band H, Ghosal G. USP1 Expression Driven by EWS::FLI1 Transcription Factor Stabilizes Survivin and Mitigates Replication Stress in Ewing Sarcoma. Mol Cancer Res 2023; 21:1186-1204. [PMID: 37478161 PMCID: PMC10618738 DOI: 10.1158/1541-7786.mcr-23-0323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/23/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023]
Abstract
In this study, we identify USP1 as a transcriptional target of EWS::FLI1 and demonstrate the requisite function of USP1 in Ewing sarcoma (EWS) cell survival in response to endogenous replication stress. EWS::FLI1 oncogenic transcription factor drives most EWS, a pediatric bone cancer. EWS cells display elevated levels of R-loops and replication stress. The mechanism by which EWS cells override activation of apoptosis or cellular senescence in response to increased replication stress is not known. We show that USP1 is overexpressed in EWS and EWS::FLI1 regulates USP1 transcript levels. USP1 knockdown or inhibition arrests EWS cell growth and induces cell death by apoptosis. Mechanistically, USP1 regulates Survivin (BIRC5/API4) protein stability and the activation of caspase-9 and caspase-3/7 in response to endogenous replication stress. Notably, USP1 inhibition sensitizes cells to doxorubicin and etoposide treatment. Together, our study demonstrates that USP1 is regulated by EWS::FLI1, the USP1-Survivin axis promotes EWS cell survival, and USP1 inhibition sensitizes cells to standard of care chemotherapy. IMPLICATIONS High USP1 and replication stress levels driven by EWS::FLI1 transcription factor in EWS are vulnerabilities that can be exploited to improve existing treatment avenues and overcome drug resistance.
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Affiliation(s)
- Halle J. Mallard
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Shibiao Wan
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Prakriti Nidhi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Yvan D. Hanscom-Trofy
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Bhopal Mohapatra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Nicholas T. Woods
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Antonio Llombart-Bosch
- Department of Pathology, Instituto Valenciano de Oncología and Patologika Laboratory, Hospital QuironSalud, Valencia, Spain
| | - Isidro Machado
- Department of Pathology, Instituto Valenciano de Oncología and Patologika Laboratory, Hospital QuironSalud, Valencia, Spain
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Natasha F. Kreiling
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Megan C. Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Donald W. Coulter
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Hamid Band
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
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5
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Selig EE, Bhura R, White MR, Akula S, Hoffman RD, Tovar CN, Xu X, Booth RE, Libich DS. Biochemical and biophysical characterization of the nucleic acid binding properties of the RNA/DNA binding protein EWS. Biopolymers 2023; 114:e23536. [PMID: 36929870 PMCID: PMC10233817 DOI: 10.1002/bip.23536] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023]
Abstract
EWS is a member of the FET family of RNA/DNA binding proteins that regulate crucial phases of nucleic acid metabolism. EWS comprises an N-terminal low-complexity domain (LCD) and a C-terminal RNA-binding domain (RBD). The RBD is further divided into three RG-rich regions, which flank an RNA-recognition motif (RRM) and a zinc finger (ZnF) domain. Recently, EWS was shown to regulate R-loops in Ewing sarcoma, a pediatric bone and soft-tissue cancer in which a chromosomal translocation fuses the N-terminal LCD of EWS to the C-terminal DNA binding domain of the transcription factor FLI1. Though EWS was shown to directly bind R-loops, the binding mechanism was not elucidated. In the current study, the RBD of EWS was divided into several constructs, which were subsequently assayed for binding to various nucleic acid structures expected to form at R-loops, including RNA stem-loops, DNA G-quadruplexes, and RNA:DNA hybrids. EWS interacted with all three nucleic acid structures with varying affinities and multiple domains contributed to binding each substrate. The RRM and RG2 region appear to bind nucleic acids promiscuously while the ZnF displayed more selectivity for single-stranded structures. With these results, the structural underpinnings of EWS recognition and binding of R-loops and other nucleic acid structures is better understood.
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Affiliation(s)
- Emily E Selig
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
| | - Roohi Bhura
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Matthew R White
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Shivani Akula
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Renee D Hoffman
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Carmel N Tovar
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Xiaoping Xu
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
| | - Rachell E Booth
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - David S Libich
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
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6
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Anderson PM, Tu ZJ, Kilpatrick SE, Trucco M, Hanna R, Chan T. Routine EWS Fusion Analysis in the Oncology Clinic to Identify Cancer-Specific Peptide Sequence Patterns That Span Breakpoints in Ewing Sarcoma and DSRCT. Cancers (Basel) 2023; 15:cancers15051623. [PMID: 36900411 PMCID: PMC10001040 DOI: 10.3390/cancers15051623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/14/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
(1) Background: EWS fusion genes are associated with Ewing sarcoma and other Ewing family tumors including desmoplastic small round tumor, DSRCT. We utilize a clinical genomics workflow to reveal real-world frequencies of EWS fusion events, cataloging events that are similar, or divergent at the EWS breakpoint. (2) Methods: EWS fusion events from our next-generation sequencing panel (NGS) samples were first sorted by breakpoint or fusion junctions to map out the frequency of breakpoints. Fusion results were illustrated as in-frame fusion peptides involving EWS and a partner gene. (3) Results: From 2471 patient pool samples for fusion analysis at the Cleveland Clinic Molecular Pathology Laboratory, we identified 182 fusion samples evolved with the EWS gene. They are clustered in several breakpoints: chr22:29683123 (65.9%), and chr22:29688595 (2.7%). About 3/4 of Ewing sarcoma and DSRCT tumors have an identical EWS breakpoint motif at Exon 7 (SQQSSSYGQQ-) fused to a specific part of FLI1 (NPSYDSVRRG or-SSLLAYNTSS), ERG (NLPYEPPRRS), FEV (NPVGDGLFKD) or WT1 (SEKPYQCDFK). Our method also worked with Caris transcriptome data, too. Our primary clinical utility is to use this information to identify neoantigens for therapeutic purposes. (4) Conclusions and future perspectives: our method allows interpretation of what peptides result from the in-frame translation of EWS fusion junctions. These sequences, coupled with HLA-peptide binding data, are used to identify potential sequences of cancer-specific immunogenic peptides for Ewing sarcoma or DSRCT patients. This information may also be useful for immune monitoring (e.g., circulating T-cells with fusion-peptide specificity) to detect vaccine candidates, responses, or residual disease.
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Affiliation(s)
- Peter M. Anderson
- Pediatric Hematology and Bone Marrow Transplant, Pediatric and Taussig Cancer Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
- Correspondence: ; Tel.: +1-216-308-2706
| | - Zheng Jin Tu
- Bioinformatics, Molecular Pathology and Cytogenomics, Department of Laboratory Medicine, Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Scott E. Kilpatrick
- Orthopedic Pathology and Center for ePathology, Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Matteo Trucco
- Pediatric Hematology and Bone Marrow Transplant, Pediatric and Taussig Cancer Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Rabi Hanna
- Pediatric Hematology and Bone Marrow Transplant, Pediatric and Taussig Cancer Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Timothy Chan
- Center for Immuno-Oncology, Department of Radiation Oncology, Taussig Cancer Institute and Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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7
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Sorokin M, Rabushko E, Rozenberg JM, Mohammad T, Seryakov A, Sekacheva M, Buzdin A. Clinically relevant fusion oncogenes: detection and practical implications. Ther Adv Med Oncol 2022; 14:17588359221144108. [PMID: 36601633 PMCID: PMC9806411 DOI: 10.1177/17588359221144108] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/22/2022] [Indexed: 12/28/2022] Open
Abstract
Mechanistically, chimeric genes result from DNA rearrangements and include parts of preexisting normal genes combined at the genomic junction site. Some rearranged genes encode pathological proteins with altered molecular functions. Those which can aberrantly promote carcinogenesis are called fusion oncogenes. Their formation is not a rare event in human cancers, and many of them were documented in numerous study reports and in specific databases. They may have various molecular peculiarities like increased stability of an oncogenic part, self-activation of tyrosine kinase receptor moiety, and altered transcriptional regulation activities. Currently, tens of low molecular mass inhibitors are approved in cancers as the drugs targeting receptor tyrosine kinase (RTK) oncogenic fusion proteins, that is, including ALK, ABL, EGFR, FGFR1-3, NTRK1-3, MET, RET, ROS1 moieties. Therein, the presence of the respective RTK fusion in the cancer genome is the diagnostic biomarker for drug prescription. However, identification of such fusion oncogenes is challenging as the breakpoint may arise in multiple sites within the gene, and the exact fusion partner is generally unknown. There is no gold standard method for RTK fusion detection, and many alternative experimental techniques are employed nowadays to solve this issue. Among them, RNA-seq-based methods offer an advantage of unbiased high-throughput analysis of only transcribed RTK fusion genes, and of simultaneous finding both fusion partners in a single RNA-seq read. Here we focus on current knowledge of biology and clinical aspects of RTK fusion genes, related databases, and laboratory detection methods.
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Affiliation(s)
| | - Elizaveta Rabushko
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia,I.M. Sechenov First Moscow State Medical
University, Moscow, Russia
| | | | - Tharaa Mohammad
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia
| | | | - Marina Sekacheva
- I.M. Sechenov First Moscow State Medical
University, Moscow, Russia
| | - Anton Buzdin
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia,I.M. Sechenov First Moscow State Medical
University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic
Chemistry, Moscow, Russia,PathoBiology Group, European Organization for
Research and Treatment of Cancer (EORTC), Brussels, Belgium
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8
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Chromatin structure in cancer. BMC Mol Cell Biol 2022; 23:35. [PMID: 35902807 PMCID: PMC9331575 DOI: 10.1186/s12860-022-00433-6] [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: 08/20/2021] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
In the past decade, we have seen the emergence of sequence-based methods to understand chromosome organization. With the confluence of in situ approaches to capture information on looping, topological domains, and larger chromatin compartments, understanding chromatin-driven disease is becoming feasible. Excitingly, recent advances in single molecule imaging with capacity to reconstruct “bulk-cell” features of chromosome conformation have revealed cell-to-cell chromatin structural variation. The fundamental question motivating our analysis of the literature is, can altered chromatin structure drive tumorigenesis? As our community learns more about rare disease, including low mutational frequency cancers, understanding “chromatin-driven” pathology will illuminate the regulatory structures of the genome. We describe recent insights into altered genome architecture in human cancer, highlighting multiple pathways toward disruptions of chromatin structure, including structural variation, noncoding mutations, metabolism, and de novo mutations to architectural regulators themselves. Our analysis of the literature reveals that deregulation of genome structure is characteristic in distinct classes of chromatin-driven tumors. As we begin to integrate the findings from single cell imaging studies and chromatin structural sequencing, we will be able to understand the diversity of cells within a common diagnosis, and begin to define structure–function relationships of the misfolded genome.
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9
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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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10
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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:cancers14194819. [PMID: 36230742 PMCID: PMC9564116 DOI: 10.3390/cancers14194819] [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: 09/02/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary The main oncogene in Ewing sarcoma directly drives a high expression of a previously unknown variant KCNN1 (encoding the KCa2.1 channel) that we also verified in samples from >200 patients. Yet, we found that the channel is not functional and does not modulate Ewing sarcoma cell behavior. We could explain this lack of functional impact by the surprising absence of any KCa2.1-carried K+ current in Ewing sarcoma cells. However, we show in a proof-of-principle study that the essential lack of a K+ conductance can be exploited by applying hypoosmotic stress and effectively and selectively killing the Ewing sarcoma cells. 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
- Correspondence:
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11
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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: 15] [Impact Index Per Article: 7.5] [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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12
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Singer DS. A new phase of the Cancer Moonshot to end cancer as we know it. Nat Med 2022; 28:1345-1347. [PMID: 35760861 PMCID: PMC9244436 DOI: 10.1038/s41591-022-01881-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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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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14
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Flores G, Grohar PJ. One oncogene, several vulnerabilities: EWS/FLI targeted therapies for Ewing sarcoma. J Bone Oncol 2021; 31:100404. [PMID: 34976713 PMCID: PMC8686064 DOI: 10.1016/j.jbo.2021.100404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 12/23/2022] Open
Abstract
EWS/FLI is the defining mutation of Ewing sarcoma. This oncogene drives malignant transformation and progression and occurs in a genetic background characterized by few other recurrent cooperating mutations. In addition, the tumor is absolutely dependent on the continued expression of EWS/FLI to maintain the malignant phenotype. However, EWS/FLI is a transcription factor and therefore a challenging drug target. The difficulty of directly targeting EWS/FLI stems from unique features of this fusion protein as well as the network of interacting proteins required to execute the transcriptional program. This network includes interacting proteins as well as upstream and downstream effectors that together reprogram the epigenome and transcriptome. While the vast number of proteins involved in this process challenge the development of a highly specific inhibitors, they also yield numerous therapeutic opportunities. In this report, we will review how this vast EWS-FLI transcriptional network has been exploited over the last two decades to identify compounds that directly target EWS/FLI and/or associated vulnerabilities.
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Affiliation(s)
- Guillermo Flores
- Van Andel Research Institute, Grand Rapids, MI, USA
- Michigan State University, College of Human Medicine, USA
| | - Patrick J Grohar
- Children's Hospital of Philadelphia, University of Pennsylvania, Perelman School of Medicine, 3501 Civic Center Blvd., Philadelphia, PA, USA
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15
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Abstract
Transcription factors (TFs) are essential mediators of epigenetic regulation and modifiers of penetrance. Studies from the past decades have revealed a sub-class of TF that is capable of remodeling closed chromatin states through targeting nucleosomal motifs. This pioneer factor (PF) class of chromatin remodeler is ATP independent in its roles in epigenetic initiation, with nucleosome-motif recognition and association with repressive chromatin regions. Increasing evidence suggests that the fundamental properties of PFs can be coopted in human cancers. We explore the role of PFs in the larger context of tissue-specific epigenetic regulation. Moreover, we highlight an emerging class of chimeric PF derived from translocation partners in human disease and PFs associated with rare tumors. In the age of site-directed genome editing and targeted protein degradation, increasing our understanding of PFs will provide access to next-generation therapy for human disease driven from altered transcriptional circuitry.
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