1
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He Y, Liu B, Yang FY, Yang Q, Xu B, Liu L, Chen Y. TAF15 downregulation contributes to the benefits of physical training on dendritic spines and working memory in aged mice. Aging Cell 2024:e14244. [PMID: 38874013 DOI: 10.1111/acel.14244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
Moderate physical training has been shown to hinder age-related memory decline. While the benefits of physical training on hippocampal memory function are well-documented, little is known about its impact on working memory, which is linked to the prelimbic cortex (PrL), one major subdivision of the prefrontal cortex. Here, we examined the effects of physical training on spatial working memory in a well-established animal model of physical training, starting at 16 months of age and continuing for 5 months (running wheel 1 h/day and 5 days/week). This training strategy improved spatial working memory in aged mice (22-month-old), which was accompanied by an increased spine density and a lower TAF15 expression in the PrL. Specifically, physical training affected both thin and mushroom-type spines on PrL pyramidal cells, and prevented age-related loss of spines on selective segments of apical dendritic branches. Correlation analysis revealed that increased TAF15-expression was detrimental to the dendritic spines. However, physical training downregulated TAF15 expression in the PrL, preserving the dendritic spines on PrL pyramidal cells and improving working memory in trained aged mice. When TAF15 was overexpressed in the PrL via a viral approach, the benefits of physical training on the dendritic spines and working memory were abolished. These data suggest that physical training at a moderate pace might downregulate TAF15 expression in the PrL, which favors the dendritic spines on PrL pyramidal cells, thereby improving spatial working memory.
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Affiliation(s)
- Yun He
- Department of Anatomy, School of Medicine, Yangtze University, Jingzhou, China
| | - Benju Liu
- Department of Anatomy, School of Medicine, Yangtze University, Jingzhou, China
| | - Fu-Yuan Yang
- Health Science Center, Yangtze University, Jingzhou, China
| | - Qun Yang
- Department of Medical Imaging, School of Medicine, Yangtze University, Jingzhou, China
| | - Benke Xu
- Department of Anatomy, School of Medicine, Yangtze University, Jingzhou, China
| | - Lian Liu
- Department of Pharmacology, School of Medicine, Yangtze University, Jingzhou, China
| | - Yuncai Chen
- Department of Anatomy, School of Medicine, Yangtze University, Jingzhou, China
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2
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Ranji P, Jonasson E, Andersson L, Filges S, Luna Santamaría M, Vannas C, Dolatabadi S, Gustafsson A, Myklebost O, Håkansson J, Fagman H, Landberg G, Åman P, Ståhlberg A. Deciphering the role of FUS::DDIT3 expression and tumor microenvironment in myxoid liposarcoma development. J Transl Med 2024; 22:389. [PMID: 38671504 PMCID: PMC11046918 DOI: 10.1186/s12967-024-05211-w] [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: 01/10/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Myxoid liposarcoma (MLS) displays a distinctive tumor microenvironment and is characterized by the FUS::DDIT3 fusion oncogene, however, the precise functional contributions of these two elements remain enigmatic in tumor development. METHODS To study the cell-free microenvironment in MLS, we developed an experimental model system based on decellularized patient-derived xenograft tumors. We characterized the cell-free scaffold using mass spectrometry. Subsequently, scaffolds were repopulated using sarcoma cells with or without FUS::DDIT3 expression that were analyzed with histology and RNA sequencing. RESULTS Characterization of cell-free MLS scaffolds revealed intact structure and a large variation of protein types remaining after decellularization. We demonstrated an optimal culture time of 3 weeks and showed that FUS::DDIT3 expression decreased cell proliferation and scaffold invasiveness. The cell-free MLS microenvironment and FUS::DDIT3 expression both induced biological processes related to cell-to-cell and cell-to-extracellular matrix interactions, as well as chromatin remodeling, immune response, and metabolism. Data indicated that FUS::DDIT3 expression more than the microenvironment determined the pre-adipocytic phenotype that is typical for MLS. CONCLUSIONS Our experimental approach opens new means to study the tumor microenvironment in detail and our findings suggest that FUS::DDIT3-expressing tumor cells can create their own extracellular niche.
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Affiliation(s)
- Parmida Ranji
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Jonasson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Lisa Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Stefan Filges
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Manuel Luna Santamaría
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Christoffer Vannas
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Oncology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Soheila Dolatabadi
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Anna Gustafsson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ola Myklebost
- Department of Tumor Biology, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Science, University of Bergen, Bergen, Norway
| | - Joakim Håkansson
- RISE Unit of Biological Function, Division Materials and Production, RISE Research Institutes of Sweden, Borås, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, Faculty of Science at University of Gothenburg, Gothenburg, Sweden
| | - Henrik Fagman
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Göran Landberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pierre Åman
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.
- Department of Clinical Genetics and Genomics, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.
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3
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Feichtner A, Enzler F, Kugler V, Hoppe K, Mair S, Kremser L, Lindner H, Huber RG, Stelzl U, Stefan E, Torres-Quesada O. Phosphorylation of the compartmentalized PKA substrate TAF15 regulates RNA-protein interactions. Cell Mol Life Sci 2024; 81:162. [PMID: 38568213 PMCID: PMC10991009 DOI: 10.1007/s00018-024-05204-4] [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: 08/18/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
Spatiotemporal-controlled second messengers alter molecular interactions of central signaling nodes for ensuring physiological signal transmission. One prototypical second messenger molecule which modulates kinase signal transmission is the cyclic-adenosine monophosphate (cAMP). The main proteinogenic cellular effectors of cAMP are compartmentalized protein kinase A (PKA) complexes. Their cell-type specific compositions precisely coordinate substrate phosphorylation and proper signal propagation which is indispensable for numerous cell-type specific functions. Here we present evidence that TAF15, which is implicated in the etiology of amyotrophic lateral sclerosis, represents a novel nuclear PKA substrate. In cross-linking and immunoprecipitation experiments (iCLIP) we showed that TAF15 phosphorylation alters the binding to target transcripts related to mRNA maturation, splicing and protein-binding related functions. TAF15 appears to be one of multiple PKA substrates that undergo RNA-binding dynamics upon phosphorylation. We observed that the activation of the cAMP-PKA signaling axis caused a change in the composition of a collection of RNA species that interact with TAF15. This observation appears to be a broader principle in the regulation of molecular interactions, as we identified a significant enrichment of RNA-binding proteins within endogenous PKA complexes. We assume that phosphorylation of RNA-binding domains adds another layer of regulation to binary protein-RNAs interactions with consequences to RNA features including binding specificities, localization, abundance and composition.
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Affiliation(s)
- Andreas Feichtner
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Florian Enzler
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
| | - Valentina Kugler
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Katharina Hoppe
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Sophia Mair
- Department of Cardiac Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
- Vascage, Center of Clinical Stroke Research, 6020, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, 138671, Singapore
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Eduard Stefan
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Omar Torres-Quesada
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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4
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [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: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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5
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Schöpf J, Uhrig S, Heilig CE, Lee KS, Walther T, Carazzato A, Dobberkau AM, Weichenhan D, Plass C, Hartmann M, Diwan GD, Carrero ZI, Ball CR, Hohl T, Kindler T, Rudolph-Hähnel P, Helm D, Schneider M, Nilsson A, Øra I, Imle R, Banito A, Russell RB, Jones BC, Lipka DB, Glimm H, Hübschmann D, Hartmann W, Fröhling S, Scholl C. Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions. Nat Commun 2024; 15:51. [PMID: 38168093 PMCID: PMC10761971 DOI: 10.1038/s41467-023-44360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Linking clinical multi-omics with mechanistic studies may improve the understanding of rare cancers. We leverage two precision oncology programs to investigate rhabdomyosarcoma with FUS/EWSR1-TFCP2 fusions, an orphan malignancy without effective therapies. All tumors exhibit outlier ALK expression, partly accompanied by intragenic deletions and aberrant splicing resulting in ALK variants that are oncogenic and sensitive to ALK inhibitors. Additionally, recurrent CKDN2A/MTAP co-deletions provide a rationale for PRMT5-targeted therapies. Functional studies show that FUS-TFCP2 blocks myogenic differentiation, induces transcription of ALK and truncated TERT, and inhibits DNA repair. Unlike other fusion-driven sarcomas, TFCP2-rearranged tumors exhibit genomic instability and signs of defective homologous recombination. DNA methylation profiling demonstrates a close relationship with undifferentiated sarcomas. In two patients, sarcoma was preceded by benign lesions carrying FUS-TFCP2, indicating stepwise sarcomagenesis. This study illustrates the potential of linking precision oncology with preclinical research to gain insight into the classification, pathogenesis, and therapeutic vulnerabilities of rare cancers.
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Affiliation(s)
- Julia Schöpf
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sebastian Uhrig
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg, and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christoph E Heilig
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kwang-Seok Lee
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Tatjana Walther
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Alexander Carazzato
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Anna Maria Dobberkau
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | | | | | - Mark Hartmann
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Gaurav D Diwan
- Bioquant, Heidelberg University, Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Zunamys I Carrero
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Claudia R Ball
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD, Dresden, Germany
- Faculty of Biology, TUD Dresden University of Technology, Dresden, Germany
| | - Tobias Hohl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Thomas Kindler
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Patricia Rudolph-Hähnel
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Dominic Helm
- Proteomics Core Facility, DKFZ, Heidelberg, Germany
| | | | - Anna Nilsson
- Pediatric Oncology and Coagulation, Karolinska University Hospital, Stockholm, Sweden
| | - Ingrid Øra
- Pediatric Oncology and Hematology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Roland Imle
- Soft-Tissue Sarcoma Junior Research Group, DKFZ, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ana Banito
- Soft-Tissue Sarcoma Junior Research Group, DKFZ, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
| | - Robert B Russell
- Bioquant, Heidelberg University, Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Barbara C Jones
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD, Dresden, Germany
- Translational Functional Cancer Genomics, DKFZ, Heidelberg, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg, and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard Domagk Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
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6
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Kaprio H, Siddiqui A, Saustila L, Heuser VD, Gardberg M. The oncogenic properties of the EWSR1::CREM fusion gene are associated with polyamine metabolism. Sci Rep 2023; 13:4884. [PMID: 36966162 PMCID: PMC10039922 DOI: 10.1038/s41598-023-31576-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
The EWSR1::CREM fusion gene, caused by a chromosomal translocation t(10;22)(p11;q12), has been discovered in divergent malignancies, ranging from low-grade to highly malignant cancers. The translocation gives rise to a chimeric protein, EWSR1::CREM. The molecular mechanisms behind the oncogenic properties of the EWSR1::CREM protein have not previously been systematically characterized. In this study, we performed transcriptional profiling of the melanoma cell line CHL-1, with depletion of endogenous EWSR1::CREM protein using siRNA mediated knockdown. We found that the expression of 712 genes was altered (Log2 fold-change ≥ 2). We performed pathway analysis to identify EWSR1::CREM mediated pathways and cell studies to examine functional differences brought upon by the knockdown. Altered pathways involved cell cycle and proliferation, this was further validated by the cell studies where cell migration was affected as well. Among the target genes with the greatest downregulation, we discovered ODC1-a well-established oncogenic enzyme that can be pharmacologically inhibited and is essential for polyamine synthesis. We found that the main effects seen upon EWSR1::CREM knockdown can be reproduced by directly silencing ODC1 expression. These findings provide novel insights into pathogenesis of tumors harboring a EWSR1::CREM fusion gene, hopefully facilitating the development of novel therapeutic strategies.
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Affiliation(s)
- Heidi Kaprio
- Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10 D, Turku, Finland.
- Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Arafat Siddiqui
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Lotta Saustila
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Vanina D Heuser
- Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10 D, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Maria Gardberg
- Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10 D, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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7
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Faustini E, Panza A, Longaretti M, Lottersberger F. Quantitative analysis of nuclear deformations and DNA damage foci dynamics by live-cell imaging. Methods Cell Biol 2023; 182:247-263. [PMID: 38359981 DOI: 10.1016/bs.mcb.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The correct repair of DNA Double Strand Breaks (DSBs) is fundamental to prevent the loss of genetic information, mutations, and chromosome rearrangements. An emerging determinant of DNA repair is chromatin mobility. However, how chromatin mobility can influence DSBs repair is still poorly understood. While increased mobility is generally associated with the correct repair by Homologous Recombination (HR) of DSBs generated in heterochromatin, it promotes the mis-repair of multiple distal DSBs by Non-Homologous End Joining (NHEJ). Here we describe a method for detecting and quantifying DSBs mobility by live-cell imaging in the context of multiple DSBs prone to mis-repair by NHEJ. In addition, we discuss a set of parameters that can be used for quantitative and qualitative analysis of nuclear deformations and to discard nuclei where the deformation could affect the analysis of DSBs mobility. While this method is based on the visualization of DSBs with the mCherry-53BP1-2 fusion protein, we believe that it can also be used to analyze the mobility of nuclear foci formed by different fluorescent proteins.
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Affiliation(s)
- Elena Faustini
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Andrea Panza
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Matteo Longaretti
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Francisca Lottersberger
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden.
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8
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Savary C, Picard C, Corradini N, Castets M. Complex Elucidation of Cells-of-Origin in Pediatric Soft Tissue Sarcoma: From Concepts to Real Life, Hide-and-Seek through Epigenetic and Transcriptional Reprogramming. Int J Mol Sci 2022; 23:6310. [PMID: 35682989 PMCID: PMC9181261 DOI: 10.3390/ijms23116310] [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: 04/11/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 02/01/2023] Open
Abstract
Soft tissue sarcoma (STS) comprise a large group of mesenchymal malignant tumors with heterogeneous cellular morphology, proliferative index, genetic lesions and, more importantly, clinical features. Full elucidation of this wide diversity remains a central question to improve their therapeutic management and the identity of cell(s)-of-origin from which these tumors arise is part of this enigma. Cellular reprogramming allows transitions of a mature cell between phenotypes, or identities, and represents one key driver of tumoral heterogeneity. Here, we discuss how cellular reprogramming mediated by driver genes in STS can profoundly reshape the molecular and morphological features of a transformed cell and lead to erroneous interpretation of its cell-of-origin. This review questions the fact that the epigenetic context in which a genetic alteration arises has to be taken into account as a key determinant of STS tumor initiation and progression. Retracing the cancer-initiating cell and its clonal evolution, notably via epigenetic approach, appears as a key lever for understanding the origin of these tumors and improving their clinical management.
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Affiliation(s)
- Clara Savary
- Childhood Cancer & Cell Death (C3), LabEx DEVweCAN, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Cécile Picard
- Department of Pathology, Hôpital Femme-Mère-Enfant, Hospices Civils de Lyon, Claude Bernard Lyon 1 University, 69002 Lyon, France;
| | - Nadège Corradini
- Department of Pediatric Oncology, Institut d’Hematologie et d’Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France;
- Department of Translational Research in Pediatric Oncology, Centre Léon Bérard, 69008 Lyon, France
| | - Marie Castets
- Childhood Cancer & Cell Death (C3), LabEx DEVweCAN, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
- Department of Translational Research in Pediatric Oncology, Centre Léon Bérard, 69008 Lyon, France
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9
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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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10
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Zhang L, Lin W, Zhou Y, Shao F, Gao Y, He J. A Complement-Related Gene Signature for Predicting Overall Survival and Immunotherapy Efficacy in Sarcoma Patients. Front Cell Dev Biol 2022; 10:765062. [PMID: 35493104 PMCID: PMC9046668 DOI: 10.3389/fcell.2022.765062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/07/2022] [Indexed: 12/24/2022] Open
Abstract
The prognoses of sarcomas are poor and the responses of them to systemic therapies are limited and controversial. Thus, there is an urgent need to stratify the risk factors and identify the patients who may benefit from systemic therapies. Here, we developed a reliable, complement-based gene signature to predict the prognosis of sarcoma patients. Survival-related complement genes were identified by univariate Cox analyses and were used to build a gene signature, which was further selected using the least absolute shrinkage and selection operator model, and determined using a stepwise Cox proportional hazards regression model. The whole sarcoma cohort of TCGA was randomly divided into a training set and a test set. The signature was constructed using the training set and validated subsequently in the test set, the whole TCGA sarcoma cohort, and another two independent cohorts from the TARGET and GEO databases, respectively. Furthermore, the prognostic value of the signature was also validated in an independent cohort from our center. This model effectively predicted prognoses across the training set, different validation cohorts, and different clinical subgroups. Next, immune cell infiltration analysis, GO and KEGG analysis, and gene set enrichment analysis were performed to explore possible underlying mechanisms of this signature. Moreover, this signature may predict the response to immunotherapy. Collectively, the current complement-related gene signature can predict overall survival and possible immunotherapy response of sarcoma patients; it may serve as a powerful prognostic tool to further optimize clinical treatment and prognosis management for sarcoma patients.
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Affiliation(s)
- Lin Zhang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weihao Lin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Shao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Qingdao Cancer Institute, Cancer Institute of the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yibo Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yibo Gao, ; Jie He,
| | - Jie He
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yibo Gao, ; Jie He,
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11
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CIC rearranged sarcomas: A Single Institution Experience of the Potential Pitfalls in Interpreting CIC FISH Results. Pathol Res Pract 2022; 231:153773. [DOI: 10.1016/j.prp.2022.153773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 11/19/2022]
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12
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Owen I, Yee D, Wyne H, Perdikari TM, Johnson V, Smyth J, Kortum R, Fawzi NL, Shewmaker F. The oncogenic transcription factor FUS-CHOP can undergo nuclear liquid-liquid phase separation. J Cell Sci 2021; 134:272045. [PMID: 34357401 DOI: 10.1242/jcs.258578] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/24/2021] [Indexed: 11/20/2022] Open
Abstract
Myxoid liposarcoma is caused by a chromosomal translocation resulting in a fusion protein comprised of the N terminus of FUS (fused in sarcoma) and the full-length transcription factor CHOP (CCAAT/enhancer-binding protein homologous protein, also known as DDIT3). FUS functions in RNA metabolism, and CHOP is a stress-induced transcription factor. The FUS-CHOP fusion protein causes unique gene expression and oncogenic transformation. Although it is clear that the FUS segment is required for oncogenic transformation, the mechanism of FUS-CHOP-induced transcriptional activation is unknown. Recently, some transcription factors and super enhancers have been proposed to undergo liquid-liquid phase separation and form membraneless compartments that recruit transcription machinery to gene promoters. Since phase separation of FUS depends on its N terminus, transcriptional activation by FUS-CHOP could result from the N terminus driving nuclear phase transitions. Here, we characterized FUS-CHOP in cells and in vitro, and observed novel phase-separating properties relative to unmodified CHOP. Our data indicate that FUS-CHOP forms phase-separated condensates that colocalize with BRD4, a marker of super enhancer condensates. We provide evidence that the FUS-CHOP phase transition is a novel oncogenic mechanism and potential therapeutic target for myxoid liposarcoma. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Izzy Owen
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814, USA
| | - Debra Yee
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814, USA
| | - Hala Wyne
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814, USA
| | | | - Victoria Johnson
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Jeremy Smyth
- Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD 20814, USA
| | - Robert Kortum
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD 20814, USA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Frank Shewmaker
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814, USA
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13
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Nicholas TR, Metcalf SA, Greulich BM, Hollenhorst PC. Androgen signaling connects short isoform production to breakpoint formation at Ewing sarcoma breakpoint region 1. NAR Cancer 2021; 3:zcab033. [PMID: 34409300 PMCID: PMC8364332 DOI: 10.1093/narcan/zcab033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 01/23/2023] Open
Abstract
Ewing sarcoma breakpoint region 1 (EWSR1) encodes a multifunctional protein that can cooperate with the transcription factor ERG to promote prostate cancer. The EWSR1 gene is also commonly involved in oncogenic gene rearrangements in Ewing sarcoma. Despite the cancer relevance of EWSR1, its regulation is poorly understood. Here we find that in prostate cancer, androgen signaling upregulates a 5′ EWSR1 isoform by promoting usage of an intronic polyadenylation site. This isoform encodes a cytoplasmic protein that can strongly promote cell migration and clonogenic growth. Deletion of an Androgen Receptor (AR) binding site near the 5′ EWSR1 polyadenylation site abolished androgen-dependent upregulation. This polyadenylation site is also near the Ewing sarcoma breakpoint hotspot, and androgen signaling promoted R-loop and breakpoint formation. RNase H overexpression reduced breakage and 5′ EWSR1 isoform expression suggesting an R-loop dependent mechanism. These data suggest that androgen signaling can promote R-loops internal to the EWSR1 gene leading to either early transcription termination, or breakpoint formation.
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Affiliation(s)
- Taylor R Nicholas
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Stephanie A Metcalf
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Benjamin M Greulich
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Peter C Hollenhorst
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
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14
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Ahmed NS, Harrell LM, Wieland DR, Lay MA, Thompson VF, Schwartz JC. Fusion protein EWS-FLI1 is incorporated into a protein granule in cells. RNA (NEW YORK, N.Y.) 2021; 27:rna.078827.121. [PMID: 34035145 PMCID: PMC8284321 DOI: 10.1261/rna.078827.121] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/18/2021] [Indexed: 05/15/2023]
Abstract
Ewing sarcoma is driven by fusion proteins containing a low complexity (LC) domain that is intrinsically disordered and a powerful transcriptional regulator. The most common fusion protein found in Ewing sarcoma, EWS-FLI1, takes its LC domain from the RNA-binding protein EWSR1 (Ewing Sarcoma RNA-binding protein 1) and a DNA-binding domain from the transcription factor FLI1 (Friend Leukemia Virus Integration 1). EWS-FLI1 can bind RNA polymerase II (RNA Pol II) and self-assemble through its low-complexity (LC) domain. The ability of RNA-binding proteins like EWSR1 to self-assemble or phase separate in cells has raised questions about the contribution of this process to EWS-FLI1 activity. We examined EWSR1 and EWS-FLI1 activity in Ewing sarcoma cells by siRNA-mediated knockdown and RNA-seq analysis. More transcripts were affected by the EWSR1 knockdown than expected and these included many EWS-FLI1 regulated genes. We reevaluated physical interactions between EWS-FLI1, EWSR1, and RNA Pol II, and employed a cross-linking based strategy to investigate protein assemblies associated with the proteins. The LC domain of EWS-FLI1 was required for the assemblies observed to form in cells. These results offer new insights into a protein assembly that may enable EWS-FLI1 to bind its wide network of protein partners and contribute to regulation of gene expression in Ewing sarcoma.
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Affiliation(s)
- Nasiha S Ahmed
- Department of Molecular and Cellular Biology, The University of Arizona, Tucson, AZ 85719
| | - Lucas M Harrell
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85719
| | - Daniel R Wieland
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85719
| | - Michelle A Lay
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85719
| | - Valery F Thompson
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85719
| | - Jacob C Schwartz
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85719
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15
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do Nascimento MLLB, Dos Reis AC, Santos JVO, Negreiros HA, da Silva FCC, Ferreira PMP, Gonçalves JCR, Dittz D, Braz DC, Nunes AMV, Cunha RLOR, Melo-Cavalcante AAC, de Castro E Sousa JM. Antiproliferative and Genotoxic Action of an Underexploited Organoteluran Derivative on Sarcoma 180 Cells. Anticancer Agents Med Chem 2021; 21:1019-1026. [PMID: 32951579 DOI: 10.2174/1871520620666200918110152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The search for novel metallic chemical compounds with toxicogenic effects has been of great importance for more efficient cancer treatment. OBJECTIVE The study evaluated the cytotoxic, genotoxic and mutagenic activity of organoteluran RF07 in the S-180 cell line. METHODS The bioassays used were cell viability with 3-(4,5-dimethyl-2-thiazole)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) test, evaluation of apoptosis and necrosis using fluorescence and flow cytometry, cytokinesisblock micronucleus test and comet assay. The compound was tested at 1; 2.5 and 5μM. RESULTS The results showed the cytotoxicity of RF07 at concentrations of 2.5, 5, 10 and 20μM when compared to the negative control. For genotoxicity tests, RF07 showed effects in all concentrations assessed by increased index and frequencies of damage and mutagenic alterations. The compound was also cytotoxic due to the significant decrease in the nuclear division index, with significant values of apoptosis and necrosis. The results of fluorescence and flow cytometry showed apoptosis as the main type of cell death caused by RF07 at 5μM, which is thought to avoid an aggressive immune response of the organism. CONCLUSION In addition to cytotoxic and genotoxic effects, RF07 creates good perspectives for future antitumor formulations.
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Affiliation(s)
- Maria L L Barreto do Nascimento
- Postgraduate Program in Pharmaceutical Sciences, Laboratory of Toxicological Genetics, Federal University of Piaui, Teresina, Brazil
| | - Antonielly Campinho Dos Reis
- Postgraduate Program in Pharmaceutical Sciences, Laboratory of Toxicological Genetics, Federal University of Piaui, Teresina, Brazil
| | - José V O Santos
- Postgraduate Program in Pharmaceutical Sciences, Laboratory of Toxicological Genetics, Federal University of Piaui, Teresina, Brazil
| | - Helber A Negreiros
- Postgraduate Program in Pharmaceutical Sciences, Laboratory of Toxicological Genetics, Federal University of Piaui, Teresina, Brazil
| | | | - Paulo M P Ferreira
- Postgraduate Program in Pharmaceutical Sciences, Laboratory of Toxicological Genetics, Federal University of Piaui, Teresina, Brazil
| | - Juan C R Gonçalves
- Department of Pharmaceutical Sciences, Federal University of Paraiba, Joao Pessoa, Brazil
| | - Dalton Dittz
- Department of Biochemistry and Pharmacology, Federal University of Piaui, Teresina, Brazil
| | - Débora C Braz
- Department of Pharmacy, University of Piaui, Teresina, Brazil
| | - Adriana M V Nunes
- Department of Biophysics and Physiology, Laboratory of Experimental Cancerology, Federal University of Piaui, Teresina, Brazil
| | - Rodrigo L O R Cunha
- Center for Natural and Human Sciences, Laboratory of Chemical Biology, Federal University of ABC, Santo Andre, Brazil
| | - Ana A C Melo-Cavalcante
- Postgraduate Program in Pharmaceutical Sciences, Laboratory of Toxicological Genetics, Federal University of Piaui, Teresina, Brazil
| | - João Marcelo de Castro E Sousa
- Postgraduate Program in Pharmaceutical Sciences, Laboratory of Toxicological Genetics, Federal University of Piaui, Teresina, Brazil
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16
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Affiliation(s)
- Nicolò Riggi
- From the Institute of Pathology, Faculty of Biology and Medicine, University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland (N.R., I.S.); and the Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, and the Broad Institute of Harvard University and the Massachusetts Institute of Technology, Cambridge - both in Massachusetts (M.L.S.)
| | - Mario L Suvà
- From the Institute of Pathology, Faculty of Biology and Medicine, University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland (N.R., I.S.); and the Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, and the Broad Institute of Harvard University and the Massachusetts Institute of Technology, Cambridge - both in Massachusetts (M.L.S.)
| | - Ivan Stamenkovic
- From the Institute of Pathology, Faculty of Biology and Medicine, University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland (N.R., I.S.); and the Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, and the Broad Institute of Harvard University and the Massachusetts Institute of Technology, Cambridge - both in Massachusetts (M.L.S.)
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17
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Wang Y, Li J, Shao C, Tang X, Du Y, Xu T, Zhao Z, Hu H, Sheng Y, Hu C, Xi Y. Systematic profiling of diagnostic and prognostic value of autophagy-related genes for sarcoma patients. BMC Cancer 2021; 21:58. [PMID: 33435917 PMCID: PMC7802146 DOI: 10.1186/s12885-020-07596-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 10/30/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Autophagy-related genes (ARGs) have been confirmed to have an important role in tumorigenesis and tumor microenvironment formation. Nevertheless, a systematic analysis of ARGs and their clinical significance in sarcoma patients is lacking. METHODS Gene expression files from The Cancer Genome Atlas (TCGA) database and Genotype-Tissue Expression (GTEx) were used to select differentially expressed genes (DEGs). Differentially expressed ARGs (DEARGs) were determined by matching the DEG and HADb gene sets, which were evaluated by functional enrichment analysis. Unsupervised clustering of the identified DEARGs was conducted, and associations with tumor microenvironment (TME), immune checkpoints, and immune cells were analyzed simultaneously. Two prognostic signatures, one for overall survival (OS) and one for disease-free survival (DFS), were established and validated in an independent set. RESULTS In total, 84 DEARGs and two clusters were identified. TME scores, five immune checkpoints, and several types of immune cells were found to be significantly different between two clusters. Two prognostic signatures incorporating DEARGs showed favorable discrimination and were successfully validated. Two nomograms combining signature and clinical variables were generated. The C-indexes were 0.818 and 0.747 for the OS and DFS nomograms, respectively. CONCLUSION This comprehensive analyses of the ARG landscape in sarcoma showed novel ARGs related to carcinogenesis and the immune microenvironment. These findings have implications for prognosis and therapeutic responses, which reveal novel potential prognostic biomarkers, promote precision medicine, and provide potential novel targets for immunotherapy.
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Affiliation(s)
- Yuanhe Wang
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China
| | - Jianyi Li
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China
| | - Cheng Shao
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China
| | - Xiaojie Tang
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China.,Department of Spinal Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, 264100, China
| | - Yukun Du
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China
| | - Tongshuai Xu
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China
| | - Zheng Zhao
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China
| | - Huiqiang Hu
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China
| | - Yingyi Sheng
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China
| | - Chuan Hu
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China.
| | - Yongming Xi
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266071, China.
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18
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Schneider N, Wieland FG, Kong D, Fischer AAM, Hörner M, Timmer J, Ye H, Weber W. Liquid-liquid phase separation of light-inducible transcription factors increases transcription activation in mammalian cells and mice. SCIENCE ADVANCES 2021; 7:7/1/eabd3568. [PMID: 33523844 PMCID: PMC7775772 DOI: 10.1126/sciadv.abd3568] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/06/2020] [Indexed: 05/10/2023]
Abstract
Light-inducible gene switches represent a key strategy for the precise manipulation of cellular events in fundamental and applied research. However, the performance of widely used gene switches is limited due to low tissue penetrance and possible phototoxicity of the light stimulus. To overcome these limitations, we engineer optogenetic synthetic transcription factors to undergo liquid-liquid phase separation in close spatial proximity to promoters. Phase separation of constitutive and optogenetic synthetic transcription factors was achieved by incorporation of intrinsically disordered regions. Supported by a quantitative mathematical model, we demonstrate that engineered transcription factor droplets form at target promoters and increase gene expression up to fivefold. This increase in performance was observed in multiple mammalian cells lines as well as in mice following in situ transfection. The results of this work suggest that the introduction of intrinsically disordered domains is a simple yet effective means to boost synthetic transcription factor activity.
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Affiliation(s)
- Nils Schneider
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
| | - Franz-Georg Wieland
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Institute of Physics, University of Freiburg, Hermann-Herder-Straße 3, 79104 Freiburg, Germany
- Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, Ernst-Zermelo-Str. 1, 79104 Freiburg, Germany
| | - Deqiang Kong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Alexandra A M Fischer
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 21a, 79104 Freiburg, Germany
| | - Maximilian Hörner
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
| | - Jens Timmer
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Institute of Physics, University of Freiburg, Hermann-Herder-Straße 3, 79104 Freiburg, Germany
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany.
- Faculty of Biology, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 21a, 79104 Freiburg, Germany
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19
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Dermawan JK, Cheng YW, Tu ZJ, Meyer A, Habeeb O, Zou Y, Goldblum JR, Billings SD, Kilpatrick SE, Reith JD, Shurtleff SA, Farkas DH, Rubin BP, Azzato EM. Diagnostic Utility of a Custom 34-Gene Anchored Multiplex PCR-Based Next-Generation Sequencing Fusion Panel for the Diagnosis of Bone and Soft Tissue Neoplasms With Identification of Novel USP6 Fusion Partners in Aneurysmal Bone Cysts. Arch Pathol Lab Med 2020; 145:851-863. [PMID: 33147323 DOI: 10.5858/arpa.2020-0336-oa] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Bone and soft tissue tumors are heterogeneous, diagnostically challenging, and often defined by gene fusions. OBJECTIVE.— To present our experience using a custom 34-gene targeted sequencing fusion panel. DESIGN.— Total nucleic acid extracted from formalin-fixed, paraffin-embedded (FFPE) tumor specimens was subjected to open-ended, nested anchored multiplex polymerase chain reaction and enrichment of 34 gene targets, thus enabling detection of known and novel fusion partners. RESULTS.— During a 12-month period, 147 patients were tested as part of routine clinical care. Tumor percentage ranged from 10% to 100% and turnaround time ranged from 3 to 15 (median, 7.9) days. The most common diagnostic groups were small round blue cell tumors, tumors of uncertain differentiation, fibroblastic/myofibroblastic tumors, and adipocytic tumors. In-frame fusion transcripts were identified in 64 of 142 cases sequenced (45%): in 62 cases, the detection of a disease-defining fusion confirmed the morphologic impression; in 2 cases, a germline TFG-GPR128 polymorphic fusion variant was detected. Several genes in the panel partnered with multiple fusion partners specific for different diagnoses, for example, EWSR1, NR4A3, FUS, NCOA2, and TFE3. Interesting examples are presented to highlight how fusion detection or lack thereof was instrumental in establishing accurate diagnoses. Novel fusion partners were detected for 2 cases of solid aneurysmal bone cysts (PTBP1-USP6, SLC38A2-USP6). CONCLUSIONS.— Multiplex detection of fusions in total nucleic acid purified from FFPE specimens facilitates diagnosis of bone and soft tissue tumors. This technology is particularly useful for morphologically challenging entities and in the absence of prior knowledge of fusion partners, and has the potential to discover novel fusion partners.
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Affiliation(s)
- Josephine K Dermawan
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
| | - Yu Wei Cheng
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
| | - Zheng Jin Tu
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
| | - Anders Meyer
- The Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City (Meyer)
| | - Omar Habeeb
- The Department of Anatomic Pathology, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand (Habeeb)
| | - Youran Zou
- The Department of Pathology, Kaiser Permanente Oakland Medical Center, Oakland, California (Zou)
| | - John R Goldblum
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
| | - Steven D Billings
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
| | - Scott E Kilpatrick
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
| | - John D Reith
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
| | - Sheila A Shurtleff
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
| | - Daniel H Farkas
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
| | - Brian P Rubin
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
| | - Elizabeth M Azzato
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Dermawan, Cheng, Tu, Goldblum, Billings, Kilpatrick, Reith, Shurtleff, Farkas, Rubin, Azzato)
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20
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Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. SCIENCE CHINA. LIFE SCIENCES 2020; 63:953-985. [PMID: 32548680 DOI: 10.1007/s11427-020-1702-x] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
Cells are compartmentalized by numerous membrane-enclosed organelles and membraneless compartments to ensure that a wide variety of cellular activities occur in a spatially and temporally controlled manner. The molecular mechanisms underlying the dynamics of membrane-bound organelles, such as their fusion and fission, vesicle-mediated trafficking and membrane contactmediated inter-organelle interactions, have been extensively characterized. However, the molecular details of the assembly and functions of membraneless compartments remain elusive. Mounting evidence has emerged recently that a large number of membraneless compartments, collectively called biomacromolecular condensates, are assembled via liquid-liquid phase separation (LLPS). Phase-separated condensates participate in various biological activities, including higher-order chromatin organization, gene expression, triage of misfolded or unwanted proteins for autophagic degradation, assembly of signaling clusters and actin- and microtubule-based cytoskeletal networks, asymmetric segregations of cell fate determinants and formation of pre- and post-synaptic density signaling assemblies. Biomacromolecular condensates can transition into different material states such as gel-like structures and solid aggregates. The material properties of condensates are crucial for fulfilment of their distinct functions, such as biochemical reaction centers, signaling hubs and supporting architectures. Cells have evolved multiple mechanisms to ensure that biomacromolecular condensates are assembled and disassembled in a tightly controlled manner. Aberrant phase separation and transition are causatively associated with a variety of human diseases such as neurodegenerative diseases and cancers. This review summarizes recent major progress in elucidating the roles of LLPS in various biological pathways and diseases.
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21
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HOXB13 controls cell state through super-enhancers. Exp Cell Res 2020; 393:112039. [PMID: 32376288 DOI: 10.1016/j.yexcr.2020.112039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 12/29/2022]
Abstract
Expression of the homeodomain transcription factor HOXB13 has been demonstrated in several malignancies but its role in tumorigenesis remains elusive. We observed high levels of HOXB13 in poorly differentiated pediatric tumors including a highly aggressive childhood neoplasm - malignant rhabdoid tumor. In a xenograft model of rhabdoid tumor, knockout of HOXB13 diminished tumor growth while partial knockdown of HOXB13 promoted differentiation of tumor cells into bone. These results suggest that HOXB13 enhances rhabdoid malignancy by interfering with mesenchymal stem cell differentiation. Consistent with this hypothesis, overexpression of HOXB13 in mesenchymal progenitor cells inhibited adipogenic, myogenic, and osteogenic differentiation. Mechanistically, we demonstrated that HOXB13 binds to super-enhancer regions regulating genes involved in differentiation and tumorigenesis.
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22
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Jo VY. EWSR1
fusions: Ewing sarcoma and beyond. Cancer Cytopathol 2020; 128:229-231. [DOI: 10.1002/cncy.22239] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/02/2020] [Indexed: 12/17/2022]
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23
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Mercatelli N, Fortini D, Palombo R, Paronetto MP. Small molecule inhibition of Ewing sarcoma cell growth via targeting the long non coding RNA HULC. Cancer Lett 2019; 469:111-123. [PMID: 31639426 DOI: 10.1016/j.canlet.2019.10.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 01/02/2023]
Abstract
Ewing sarcomas (ES) are aggressive pediatric cancers of bone and soft tissues characterized by in frame chromosomal translocations giving rise to chimeric transcription factors, such as EWS-FLI1. An emerging strategy to block EWS-FLI1 activity is represented by the small molecule YK-4-279, which binds to EWS-FLI1 and alters its transcriptional activity. The specific effectors of the anti-oncogenic activity of YK-4-279 are still largely unknown. Herein, by performing a high-throughput screening we identify the lncRNA HULC (Highly Upregulated in Liver Cancer) as a prominent target of YK-4-279 activity in ES cells. High levels of HULC correlate with ES aggressiveness, whereas HULC depletion reduces ES cell growth. Mechanistically, we find that HULC promotes the expression of TWIST1 oncogene by sponging miR-186. Downregulation of HULC upon treatment with YK-4-279 reduces the expression of TWIST1 by unleashing miR-186 and favoring its binding to TWIST1 transcripts. Notably, high levels of miR-186 and low levels of TWIST1 correlate with better prognosis in ES patients. Our results disclose a novel oncogenic regulatory circuit mediated by HULC lncRNA that is disrupted by the small molecule YK-4-279, with promising therapeutic implications for ES treatment.
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Affiliation(s)
- Neri Mercatelli
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, Rome, 00143, Italy.
| | - Diana Fortini
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, Rome, 00143, Italy
| | - Ramona Palombo
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, Rome, 00143, Italy
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, Rome, 00143, Italy; Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135, Rome, Italy.
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24
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Andersson MK, Åman P, Stenman G. IGF2/IGF1R Signaling as a Therapeutic Target in MYB-Positive Adenoid Cystic Carcinomas and Other Fusion Gene-Driven Tumors. Cells 2019; 8:cells8080913. [PMID: 31426421 PMCID: PMC6721700 DOI: 10.3390/cells8080913] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 12/12/2022] Open
Abstract
Chromosome rearrangements resulting in pathogenetically important gene fusions are a common feature of many cancers. They are often potent oncogenic drivers and have key functions in central cellular processes and pathways and encode transcription factors, transcriptional co-regulators, growth factor receptors, tyrosine kinases, and chromatin modifiers. In addition to being useful diagnostic biomarkers, they are also targets for development of new molecularly targeted therapies. Studies in recent decades have shown that several oncogenic gene fusions interact with the insulin-like growth factor (IGF) signaling pathway. For example, the MYB-NFIB fusion in adenoid cystic carcinoma is regulated by IGF1R through an autocrine loop, and IGF1R is a downstream target of the EWSR1-WT1 and PAX3-FKHR fusions in desmoplastic small round cell tumors and alveolar rhabdomyosarcoma, respectively. Here, we will discuss the mechanisms behind the interactions between oncogenic gene fusions and the IGF signaling pathway. We will also discuss the role of therapeutic inhibition of IGF1R in fusion gene driven malignancies.
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Affiliation(s)
- Mattias K Andersson
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, 405 30 Gothenburg, Sweden.
| | - Pierre Åman
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Göran Stenman
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, 405 30 Gothenburg, Sweden
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25
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Murthy AC, Dignon GL, Kan Y, Zerze GH, Parekh SH, Mittal J, Fawzi NL. Molecular interactions underlying liquid-liquid phase separation of the FUS low-complexity domain. Nat Struct Mol Biol 2019; 26:637-648. [PMID: 31270472 PMCID: PMC6613800 DOI: 10.1038/s41594-019-0250-x] [Citation(s) in RCA: 386] [Impact Index Per Article: 77.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
The low complexity domain of the RNA-binding protein FUS (FUS LC) mediates liquid-liquid phase separation (LLPS), but interactions between the repetitive SYGQ-rich sequence of FUS LC that stabilize the liquid phase are not known in detail. By combining NMR and Raman spectroscopy, mutagenesis, and molecular simulation, we demonstrate that heterogeneous interactions involving all residue types underlie LLPS of human FUS LC. We find no evidence that FUS LC adopts conformations with traditional secondary structure elements in the condensed phase, rather it maintains conformational heterogeneity. We show that hydrogen bonding, π/sp2 and hydrophobic interactions all contribute to stabilizing LLPS of FUS LC. In addition to contributions from tyrosine residues, we find that glutamine residues participate in contacts leading to LLPS of FUS LC. These results support a model in which FUS LC forms dynamic, multivalent interactions via multiple residue types and remains disordered in the densely packed liquid phase.
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Affiliation(s)
- Anastasia C Murthy
- Graduate Program in Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - Yelena Kan
- LUT School of Engineering Science, LUT University, Lappeenranta, Finland.,Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz, Germany
| | - Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Sapun H Parekh
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz, Germany.,Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA.
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA.
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26
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Abstract
Among the various genes that can be rearranged in soft tissue neoplasms associated with nonrandom chromosomal translocations, EWSR1 is the most frequent one to partner with other genes to generate recurrent fusion genes. This leads to a spectrum of clinically and pathologically diverse mesenchymal and nonmesenchymal neoplasms, variably manifesting as small round cell, spindle cell, clear cell or adipocytic tumors, or tumors with distinctive myxoid stroma. This review summarizes the growing list of mesenchymal neoplasms that are associated with EWSR1 gene rearrangements.
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Affiliation(s)
- Khin Thway
- Sarcoma Unit, Royal Marsden Hospital, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK.
| | - Cyril Fisher
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital NHS Foundation Trust, Robert Aitken Institute for Clinical Research, University of Birmingham, Birmingham B15 2TT, UK
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27
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Palombo R, Frisone P, Fidaleo M, Mercatelli N, Sette C, Paronetto MP. The Promoter-Associated Noncoding RNA pncCCND1_B Assembles a Protein-RNA Complex to Regulate Cyclin D1 Transcription in Ewing Sarcoma. Cancer Res 2019; 79:3570-3582. [PMID: 31072811 DOI: 10.1158/0008-5472.can-18-2403] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/05/2018] [Accepted: 05/03/2019] [Indexed: 11/16/2022]
Abstract
Most Ewing sarcomas are characterized by the in-frame chromosomal translocation t(11;22) generating the EWS-FLI1 oncogene. EWS-FLI1 protein interacts with the RNA helicase DHX9 and affects transcription and processing of genes involved in neoplastic transformation, including CCND1 (the cyclin D1 gene), which contributes to cell-cycle dysregulation in cancer. In this study, we found that CCND1 expression is significantly higher in patients with Ewing sarcoma compared with other sarcomas and that the pncCCND1_B RNA, a previously uncharacterized CCND1 promoter-associated noncoding (pnc) transcript, is expressed in Ewing sarcoma cells. PncCCND1_B interacted with the RNA-binding protein Sam68 and repressed CCND1 expression. Notably, knockdown of Sam68 affected pncCCND1_B subcellular localization and cyclin D1 expression. Pharmacologic impairment of DHX9/EWS-FLI1 interaction promoted RNA-dependent association of Sam68 with DHX9 and recruitment of Sam68 to the CCND1 promoter, thus repressing it. Conversely, mitogenic stimulation of Ewing sarcoma cells with IGF1 impaired Sam68/DHX9 interaction and positively regulated CCND1 expression. These studies uncover a fine-tuned modulation of the proto-oncogene CCND1 in Ewing sarcoma cells via alternative complexes formed by DHX9 with either EWS-FLI1 or pncCCND1_B-Sam68. SIGNIFICANCE: A pncRNA-based mechanism represses expression of CCND1 through the formation of a protein-RNA complex and provides new therapeutic opportunities for patients with Ewing sarcoma.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/14/3570/F1.large.jpg.
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Affiliation(s)
- Ramona Palombo
- Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, Rome, Italy
| | - Paola Frisone
- Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, Rome, Italy
| | - Marco Fidaleo
- Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, Rome, Italy
| | - Neri Mercatelli
- Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, Rome, Italy
| | - Claudio Sette
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, Rome, Italy. .,Department of Movement, Human and Health Sciences, University of Rome "Foro Italico," Piazza Lauro de Bosis 6, Rome, Italy
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28
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Sheth J, Arnoldo A, Zhong Y, Marrano P, Pereira C, Ryall S, Thorner P, Hawkins C, Somers GR. Sarcoma Subgrouping by Detection of Fusion Transcripts Using NanoString nCounter Technology. Pediatr Dev Pathol 2019; 22:205-213. [PMID: 30089422 DOI: 10.1177/1093526618790747] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND NanoString technology is an innovative barcode-based system that requires less tissue than traditional techniques and can test for multiple fusion transcripts in a single reaction. The objective of this study was to determine the utility of NanoString technology in the detection of sarcoma-specific fusion transcripts in pediatric sarcomas. DESIGN Probe pairs for the most common pediatric sarcoma fusion transcripts were designed for the assay. The NanoString assay was used to test 22 specific fusion transcripts in 45 sarcoma samples that had exhibited one of these fusion genes previously by reverse transcription polymerase chain reaction (RT-PCR). A mixture of frozen (n = 18), formalin-fixed, paraffin-embedded (FFPE) tissue (n = 23), and rapid extract template (n = 4) were used for testing. RESULTS Each of the 22 transcripts tested was detected in at least one of the 45 tumor samples. The results of the NanoString assay were 100% concordant with the previous RT-PCR results for the tumor samples, and the technique was successful using both FFPE and rapid extract method. CONCLUSION Multiplexed interrogation for sarcoma-specific fusion transcripts using NanoString technology is a reliable approach for molecular diagnosis of pediatric sarcomas and works well with FFPE tissues. Future work will involve validating additional sarcoma fusion transcripts as well as determining the optimal workflow for diagnostic purposes.
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Affiliation(s)
- Javal Sheth
- 1 Division of Pathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anthony Arnoldo
- 1 Division of Pathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yunan Zhong
- 1 Division of Pathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Paula Marrano
- 1 Division of Pathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Carlos Pereira
- 1 Division of Pathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Scott Ryall
- 2 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Paul Thorner
- 1 Division of Pathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada.,2 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- 1 Division of Pathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada.,2 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Gino R Somers
- 1 Division of Pathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada.,2 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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29
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Lindén M, Thomsen C, Grundevik P, Jonasson E, Andersson D, Runnberg R, Dolatabadi S, Vannas C, Luna Santamarίa M, Fagman H, Ståhlberg A, Åman P. FET family fusion oncoproteins target the SWI/SNF chromatin remodeling complex. EMBO Rep 2019; 20:embr.201845766. [PMID: 30962207 PMCID: PMC6500973 DOI: 10.15252/embr.201845766] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/06/2019] [Accepted: 03/11/2019] [Indexed: 12/15/2022] Open
Abstract
Members of the human FET family of RNA‐binding proteins, comprising FUS, EWSR1, and TAF15, are ubiquitously expressed and engage at several levels of gene regulation. Many sarcomas and leukemias are characterized by the expression of fusion oncogenes with FET genes as 5′ partners and alternative transcription factor‐coding genes as 3′ partners. Here, we report that the N terminus of normal FET proteins and their oncogenic fusion counterparts interact with the SWI/SNF chromatin remodeling complex. In contrast to normal FET proteins, increased fractions of FET oncoproteins bind SWI/SNF, indicating a deregulated and enhanced interaction in cancer. Forced expression of FET oncogenes caused changes of global H3K27 trimethylation levels, accompanied by altered gene expression patterns suggesting a shift in the antagonistic balance between SWI/SNF and repressive polycomb group complexes. Thus, deregulation of SWI/SNF activity could provide a unifying pathogenic mechanism for the large group of tumors caused by FET fusion oncoproteins. These results may help to develop common strategies for therapy.
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Affiliation(s)
- Malin Lindén
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christer Thomsen
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pernilla Grundevik
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Emma Jonasson
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Andersson
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Rikard Runnberg
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Soheila Dolatabadi
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christoffer Vannas
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Manuel Luna Santamarίa
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Henrik Fagman
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anders Ståhlberg
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden .,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Pierre Åman
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden .,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
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30
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Dolatabadi S, Jonasson E, Lindén M, Fereydouni B, Bäcksten K, Nilsson M, Martner A, Forootan A, Fagman H, Landberg G, Åman P, Ståhlberg A. JAK-STAT signalling controls cancer stem cell properties including chemotherapy resistance in myxoid liposarcoma. Int J Cancer 2019; 145:435-449. [PMID: 30650179 PMCID: PMC6590236 DOI: 10.1002/ijc.32123] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 12/03/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022]
Abstract
Myxoid liposarcoma (MLS) shows extensive intratumoural heterogeneity with distinct subpopulations of tumour cells. Despite improved survival of MLS patients, existing therapies have shortcomings as they fail to target all tumour cells. The nature of chemotherapy‐resistant cells in MLS remains unknown. Here, we show that MLS cell lines contained subpopulations of cells that can form spheres, efflux Hoechst dye and resist doxorubicin, all properties attributed to cancer stem cells (CSCs). By single‐cell gene expression, western blot, phospho‐kinase array, immunoprecipitation, immunohistochemistry, flow cytometry and microarray analysis we showed that a subset of MLS cells expressed JAK–STAT genes with active signalling. JAK1/2 inhibition via ruxolitinib decreased, while stimulation with LIF increased, phosphorylation of STAT3 and the number of cells with CSC properties indicating that JAK–STAT signalling controlled the number of cells with CSC features. We also show that phosphorylated STAT3 interacted with the SWI/SNF complex. We conclude that MLS contains JAK–STAT‐regulated subpopulations of cells with CSC features. Combined doxorubicin and ruxolitinib treatment targeted both proliferating cells as well as cells with CSC features, providing new means to circumvent chemotherapy resistance in treatment of MLS patients. What's new? Despite improved survival of patients, existing therapies for Myxoid liposarcoma (MLS) present shortcomings as they fail to target all tumour cells. The nature of chemotherapy‐resistant cells in MLS remains unknown, however. Here, the authors show that myxoid liposarcomas are heterogeneous and contain subpopulations of cells with stem cell properties, including chemotherapy resistance. Moreover, JAK‐STAT signalling is active in MLS and regulates the size of the cancer stem cells‐like subpopulation via the SWI/SNF complex. The results shed light on the mechanisms of therapy resistance in MLS and point to JAK‐STAT inhibitors as a new avenue for targeted MLS therapies.
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Affiliation(s)
- Soheila Dolatabadi
- Sahlgrenska Cancer Center, Department of Pathology and GeneticsInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Emma Jonasson
- Sahlgrenska Cancer Center, Department of Pathology and GeneticsInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Malin Lindén
- Sahlgrenska Cancer Center, Department of Pathology and GeneticsInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Bentolhoda Fereydouni
- Sahlgrenska Cancer Center, Department of Pathology and GeneticsInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Karin Bäcksten
- Sahlgrenska Cancer Center, Department of Pathology and GeneticsInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Malin Nilsson
- TIMM Laboratory, Sahlgrenska Cancer CenterUniversity of GothenburgGothenburgSweden
| | - Anna Martner
- TIMM Laboratory, Sahlgrenska Cancer CenterUniversity of GothenburgGothenburgSweden
| | - Amin Forootan
- Sahlgrenska Cancer Center, Department of Pathology and GeneticsInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
- MultiD Analysis ABGothenburgSweden
| | - Henrik Fagman
- Sahlgrenska Cancer Center, Department of Pathology and GeneticsInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
- Department of Clinical Pathology and GeneticsSahlgrenska University HospitalGothenburgSweden
| | - Göran Landberg
- Sahlgrenska Cancer Center, Department of Pathology and GeneticsInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Pierre Åman
- Sahlgrenska Cancer Center, Department of Pathology and GeneticsInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Anders Ståhlberg
- Sahlgrenska Cancer Center, Department of Pathology and GeneticsInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
- Department of Clinical Pathology and GeneticsSahlgrenska University HospitalGothenburgSweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of GothenburgGothenburgSweden
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31
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Xu J, Du Y, Liu WJ, Li L, Li Y, Wang XF, Yi HF, Shan CK, Xia GM, Liu XJ, Zhen YS. Intensive fibrosarcoma-binding capability of the reconstituted analog and its antitumor activity. Drug Deliv 2018; 25:102-111. [PMID: 29250984 PMCID: PMC6058573 DOI: 10.1080/10717544.2017.1410261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Fibrosarcomas are highly aggressive malignant tumors. It is urgently needed to explore targeted drugs and modalities for more effective therapy. Matrix metalloproteinases (MMPs) play important roles in tumor progression and metastasis, while several MMPs are highly expressed in fibrosarcomas. In addition, tissue inhibitor of metalloproteinase 2 (TIMP2) displays specific interaction with MMPs. Therefore, TIMP2 may play an active role in the development of fibrosarcoma-targeting agents. In the current study, a TIMP2-based recombinant protein LT and its enediyne-integrated analog LTE were prepared; furthermore, the fibrosarcoma-binding intensity and antitumor activity were investigated. As shown, intense and selective binding capability of the protein LT to human fibrosarcoma specimens was confirmed by tissue microarray. Moreover, LTE, the enediyne-integrated analog of LT, exerted highly potent cytotoxicity to fibrosarcoma HT1080 cells, induced apoptosis, and caused G2/M arrest. LTE at 0.1 nM markedly suppressed the migration and invasion of HT1080 cells. LTE at tolerated dose of 0.6 mg/kg inhibited the tumor growth of fibrosarcoma xenograft in athymic mice. The study provides evidence that the TIMP2-based reconstituted analog LTE may be useful as a targeted drug for fibrosarcome therapy.
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Affiliation(s)
- Jian Xu
- a Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Yue Du
- a Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Wen-Juan Liu
- a Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China.,b Shandong Provincial Key Laboratory of Radiation Oncology , Shandong Cancer Hospital and Institute, Shandong Cancer Hospital affiliated to Shandong University Shandong Academy of Medical Sciences , Jinan , China
| | - Liang Li
- a Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Yi Li
- a Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Xiao-Fei Wang
- a Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Hong-Fei Yi
- c West China Hospital, Sichuan University and Collaborative Innovation Center , Chengdu , China
| | - Chuan-Kun Shan
- a Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Gui-Min Xia
- a Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Xiu-Jun Liu
- a Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Yong-Su Zhen
- a Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
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32
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Xiong D, Wu YB, Jin C, Li JJ, Gu J, Liao YF, Long X, Zhu SQ, Wu HB, Xu JJ, Ding JY. Elevated FUS/TLS expression is negatively associated with E-cadherin expression and prognosis of patients with non-small cell lung cancer. Oncol Lett 2018; 16:1791-1800. [PMID: 30008867 DOI: 10.3892/ol.2018.8816] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 11/23/2017] [Indexed: 01/02/2023] Open
Abstract
Fused in sarcoma/translocated in liposarcoma (FUS/TLS), a ubiquitous and multifunctional DNA and RNA-binding protein, contributes an important function in cancer and neurodegenerative disease; however, its role in lung cancer remains unclear. In the present study, the expression of FUS/TLS in non-small cell lung cancer (NSCLC) and the significance of FUS/TLS for predicting the clinical outcome of patients with NSCLC, was examined. FUS/TLS expression was investigated in NSCLC tissues and their matched adjacent non-tumorous tissues by reverse transcription-quantitative polymerase chain reaction, western blotting, and immunohistochemistry. Tissue microarrays representing 208 patients with NSCLC were used to determine the expression pattern and associations with FUS/TLS using immunohistochemistry. Prognostic significance was assessed by Kaplan-Meier survival estimates and log-rank tests. Data revealed that FUS/TLS expression was elevated in NSCLC tissues compared with corresponding normal tissue mRNA (9.27±0.73 vs. 6.15±0.60) and protein (3.32±0.75 vs. 0.30±0.07) levels. In tissue microarrays, FUS/TLS was highly expressed in 103 (49.5%, 103/208) NSCLC tissues compared with adjacent normal lung tissues (28.4%, 59/208). Overexpression of FUS/TLS was associated with higher tumor node metastasis stage (P=0.016), poorer differentiation (P=0.008), large tumor size (P=0.019) and predicted poor prognosis (P=0.005) in patients with NSCLC. Notably, correlation analysis revealed a significant inverse association between the expression of FUS/TLS and E-cadherin (r2=0.51; P=0.036). Furthermore, patients with NSCLC with high FUS/TLS and impaired E-cadherin expression had a notably poor prognosis (P=4.01×10-4). Thus, the results from the present study indicate that elevated FUS/TLS expression promotes NSCLC progression. FUS/TLS, alone or in combination with E-cadherin, is a novel prognostic predictor for patients with NSCLC.
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Affiliation(s)
- Dian Xiong
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China.,Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Yong-Bing Wu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Chun Jin
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Ji-Jun Li
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China.,Department of Cardio-Thoracic Surgery, Kashgar Prefecture Second People's Hospital, Kashgar, Xinjiang 844000, P.R. China
| | - Jie Gu
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Yun-Fei Liao
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Xiang Long
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Shu-Qiang Zhu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Hai-Bo Wu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Jian-Jun Xu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Jian-Yong Ding
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
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33
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Gorthi A, Romero JC, Loranc E, Cao L, Lawrence LA, Goodale E, Iniguez AB, Bernard X, Masamsetti VP, Roston S, Lawlor ER, Toretsky JA, Stegmaier K, Lessnick SL, Chen Y, Bishop AJR. EWS-FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma. Nature 2018; 555:387-391. [PMID: 29513652 PMCID: PMC6318124 DOI: 10.1038/nature25748] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/11/2018] [Indexed: 02/06/2023]
Abstract
Ewing sarcoma is an aggressive paediatric cancer of the bone and soft tissue. It results from a chromosomal translocation, predominantly t(11;22)(q24:q12), that fuses the N-terminal transactivation domain of the constitutively expressed EWSR1 protein with the C-terminal DNA binding domain of the rarely expressed FLI1 protein. Ewing sarcoma is highly sensitive to genotoxic agents such as etoposide, but the underlying molecular basis of this sensitivity is unclear. Here we show that Ewing sarcoma cells display alterations in regulation of damage-induced transcription, accumulation of R-loops and increased replication stress. In addition, homologous recombination is impaired in Ewing sarcoma owing to an enriched interaction between BRCA1 and the elongating transcription machinery. Finally, we uncover a role for EWSR1 in the transcriptional response to damage, suppressing R-loops and promoting homologous recombination. Our findings improve the current understanding of EWSR1 function, elucidate the mechanistic basis of the sensitivity of Ewing sarcoma to chemotherapy (including PARP1 inhibitors) and highlight a class of BRCA-deficient-like tumours.
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Affiliation(s)
- Aparna Gorthi
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
| | - July Carolina Romero
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
| | - Eva Loranc
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
| | - Lin Cao
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
| | - Liesl A Lawrence
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
| | - Elicia Goodale
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
| | - Amanda Balboni Iniguez
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Xavier Bernard
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
| | - V Pragathi Masamsetti
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
| | - Sydney Roston
- Departments of Oncology and Pediatrics, Georgetown University, Washington DC 20057, USA
| | - Elizabeth R Lawlor
- Departments of Pediatrics and Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jeffrey A Toretsky
- Departments of Oncology and Pediatrics, Georgetown University, Washington DC 20057, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
- Mays Cancer Center, University of Texas Health at San Antonio, Texas 78229, USA
- Department of Epidemiology and Biostatistics, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
| | - Alexander J R Bishop
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, Texas 78229, USA
- Mays Cancer Center, University of Texas Health at San Antonio, Texas 78229, USA
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34
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Svetoni F, De Paola E, La Rosa P, Mercatelli N, Caporossi D, Sette C, Paronetto MP. Post-transcriptional regulation of FUS and EWS protein expression by miR-141 during neural differentiation. Hum Mol Genet 2018; 26:2732-2746. [PMID: 28453628 DOI: 10.1093/hmg/ddx160] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/21/2017] [Indexed: 12/31/2022] Open
Abstract
Brain development involves proliferation, migration and specification of neural progenitor cells, culminating in neuronal circuit formation. Mounting evidence indicates that improper regulation of RNA binding proteins (RBPs), including members of the FET (FUS, EWS, TAF15) family, results in defective cortical development and/or neurodegenerative disorders. However, in spite of their physiological relevance, the precise pattern of FET protein expression in developing neurons is largely unknown. Herein, we found that FUS, EWS and TAF15 expression is differentially regulated during brain development, both in time and in space. In particular, our study identifies a fine-tuned regulation of FUS and EWS during neuronal differentiation, whereas TAF15 appears to be more constitutively expressed. Mechanistically FUS and EWS protein expression is regulated at the post-transcriptional level during neuron differentiation and brain development. Moreover, we identified miR-141 as a key regulator of these FET proteins that modulate their expression levels in differentiating neuronal cells. Thus, our studies uncover a novel link between post-transcriptional regulation of FET proteins expression and neurogenesis.
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Affiliation(s)
- Francesca Svetoni
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Elisa De Paola
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Piergiorgio La Rosa
- Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Neri Mercatelli
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Daniela Caporossi
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy
| | - Claudio Sette
- Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
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35
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Identification of inhibitors regulating cell proliferation and FUS-DDIT3 expression in myxoid liposarcoma using combined DNA, mRNA, and protein analyses. J Transl Med 2018; 98:957-967. [PMID: 29588491 PMCID: PMC6070472 DOI: 10.1038/s41374-018-0046-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 02/13/2018] [Accepted: 02/20/2018] [Indexed: 12/22/2022] Open
Abstract
FUS-DDIT3 belongs to the FET (FUS, EWSR1, and TAF15) family of fusion oncogenes, which collectively are considered to be key players in tumor development. Even though over 90% of all myxoid liposarcomas (MLS) have a FUS-DDIT3 gene fusion, there is limited understanding of the signaling pathways that regulate its expression. In order to study cell proliferation and FUS-DDIT3 regulation at mRNA and protein levels, we first developed a direct cell lysis approach that allows DNA, mRNA, and protein to be analyzed in the same sample using quantitative PCR, reverse transcription quantitative qPCR and proximity ligation assay, respectively. We screened 70 well-characterized kinase inhibitors and determined their effects on cell proliferation and expression of FUS-DDIT3 and FUS at both mRNA and protein levels in the MLS 402-91 cell line, where twelve selected inhibitors were evaluated further in two additional MLS cell lines. Both FUS-DDIT3 and FUS mRNA expression correlated with cell proliferation and both transcripts were co-regulated in most conditions, indicating that the common 5' FUS promotor is important in transcriptional regulation. In contrast, FUS-DDIT3 and FUS protein levels displayed more cell line dependent expression. Furthermore, most JAK inhibitors caused FUS-DDIT3 downregulation at both mRNA and protein levels. In conclusion, defining factors that regulate FUS-DDIT3 expression opens new means to understand MLS development at the molecular level.
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36
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Janke AM, Seo DH, Rahmanian V, Conicella AE, Mathews KL, Burke KA, Mittal J, Fawzi NL. Lysines in the RNA Polymerase II C-Terminal Domain Contribute to TAF15 Fibril Recruitment. Biochemistry 2017; 57:2549-2563. [PMID: 28945358 DOI: 10.1021/acs.biochem.7b00310] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many cancer-causing chromosomal translocations result in transactivating protein products encoding FET family (FUS, EWSR1, TAF15) low-complexity (LC) domains fused to a DNA binding domain from one of several transcription factors. Recent work demonstrates that higher-order assemblies of FET LC domains bind the carboxy-terminal domain of the large subunit of RNA polymerase II (RNA pol II CTD), suggesting FET oncoproteins may mediate aberrant transcriptional activation by recruiting RNA polymerase II to promoters of target genes. Here we use nuclear magnetic resonance (NMR) spectroscopy and hydrogel fluorescence microscopy localization and fluorescence recovery after photobleaching to visualize atomic details of a model of this process, interactions of RNA pol II CTD with high-molecular weight TAF15 LC assemblies. We report NMR resonance assignments of the intact degenerate repeat half of human RNA pol II CTD alone and verify its predominant intrinsic disorder by molecular simulation. By measuring NMR spin relaxation and dark-state exchange saturation transfer, we characterize the interaction of RNA pol II CTD with amyloid-like hydrogel fibrils of TAF15 and hnRNP A2 LC domains and observe that heptads far from the acidic C-terminal tail of RNA pol II CTD bind TAF15 fibrils most avidly. Mutation of CTD lysines in heptad position 7 to consensus serines reduced the overall level of TAF15 fibril binding, suggesting that electrostatic interactions contribute to complex formation. Conversely, mutations of position 7 asparagine residues and truncation of the acidic tail had little effect. Thus, weak, multivalent interactions between TAF15 fibrils and heptads throughout RNA pol II CTD collectively mediate complex formation.
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Affiliation(s)
- Abigail M Janke
- Department of Molecular Pharmacology, Physiology, and Biotechnology , Brown University , Providence , Rhode Island 02921 , United States
| | - Da Hee Seo
- Department of Molecular Pharmacology, Physiology, and Biotechnology , Brown University , Providence , Rhode Island 02921 , United States
| | - Vahid Rahmanian
- Department of Chemical and Biomolecular Engineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Alexander E Conicella
- Graduate Program in Molecular Biology, Cell Biology and Biochemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Kaylee L Mathews
- Graduate Program in Molecular Biology, Cell Biology and Biochemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Kathleen A Burke
- Department of Molecular Pharmacology, Physiology, and Biotechnology , Brown University , Providence , Rhode Island 02921 , United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology , Brown University , Providence , Rhode Island 02921 , United States.,Graduate Program in Molecular Biology, Cell Biology and Biochemistry , Brown University , Providence , Rhode Island 02912 , United States
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37
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Degrauwe N, Suvà ML, Janiszewska M, Riggi N, Stamenkovic I. IMPs: an RNA-binding protein family that provides a link between stem cell maintenance in normal development and cancer. Genes Dev 2017; 30:2459-2474. [PMID: 27940961 PMCID: PMC5159662 DOI: 10.1101/gad.287540.116] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review by Degrauwe et al. summarizes our current understanding of the functions of IMPs during normal development and focuses on a series of recent observations that have provided new insight into how their physiological functions enable IMPs to play a potentially key role in cancer stem cell maintenance and tumor growth. IMPs, also known as insulin-like growth factor 2 (IGF2) messenger RNA (mRNA)-binding proteins (IGF2BPs), are highly conserved oncofetal RNA-binding proteins (RBPs) that regulate RNA processing at several levels, including localization, translation, and stability. Three mammalian IMP paralogs (IMP1–3) have been identified that are expressed in most organs during embryogenesis, where they are believed to play an important role in cell migration, metabolism, and stem cell renewal. Whereas some IMP2 expression is retained in several adult mouse organs, IMP1 and IMP3 are either absent or expressed at very low levels in most tissues after birth. However, all three paralogs can be re-expressed upon malignant transformation and are found in a broad range of cancer types where their expression often correlates with poor prognosis. IMPs appear to resume their physiological functions in malignant cells, which not only contribute to tumor progression but participate in the establishment and maintenance of tumor cell hierarchies. This review summarizes our current understanding of the functions of IMPs during normal development and focuses on a series of recent observations that have provided new insight into how their physiological functions enable IMPs to play a potentially key role in cancer stem cell maintenance and tumor growth.
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Affiliation(s)
- Nils Degrauwe
- Department of Medicine, Centre Hospitalier Universitaire Vaudois/University of Lausanne, Lausanne CH-1011, Switzerland
| | - Mario-Luca Suvà
- Molecular Pathology Unit, Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129, USA
| | - Michalina Janiszewska
- Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Nicolo Riggi
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois/University of Lausanne, Lausanne CH-1011, Switzerland
| | - Ivan Stamenkovic
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois/University of Lausanne, Lausanne CH-1011, Switzerland
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38
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Li T, Zhang F, Cao Y, Ning S, Bi Y, Xue W, Ren L. Primary Ewing's sarcoma/primitive neuroectodermal tumor of the ileum: case report of a 16-year-old Chinese female and literature review. Diagn Pathol 2017; 12:37. [PMID: 28472972 PMCID: PMC5418692 DOI: 10.1186/s13000-017-0626-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/17/2017] [Indexed: 12/21/2022] Open
Abstract
Background Ewing’s sarcoma (ES) and primitive neuroectodermal tumors (PNET) are closely related tumors. Although soft tissue ES/PNET are common in clinical practice, they are rare in the small intestine. Because of the absence of characteristic clinical symptoms, they are easily misdiagnosed as other benign or malignant diseases. Case presentation Here, we present the case of a 16-year-old female who complained of anemia and interval hematochezia. Her serum test results showed only a slight elevation of CA-125 and a low level of hemoglobin. Computer tomography and magnetic resonance imaging revealed a cystic and solid mass in the lower abdominal quadrant and pelvic region, which prompted suspicion of a malignant gastrointestinal stromal tumor of the small intestine. After resection, the tumor’s histology and immunohistochemistry (positive for CD99, vimentin and synaptophysin) results suggested ES/PNET. Fluorescent in situ hybridization tests proved the breakpoint rearrangement of the EWSR1 gene in chr 22.Ultrastructural analysis revealed neurosecretory and glycogen granules in the tumor cell cytoplasm. Conclusions Together, these data supported the diagnosis of a rare case of localized ES/PNET in the small intestine without adjuvant chemo- or radiotherapy. To our knowledge, this is the first report from China of a primary small bowel ES/PNET in the English-language literature. In addition, on the basis of findings from previous publications and the current case, the optimal treatment for localized gastrointestinal ES/PNET is discussed.
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Affiliation(s)
- Teng Li
- Department of Pathology, The General Hospital of Air force, PLA, Fucheng Road 30th, Beijing, China
| | - Fang Zhang
- Department of Pathology, The General Hospital of Air force, PLA, Fucheng Road 30th, Beijing, China
| | - Yarui Cao
- Department of Pathology, The General Hospital of Air force, PLA, Fucheng Road 30th, Beijing, China
| | - Shoubin Ning
- Department of Gastroenterology, The General Hospital of Air force, PLA, Fucheng Road 30th, Beijing, China
| | - Yongmin Bi
- Department of Radio and Imaging, The General Hospital of Air force, PLA, Fucheng Road 30th, Beijing, China
| | - Weicheng Xue
- Department of Pathology, Beijing Cancer Hospital, Fucheng Road 52nd, Beijing, China
| | - Li Ren
- Department of Pathology, The General Hospital of Air force, PLA, Fucheng Road 30th, Beijing, China.
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39
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Autophagy as a potential target for sarcoma treatment. Biochim Biophys Acta Rev Cancer 2017; 1868:40-50. [PMID: 28242349 DOI: 10.1016/j.bbcan.2017.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/23/2017] [Accepted: 02/23/2017] [Indexed: 02/05/2023]
Abstract
Autophagy is a constitutively active, evolutionary conserved, catabolic process for maintaining homeostasis in cellular stress responses and cell survival. Although its mechanism has not been fully illustrated, recent work on autophagy in various types of sarcomas has demonstrated that autophagy exerts an important role in sarcoma cell growth and proliferation, in pro-survival response to therapies and stresses, and in therapeutic resistance of sarcoma. Thus, the autophagic process is being seen as a possibly novel therapeutic target of sarcoma. Additionally, some co-regulators of autophagy have also been investigated as promising biomarkers for the diagnosis and prognosis of sarcoma. In this review, we summarize contemporary advances in the role of autophagy in sarcoma and discuss the potential of autophagy as a new target for sarcoma treatment.
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40
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Loke BN, Lee VKM, Sudhanshi J, Wong MK, Kuick CH, Puhaindran M, Chang KTE. Novel exon–exon breakpoint inCIC-DUX4fusion sarcoma identified by anchored multiplex PCR (Archer FusionPlex Sarcoma Panel). J Clin Pathol 2017; 70:697-701. [DOI: 10.1136/jclinpath-2016-204247] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/26/2022]
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Abstract
Better diagnostic biomarkers and therapeutic options are still necessary for patients with sarcomas due to the current limitations of diagnosis and treatment. Exosomes are small extracellular membrane vesicles that are released by various cells and are found in most body fluids. Tumor-derived exosomes have been proven to mediate tumorigenesis, intercellular communication, microenvironment modulation, and metastasis in different cancers, including in sarcomas. Recently, exosomes have been considered as potential biomarkers for sarcoma diagnosis and prognosis, and as possible targets for sarcoma therapy. Moreover, due to their specific cell tropism and bioavailability, exosomes can also be engineered as vehicles for drug delivery. In this review, we discuss recent advances in the roles of tumor-derived exosomes in sarcoma and their potential clinical applications.
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Åman P, Dolatabadi S, Svec D, Jonasson E, Safavi S, Andersson D, Grundevik P, Thomsen C, Ståhlberg A. Regulatory mechanisms, expression levels and proliferation effects of the FUS-DDIT3 fusion oncogene in liposarcoma. J Pathol 2016; 238:689-99. [PMID: 26865464 DOI: 10.1002/path.4700] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/06/2016] [Accepted: 02/01/2016] [Indexed: 12/28/2022]
Abstract
Fusion oncogenes are among the most common types of oncogene in human cancers. The gene rearrangements result in new combinations of regulatory elements and functional protein domains. Here we studied a subgroup of sarcomas and leukaemias characterized by the FET (FUS, EWSR1, TAF15) family of fusion oncogenes, including FUS-DDIT3 in myxoid liposarcoma (MLS). We investigated the regulatory mechanisms, expression levels and effects of FUS-DDIT3 in detail. FUS-DDIT3 showed a lower expression than normal FUS at both the mRNA and protein levels, and single-cell analysis revealed a lack of correlation between FUS-DDIT3 and FUS expression. FUS-DDIT3 transcription was regulated by the FUS promotor, while its mRNA stability depended on the DDIT3 sequence. FUS-DDIT3 protein stability was regulated by protein interactions through the FUS part, rather than the leucine zipper containing DDIT3 part. In addition, in vitro as well as in vivo FUS-DDIT3 protein expression data displayed highly variable expression levels between individual MLS cells. Combined mRNA and protein analyses at the single-cell level showed that FUS-DDIT3 protein expression was inversely correlated to the expression of cell proliferation-associated genes. We concluded that FUS-DDIT3 is uniquely regulated at the transcriptional as well as the post-translational level and that its expression level is important for MLS tumour development. The FET fusion oncogenes are potentially powerful drug targets and detailed knowledge about their regulation and functions may help in the development of novel treatments.
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Cell Proliferation
- Gene Expression Regulation, Neoplastic
- Half-Life
- Humans
- Liposarcoma, Myxoid/genetics
- Liposarcoma, Myxoid/metabolism
- Liposarcoma, Myxoid/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic
- Protein Binding
- Protein Processing, Post-Translational
- Protein Stability
- RNA Stability
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Signal Transduction
- Time Factors
- Transcription, Genetic
- Transfection
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Affiliation(s)
- Pierre Åman
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Soheila Dolatabadi
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - David Svec
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Emma Jonasson
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Setareh Safavi
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Daniel Andersson
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Pernilla Grundevik
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Christer Thomsen
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Cancer Centre, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Sweden
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43
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Preusse M, Marr C, Saunders S, Maticzka D, Lickert H, Backofen R, Theis F. SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins. RNA Biol 2016; 12:998-1009. [PMID: 26383775 PMCID: PMC4615630 DOI: 10.1080/15476286.2015.1068496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
microRNAs and microRNA-independent RNA-binding proteins are 2 classes of post-transcriptional regulators that have been shown to cooperate in gene-expression regulation. We compared the genome-wide target sets of microRNAs and RBPs identified by recent CLIP-Seq technologies, finding that RBPs have distinct target sets and favor gene interaction network hubs. To identify microRNAs and RBPs with a similar functional context, we developed simiRa, a tool that compares enriched functional categories such as pathways and GO terms. We applied simiRa to the known functional cooperation between Pumilio family proteins and miR-221/222 in the regulation of tumor supressor gene p27 and show that the cooperation is reflected by similar enriched categories but not by target genes. SimiRa also predicts possible cooperation of microRNAs and RBPs beyond direct interaction on the target mRNA for the nuclear RBP TAF15. To further facilitate research into cooperation of microRNAs and RBPs, we made simiRa available as a web tool that displays the functional neighborhood and similarity of microRNAs and RBPs: http://vsicb-simira.helmholtz-muenchen.de.
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Affiliation(s)
- Martin Preusse
- a Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Computational Biology ; Neuherberg , Germany.,b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany
| | - Carsten Marr
- a Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Computational Biology ; Neuherberg , Germany
| | - Sita Saunders
- c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany
| | - Daniel Maticzka
- c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany
| | - Heiko Lickert
- b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany.,d Medical Faculty; Technische Universität München ; Munich , Germany
| | - Rolf Backofen
- c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany.,e BIOSS Center for Biological Signaling Studies; Cluster of Excellence; University of Freiburg ; Freiburg , Germany
| | - Fabian Theis
- b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany.,f Technische Universität München; Center for Mathematics; Chair of Mathematical Modeling of Biological Systems ; Garching , Germany
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44
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Jadhav S, Ajay AK, Trivedi P, Seematti J, Pellegrini K, Craciun F, Vaidya VS. RNA-binding Protein Musashi Homologue 1 Regulates Kidney Fibrosis by Translational Inhibition of p21 and Numb mRNA. J Biol Chem 2016; 291:14085-14094. [PMID: 27129280 DOI: 10.1074/jbc.m115.713289] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Indexed: 11/06/2022] Open
Abstract
RNA-binding proteins (RBPs) are recognized as key posttranscriptional regulators that not only modulate the spatiotemporal expression of genes during organism development but also regulate disease pathogenesis. Very limited information exists on the potential role of RBPs in modulating kidney fibrosis, which is a major hallmark of chronic kidney disease. Here, we report a novel mechanism in kidney fibrosis involving a RBP, Musashi homologue 1 (Msi1), which is expressed in tubular epithelial cells. Using two mechanistically distinct mouse models of kidney fibrosis, we show that Msi1 protein levels are significantly down-regulated in the kidneys following fibrosis. We found that Msi1 functions by negatively regulating the translation of its target mRNAs, p21 and Numb, whose protein levels are markedly increased in kidney fibrosis. Also, Msi1 overexpression and knockdown in kidney epithelial cells cause p21- and Numb-mediated cell cycle arrest. Furthermore, we observed that Numb looses its characteristic membrane localization in fibrotic kidneys and therefore is likely unable to inhibit Notch resulting in tubular cell death. Oleic acid is a known inhibitor of Msi1 and injecting oleic acid followed by unilateral ureteral obstruction surgery in mice resulted in enhanced fibrosis compared with the control group, indicating that inhibiting Msi1 activity renders the mice more susceptible to fibrosis. Given that deregulated fatty acid metabolism plays a key role in kidney fibrosis, these results demonstrate a novel connection between fatty acid and Msi1, an RNA-binding protein, in kidney fibrosis.
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Affiliation(s)
- Shreyas Jadhav
- Department of Medicine, Renal Division, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Amrendra K Ajay
- Department of Medicine, Renal Division, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Priyanka Trivedi
- Department of Medicine, Renal Division, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Jenifer Seematti
- Department of Medicine, Renal Division, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Kathryn Pellegrini
- Department of Medicine, Renal Division, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Florin Craciun
- Department of Medicine, Renal Division, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Vishal S Vaidya
- Department of Medicine, Renal Division, Brigham and Women's Hospital, Boston, Massachusetts 02115,; Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, Massachusetts 02115; Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115.
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45
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Lye KL, Nordin N, Vidyadaran S, Thilakavathy K. Mesenchymal stem cells: From stem cells to sarcomas. Cell Biol Int 2016; 40:610-8. [PMID: 26992453 DOI: 10.1002/cbin.10603] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/14/2016] [Indexed: 12/15/2022]
Abstract
Mesenchymal stem cells (MSCs) have garnered vast interests in clinical settings, especially in regenerative medicine due to their unique properties-they are reliably isolated and expanded from various tissue sources; they are able to differentiate into mesodermal tissues such as bones, cartilages, adipose tissues, and muscles; and they have unique immunosuppressive properties. However, there are some concerns pertaining to the role of MSCs in the human body. On one hand, they are crucial component in the regeneration and repair of the human body. On the contrary, they are shown to transform into sarcomas. Although the exact mechanisms are still unknown, many new leads have pointed to the belief that MSCs do play a role in sarcomagenesis. This review focuses on the current updates and findings of the role of MSCs in their transformation process into sarcomas.
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Affiliation(s)
- Kwan Liang Lye
- Medical Genetics Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Norshariza Nordin
- Medical Genetics Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Sharmili Vidyadaran
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Karuppiah Thilakavathy
- Medical Genetics Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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46
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Xiang S, Kato M, Wu LC, Lin Y, Ding M, Zhang Y, Yu Y, McKnight SL. The LC Domain of hnRNPA2 Adopts Similar Conformations in Hydrogel Polymers, Liquid-like Droplets, and Nuclei. Cell 2016; 163:829-39. [PMID: 26544936 DOI: 10.1016/j.cell.2015.10.040] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/25/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
Abstract
Many DNA and RNA regulatory proteins contain polypeptide domains that are unstructured when analyzed in cell lysates. These domains are typified by an over-representation of a limited number of amino acids and have been termed prion-like, intrinsically disordered or low-complexity (LC) domains. When incubated at high concentration, certain of these LC domains polymerize into labile, amyloid-like fibers. Here, we report methods allowing the generation of a molecular footprint of the polymeric state of the LC domain of hnRNPA2. By deploying this footprinting technique to probe the structure of the native hnRNPA2 protein present in isolated nuclei, we offer evidence that its LC domain exists in a similar conformation as that described for recombinant polymers of the protein. These observations favor biologic utility to the polymerization of LC domains in the pathway of information transfer from gene to message to protein.
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Affiliation(s)
- Siheng Xiang
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Leeju C Wu
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yi Lin
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ming Ding
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yajie Zhang
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yonghao Yu
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
| | - Steven L McKnight
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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47
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Liu T, Shen JK, Li Z, Choy E, Hornicek FJ, Duan Z. Development and potential applications of CRISPR-Cas9 genome editing technology in sarcoma. Cancer Lett 2016; 373:109-118. [PMID: 26806808 DOI: 10.1016/j.canlet.2016.01.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 02/07/2023]
Abstract
Sarcomas include some of the most aggressive tumors and typically respond poorly to chemotherapy. In recent years, specific gene fusion/mutations and gene over-expression/activation have been shown to drive sarcoma pathogenesis and development. These emerging genomic alterations may provide targets for novel therapeutic strategies and have the potential to transform sarcoma patient care. The RNA-guided nuclease CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein-9 nuclease) is a convenient and versatile platform for site-specific genome editing and epigenome targeted modulation. Given that sarcoma is believed to develop as a result of genetic alterations in mesenchymal progenitor/stem cells, CRISPR-Cas9 genome editing technologies hold extensive application potentials in sarcoma models and therapies. We review the development and mechanisms of the CRISPR-Cas9 system in genome editing and introduce its application in sarcoma research and potential therapy in clinic. Additionally, we propose future directions and discuss the challenges faced with these applications, providing concise and enlightening information for readers interested in this area.
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Affiliation(s)
- Tang Liu
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States; Department of Orthopaedic, the 2nd Xiangya Hospital of Central South University, 139 Renmin Road, Changsha, Hunan 410011, China
| | - Jacson K Shen
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States
| | - Zhihong Li
- Department of Orthopaedic, the 2nd Xiangya Hospital of Central South University, 139 Renmin Road, Changsha, Hunan 410011, China
| | - Edwin Choy
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States
| | - Francis J Hornicek
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States
| | - Zhenfeng Duan
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States.
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48
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Aggregation of FET Proteins as a Pathological Change in Amyotrophic Lateral Sclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:1-12. [DOI: 10.1007/5584_2016_32] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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49
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Burke KA, Janke AM, Rhine CL, Fawzi NL. Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II. Mol Cell 2015; 60:231-41. [PMID: 26455390 DOI: 10.1016/j.molcel.2015.09.006] [Citation(s) in RCA: 626] [Impact Index Per Article: 69.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 08/10/2015] [Accepted: 08/31/2015] [Indexed: 12/14/2022]
Abstract
Phase-separated states of proteins underlie ribonucleoprotein (RNP) granules and nuclear RNA-binding protein assemblies that may nucleate protein inclusions associated with neurodegenerative diseases. We report that the N-terminal low-complexity domain of the RNA-binding protein Fused in Sarcoma (FUS LC) is structurally disordered and forms a liquid-like phase-separated state resembling RNP granules. This state directly binds the C-terminal domain of RNA polymerase II. Phase-separated FUS lacks static structures as probed by fluorescence microscopy, indicating they are distinct from both protein inclusions and hydrogels. We use solution nuclear magnetic resonance spectroscopy to directly probe the dynamic architecture within FUS liquid phase-separated assemblies. Importantly, we find that FUS LC retains disordered secondary structure even in the liquid phase-separated state. Therefore, we propose that disordered protein granules, even those made of aggregation-prone prion-like domains, are dynamic and disordered molecular assemblies with transiently formed protein-protein contacts.
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Affiliation(s)
- Kathleen A Burke
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Abigail M Janke
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Christy L Rhine
- Graduate Program in Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA.
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50
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Sarver AE, Sarver AL, Thayanithy V, Subramanian S. Identification, by systematic RNA sequencing, of novel candidate biomarkers and therapeutic targets in human soft tissue tumors. J Transl Med 2015; 95:1077-88. [PMID: 26121316 DOI: 10.1038/labinvest.2015.80] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/17/2015] [Accepted: 05/11/2015] [Indexed: 01/14/2023] Open
Abstract
Human sarcomas comprise a heterogeneous group of more than 50 subtypes broadly classified into two groups: bone and soft tissue sarcomas. Such heterogeneity and their relative rarity have made them challenging targets for classification, biomarker identification, and development of improved treatment strategies. In this study, we used RNA sequencing to analyze 35 primary human tissue samples representing 13 different sarcoma subtypes, along with benign schwannoma, and normal bone and muscle tissues. For each sarcoma subtype, we detected unique messenger RNA (mRNA) expression signatures, which we further subjected to bioinformatic functional analysis, upstream regulatory analysis, and microRNA (miRNA) targeting analysis. We found that, for each sarcoma subtype, significantly upregulated genes and their deduced upstream regulators included not only previously implicated known players but also novel candidates not previously reported to be associated with sarcoma. For example, the schwannoma samples were characterized by high expression of not only the known associated proteins GFAP and GAP43 but also the novel player GJB6. Further, when we integrated our expression profiles with miRNA expression data from each sarcoma subtype, we were able to deduce potential key miRNA-gene regulator relationships for each. In the Ewing's sarcoma and fibromatosis samples, two sarcomas where miR-182-5p is significantly downregulated, multiple predicted targets were significantly upregulated, including HMCN1, NKX2-2, SCNN1G, and SOX2. In conclusion, despite the small number of samples per sarcoma subtype, we were able to identify key known players; concurrently, we discovered novel genes that may prove to be important in the molecular classification of sarcomas and in the development of novel treatments.
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Affiliation(s)
- Anne E Sarver
- Division of Basic and Translational Research, Department of Surgery, University of Minnesota Medical School, University of Minnesota, Minneapolis, MN, USA
| | - Aaron L Sarver
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Venugopal Thayanithy
- Division of Basic and Translational Research, Department of Surgery, University of Minnesota Medical School, University of Minnesota, Minneapolis, MN, USA
| | - Subbaya Subramanian
- Division of Basic and Translational Research, Department of Surgery, University of Minnesota Medical School, University of Minnesota, Minneapolis, MN, USA
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