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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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2
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Wachtel M, Surdez D, Grünewald TGP, Schäfer BW. Functional Classification of Fusion Proteins in Sarcoma. Cancers (Basel) 2024; 16:1355. [PMID: 38611033 PMCID: PMC11010897 DOI: 10.3390/cancers16071355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Sarcomas comprise a heterogeneous group of malignant tumors of mesenchymal origin. More than 80 entities are associated with different mesenchymal lineages. Sarcomas with fibroblastic, muscle, bone, vascular, adipocytic, and other characteristics are distinguished. Nearly half of all entities contain specific chromosomal translocations that give rise to fusion proteins. These are mostly pathognomonic, and their detection by various molecular techniques supports histopathologic classification. Moreover, the fusion proteins act as oncogenic drivers, and their blockade represents a promising therapeutic approach. This review summarizes the current knowledge on fusion proteins in sarcoma. We categorize the different fusion proteins into functional classes, including kinases, epigenetic regulators, and transcription factors, and describe their mechanisms of action. Interestingly, while fusion proteins acting as transcription factors are found in all mesenchymal lineages, the others have a more restricted pattern. Most kinase-driven sarcomas belong to the fibroblastic/myofibroblastic lineage. Fusion proteins with an epigenetic function are mainly associated with sarcomas of unclear differentiation, suggesting that epigenetic dysregulation leads to a major change in cell identity. Comparison of mechanisms of action reveals recurrent functional modes, including antagonism of Polycomb activity by fusion proteins with epigenetic activity and recruitment of histone acetyltransferases by fusion transcription factors of the myogenic lineage. Finally, based on their biology, we describe potential approaches to block the activity of fusion proteins for therapeutic intervention. Overall, our work highlights differences as well as similarities in the biology of fusion proteins from different sarcomas and provides the basis for a functional classification.
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Affiliation(s)
- Marco Wachtel
- Department of Oncology and Children’s Research Center, University Children’s Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Didier Surdez
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), CH-8008 Zurich, Switzerland
| | - Thomas G. P. Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Hopp-Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership between DKFZ and Heidelberg University Hospital, 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Beat W. Schäfer
- Department of Oncology and Children’s Research Center, University Children’s Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
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3
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Beird HC, Wu CC, Nakazawa M, Ingram D, Daniele JR, Lazcano R, Little L, Davies C, Daw NC, Wani K, Wang WL, Song X, Gumbs C, Zhang J, Rubin B, Conley A, Flanagan AM, Lazar AJ, Futreal PA. Complete loss of TP53 and RB1 is associated with complex genome and low immune infiltrate in pleomorphic rhabdomyosarcoma. HGG ADVANCES 2023; 4:100224. [PMID: 37593416 PMCID: PMC10428123 DOI: 10.1016/j.xhgg.2023.100224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/14/2023] [Indexed: 08/19/2023] Open
Abstract
Rhabdomyosarcoma accounts for roughly 1% of adult sarcomas, with pleomorphic rhabdomyosarcoma (PRMS) as the most common subtype. Survival outcomes remain poor for patients with PRMS, and little is known about the molecular drivers of this disease. To better characterize PRMS, we performed a broad array of genomic and immunostaining analyses on 25 patient samples. In terms of gene expression and methylation, PRMS clustered more closely with other complex karyotype sarcomas than with pediatric alveolar and embryonal rhabdomyosarcoma. Immune infiltrate levels in PRMS were among the highest observed in multiple sarcoma types and contrasted with low levels in other rhabdomyosarcoma subtypes. Lower immune infiltrate was associated with complete loss of both TP53 and RB1. This comprehensive characterization of the genetic, epigenetic, and immune landscape of PRMS provides a roadmap for improved prognostications and therapeutic exploration.
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Affiliation(s)
- Hannah C. Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Nakazawa
- Department of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Davis Ingram
- Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joseph R. Daniele
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rossana Lazcano
- Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher Davies
- Research Department of Pathology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Najat C. Daw
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Khalida Wani
- Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei-Lien Wang
- Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brian Rubin
- Institute Chair, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anthony Conley
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Adrienne M. Flanagan
- Research Department of Pathology, UCL Cancer Institute, London WC1E 6DD, UK
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Alexander J. Lazar
- Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - P. Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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4
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Darbo E, Pérot G, Darmusey L, Le Guellec S, Leroy L, Gaston L, Desplat N, Thébault N, Merle C, Rochaix P, Valentin T, Ferron G, Chevreau C, Bui B, Stoeckle E, Ranchere-Vince D, Méeus P, Terrier P, Piperno-Neumann S, Collin F, De Pinieux G, Duffaud F, Coindre JM, Blay JY, Chibon F. Distinct Cellular Origins and Differentiation Process Account for Distinct Oncogenic and Clinical Behaviors of Leiomyosarcomas. Cancers (Basel) 2023; 15:cancers15020534. [PMID: 36672483 PMCID: PMC9856933 DOI: 10.3390/cancers15020534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/02/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
In leiomyosarcoma (LMS), a very aggressive disease, a relatively transcriptionally uniform subgroup of well-differentiated tumors has been described and is associated with poor survival. The question raised how differentiation and tumor progression, two apparently antagonist processes, coexist and allow tumor malignancy. We first identified the most transcriptionally homogeneous LMS subgroup in three independent cohorts, which we named 'hLMS'. The integration of multi-omics data and functional analysis suggests that hLMS originate from vascular smooth muscle cells and show that hLMS transcriptional program reflects both modulations of smooth muscle contraction activity controlled by MYOCD/SRF regulatory network and activation of the cell cycle activity controlled by E2F/RB1 pathway. We propose that the phenotypic plasticity of vascular smooth muscle cells coupled with MYOCD/SRF pathway amplification, essential for hLMS survival, concomitant with PTEN absence and RB1 alteration, could explain how hLMS balance this uncommon interplay between differentiation and aggressiveness.
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Affiliation(s)
- Elodie Darbo
- INSERM U1218 ACTION, Institut Bergonié, 33000 Bordeaux, France
- CNRS UMR5800, LaBRI, 33400 Talence, France
- Department of Medical and Biological Sciences, Université de Bordeaux, 33000 Bordeaux, France
| | - Gaëlle Pérot
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Centre Hospitalier Universitaire (CHU) de Toulouse, IUCT-Oncopole, 31000 Toulouse, France
| | - Lucie Darmusey
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
- Department of Medical and Biological Sciences, University of Toulouse 3, 31000 Toulouse, France
| | - Sophie Le Guellec
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Laura Leroy
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Laëtitia Gaston
- Department of Medical Genetics, CHU de Bordeaux, 33000 Bordeaux, France
| | - Nelly Desplat
- INSERM U1218 ACTION, Institut Bergonié, 33000 Bordeaux, France
| | - Noémie Thébault
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Candice Merle
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
- Department of Medical and Biological Sciences, University of Toulouse 3, 31000 Toulouse, France
| | - Philippe Rochaix
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Thibaud Valentin
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Oncology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Gwenaël Ferron
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Surgical Oncology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Christine Chevreau
- Department of Oncology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Binh Bui
- Department of Oncology, Institut Bergonié, 33000 Bordeaux, France
| | | | | | - Pierre Méeus
- Department of Surgery, Centre Léon Bérard, 69000 Lyon, France
| | - Philippe Terrier
- Department of Pathology, Institut Gustave Roussy, 94800 Villejuif, France
| | | | - Françoise Collin
- Department of Pathology, Centre Georges-François Leclerc, 21000 Dijon, France
| | - Gonzague De Pinieux
- Department of Pathology, Hôpital Universitaire Trousseau, 37170 Tours, France
| | - Florence Duffaud
- Medical Oncology Unit, APHM Hôpital La Timone, Aix Marseille University, 13000 Marseille, France
| | - Jean-Michel Coindre
- INSERM U1218 ACTION, Institut Bergonié, 33000 Bordeaux, France
- Department of Pathology, Institut Bergonié, 33000 Bordeaux, France
| | - Jean-Yves Blay
- Department of Medical Oncology, Centre Léon Bérard, 69000 Lyon, France
- INSERM U1052, CNRS 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, 69000 Lyon, France
| | - Frédéric Chibon
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
- Correspondence: ; Tel.: +33-0582741765
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5
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PANAGOPOULOS IOANNIS, HEIM SVERRE. Neoplasia-associated Chromosome Translocations Resulting in Gene Truncation. Cancer Genomics Proteomics 2022; 19:647-672. [PMID: 36316036 PMCID: PMC9620447 DOI: 10.21873/cgp.20349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022] Open
Abstract
Chromosomal translocations in cancer as well as benign neoplasias typically lead to the formation of fusion genes. Such genes may encode chimeric proteins when two protein-coding regions fuse in-frame, or they may result in deregulation of genes via promoter swapping or translocation of the gene into the vicinity of a highly active regulatory element. A less studied consequence of chromosomal translocations is the fusion of two breakpoint genes resulting in an out-of-frame chimera. The breaks then occur in one or both protein-coding regions forming a stop codon in the chimeric transcript shortly after the fusion point. Though the latter genetic events and mechanisms at first awoke little research interest, careful investigations have established them as neither rare nor inconsequential. In the present work, we review and discuss the truncation of genes in neoplastic cells resulting from chromosomal rearrangements, especially from seemingly balanced translocations.
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Affiliation(s)
- IOANNIS PANAGOPOULOS
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - SVERRE HEIM
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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6
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Chłopek M, Lasota J, Thompson LDR, Szczepaniak M, Kuźniacka A, Hińcza K, Kubicka K, Kaczorowski M, Newford M, Liu Y, Agaimy A, Biernat W, Durzyńska M, Dziuba I, Hartmann A, Inaguma S, Iżycka-Świeszewska E, Kato H, Kopczyński J, Michal M, Michal M, Pęksa R, Prochorec-Sobieszek M, Starzyńska A, Takahashi S, Wasąg B, Kowalik A, Miettinen M. Alterations in key signaling pathways in sinonasal tract melanoma. A molecular genetics and immunohistochemical study of 90 cases and comprehensive review of the literature. Mod Pathol 2022; 35:1609-1617. [PMID: 35978013 DOI: 10.1038/s41379-022-01122-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 11/09/2022]
Abstract
Sinonasal mucosal melanoma is a rare tumor arising within the nasal cavity, paranasal sinuses, or nasopharynx (sinonasal tract). This study evaluated 90 cases diagnosed in 29 males and 61 females with median age 68 years. Most tumors involved the nasal cavity and had an epithelioid morphology. Spectrum of research techniques used in this analysis includes targeted-DNA and -RNA next-generation sequencing, Sanger sequencing, fluorescence in situ hybridization and immunohistochemistry. Sinonasal melanomas were commonly driven by RAS (38/90, 42%), especially NRAS (n = 36) mutations and rarely (4/90, 4%) displayed BRAF pathogenic variants. BRAF/RAS mutants were more frequent among paranasal sinuses (10/14, 71%) than nasal (26/64, 41%) tumors. BRAF/RAS-wild type tumors occasionally harbored alterations of the key components and regulators of Ras-MAPK signaling pathway: NF1 mutations (1/17, 6%) or NF1 locus deletions (1/25, 4%), SPRED1 (3/25, 12%), PIK3CA (3/50, 6%), PTEN (4/50, 8%) and mTOR (1/50, 2%) mutations. These mutations often occurred in a mutually exclusive manner. In several tumors some of which were NRAS mutants, TP53 was deleted (6/48, 13%) and/or mutated (5/90, 6%). Variable nuclear accumulation of TP53, mirrored by elevated nuclear MDM2 expression was seen in >50% of cases. Furthermore, sinonasal melanomas (n = 7) including RAS/BRAF-wild type tumors (n = 5) harbored alterations of the key components and regulators of canonical WNT-pathway: APC (4/90, 4%), CTNNB1 (3/90, 3%) and AMER1 (1/90, 1%). Both, TERT promoter mutations (5/53, 9%) and fusions (2/40, 5%) were identified. The latter occurred in BRAF/RAS-wild type tumors. No oncogenic fusion gene transcripts previously reported in cutaneous melanomas were detected. Eight tumors including 7 BRAF/RAS-wild type cases expressed ADCK4::NUMBL cis-fusion transcripts. In summary, this study documented mutational activation of NRAS and other key components and regulators of Ras-MAPK signaling pathway such as SPRED1 in a majority of sinonasal melanomas.
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Affiliation(s)
- Małgorzata Chłopek
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | - Jerzy Lasota
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.
| | | | | | - Alina Kuźniacka
- Department of Biology and Genetics, Medical University of Gdańsk, Gdańsk, Poland
| | - Kinga Hińcza
- Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | - Kamila Kubicka
- Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | - Maciej Kaczorowski
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Department of Clinical and Experimental Pathology, Wrocław Medical University, Wrocław, Poland
| | - Michael Newford
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Yalan Liu
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Abbas Agaimy
- Institute of Pathology, University Hospital of Erlangen, Erlangen, Germany
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Monika Durzyńska
- Department of Pathology, The Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Ireneusz Dziuba
- Faculty of Medicine, University of Technology, Katowice, Poland
| | - Arndt Hartmann
- Institute of Pathology, University Hospital of Erlangen, Erlangen, Germany
| | - Shingo Inaguma
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Ewa Iżycka-Świeszewska
- Department of Pathology and Neuropathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Hiroyuki Kato
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Janusz Kopczyński
- Department of Surgical Pathology, Holycross Cancer Center, Kielce, Poland
| | - Michal Michal
- Sikl's Department of Pathology, University Hospital, Charles University in Prague, Medical Faculty in Plzeň, Plzeň, Czech Republic
| | - Michael Michal
- Sikl's Department of Pathology, University Hospital, Charles University in Prague, Medical Faculty in Plzeň, Plzeň, Czech Republic
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Monika Prochorec-Sobieszek
- Department of Pathology, The Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Anna Starzyńska
- Department of Oral Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Bartosz Wasąg
- Department of Biology and Genetics, Medical University of Gdańsk, Gdańsk, Poland
| | - Artur Kowalik
- Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland.,Division of Medical Biology, Institute of Biology Jan Kochanowski University, Kielce, Poland
| | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
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7
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Istl AC, Gronchi A. Neoadjuvant Therapy for Primary Resectable Retroperitoneal Sarcomas-Looking Forward. Cancers (Basel) 2022; 14:cancers14071831. [PMID: 35406603 PMCID: PMC8998126 DOI: 10.3390/cancers14071831] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/23/2022] [Accepted: 03/26/2022] [Indexed: 01/25/2023] Open
Abstract
Simple Summary This review summarizes the current evidence around neoadjuvant radiotherapy and systemic therapy for retroperitoneal sarcoma (RPS). While surgery is the cornerstone of treatment for these tumors, data from prospective studies, retrospective studies, early phase trials, and—most recently—our first phase III randomized trial for RPS suggest there are clinical scenarios in which neoadjuvant therapy may provide benefit. This review evaluates the STRASS results in the setting of other recent studies, identifies active trials of interest, and suggests future directions of study in this field. The intersection of STRASS and STRASS2 is considered and a summary of current acceptable approaches to neoadjuvant therapy for RPS is provided. Abstract The cornerstone of therapy for primary retroperitoneal sarcomas (RPS) is complete surgical resection, best achieved by resecting the tumor en bloc with adherent structures even if not overtly infiltrated. Until recently, trials designed to elucidate the role of neoadjuvant radiation or chemotherapy for RPS have been unable to achieve sufficient enrollment. The completion of the STRASS trial, which explored neoadjuvant radiotherapy for primary resectable RPS, is a major milestone in RPS research, but has prompted further questions about histology-driven treatment paradigms for RPS. Though it was ultimately a negative trial with respect to its primary endpoint of abdominal recurrence-free survival, STRASS produced a signal that suggested improved abdominal recurrence-free survival with neoadjuvant radiotherapy (RT) for patients with liposarcoma (LPS). No effect was seen for leiomyosarcoma (LMS) or high-grade dedifferentiated (DD) LPS, consistent with recent literature suggesting LMS and high-grade DD-LPS have a predominant pattern of distant rather than local failure. These results, along with those from other recent studies conducted at the bench and the bedside, emphasize the importance of a histology-specific approach to RPS research. Recent evidence for patterns of distant failure in LMS and high-grade DD-LPS has prompted the initiation of STRASS2, a study of neoadjuvant chemotherapy for these histologies. As this study unfolds, evidence may emerge for novel systemic therapy options in specific sarcoma histotypes given the explosion in targeted and immunotherapeutic applications over the last decade. This article reviews current and recent evidence around neoadjuvant radiation and chemotherapy as well as avenues for future study to optimize these treatment approaches.
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Affiliation(s)
- Alexandra C. Istl
- Division of Surgical Oncology, Johns Hopkins Hospital, Baltimore, MD 21287, USA;
| | - Alessandro Gronchi
- Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy
- Correspondence:
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8
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Kunieda J, Yamashita K, Togashi Y, Baba S, Sakata S, Inamura K, Ae K, Matsumoto S, Machinami R, Kitagawa M, Takeuchi K. High prevalence of TERT aberrations in myxoid liposarcoma: TERT reactivation may play a crucial role in tumorigenesis. Cancer Sci 2021; 113:1078-1089. [PMID: 34971481 PMCID: PMC8898734 DOI: 10.1111/cas.15256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 11/28/2022] Open
Abstract
Myxoid liposarcoma (MLPS) is genetically characterized by FUS‐DDIT3 or EWSR1‐DDIT3 gene fusion and the high frequency of hotspot mutations (C228T or C250T) in the promoter region of telomerase reverse transcriptase (TERT) that encodes the TERT protein. The latter leads to telomerase reactivation, a mechanism of telomere maintenance. Although the TERT promoter hotspot mutation is a poor prognostic factor in various tumors, its effect on MLPS has not been reported in detail. In the present study, we examined the clinicopathological characteristics, prognosis, and telomere maintenance mechanisms in 83 primary tumor samples of MLPS, which were resected surgically at the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan, from 2008 to 2020. TERT promoter hotspot mutations were observed in 77% (63/82) cases, and alternative lengthening of telomeres (ALT) was absent in all cases. Among the cases without TERT promoter hotspot mutations, TERT rearrangements, and minor point mutations in the TERT promoter region were found in 3 and 2 cases, respectively. TERT mRNA expression was observed consistently even in patients for whom no genomic TERT aberrations were detected, and the presence of TERT promoter hotspot mutation did not correlate significantly with either overall and metastasis‐free survival (P = .56, P = .83, respectively) or clinicopathological features. Therefore, patients with MLPS characteristically shows TERT expression and a high prevalence of TERT aberrations. Our findings suggest that TERT aberration is not prognostic factor, but might occur at an early stage and play a key role in tumorigenesis.
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Affiliation(s)
- Junko Kunieda
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kyoko Yamashita
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuki Togashi
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoko Baba
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiji Sakata
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kentaro Inamura
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Keisuke Ae
- Department of Orthopedic Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiichi Matsumoto
- Department of Orthopedic Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Rikuo Machinami
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Pathology, Kawakita General Hospital, Tokyo, Japan
| | - Masanobu Kitagawa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kengo Takeuchi
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.,Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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9
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Hames-Fathi S, Nottley SWG, Pillay N. Unravelling undifferentiated soft tissue sarcomas: insights from genomics. Histopathology 2021; 80:109-121. [DOI: 10.1111/his.14446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Shadi Hames-Fathi
- Research Department of Pathology University College London UCL Cancer Institute LondonUK
| | - Steven W G Nottley
- Research Department of Pathology University College London UCL Cancer Institute LondonUK
| | - Nischalan Pillay
- Research Department of Pathology University College London UCL Cancer Institute LondonUK
- Department of Cellular and Molecular Pathology Royal National Orthopaedic Hospital NHS Trust Stanmore UK
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10
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Guo X, Chen T, Chen S, Song C, Shan D, Xu S, Xu S. Case Report: Identification of Multiple TERT and FGFR2 Gene Fusions in a Pineal Region Glioblastoma Case. Front Oncol 2021; 11:739309. [PMID: 34976798 PMCID: PMC8716851 DOI: 10.3389/fonc.2021.739309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
As an oncogenic somatic variant, telomerase reverse transcriptase promoter (TERTp) mutations are frequently observed in adult glioblastoma (GBM). Alternatively, we report the first case of glioblastoma with TERT amplification accompanied by multiple TERT and FGFR2 gene fusions instead of TERTp mutation. A 55-year-old woman presented with dizziness, headache, and diplopia for three weeks. Magnetic resonance imaging (MRI) demonstrated a heterogeneously enhancing lobulated mass centered in the pineal region. Partial tumor resection and ventriculoperitoneal shunt were achieved, and the residual tumor was then treated with standard radiation. The tumor was diagnosed as GBM, IDH-wild type, WHO grade IV, and the Ki67 proliferation index was high (30–40%). Intriguingly, TERT amplification without TERTp mutation was identified via next generation sequencing (NGS). Further analysis revealed multiple TERT (TERT–NUBPL, MARCH6–TERT, and CJD4–TERT) and FGFR2 (CXCL17–FGFR2, SIPA1L3–FGFR2, FGFR2–SIPA1L3, and FGFR2–CEACAM1) gene fusions. After the surgery, the patient’s condition deteriorated rapidly due to the malignant nature of the tumor and she died with an overall survival of 3 months. Our report provides the molecular clue for a novel telomerase activation and maintenance mechanism in GBM.
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Affiliation(s)
- Xing Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Teng Chen
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Shiming Chen
- Department of Pathology, Qilu Hospital, Shandong University, Jinan, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Dezhi Shan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Shujun Xu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Shuo Xu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
- *Correspondence: Shuo Xu,
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11
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Yoon JY, Jiang W, Orr CR, Rushton C, Gargano S, Song SJ, Modi M, Hozack B, Abraham J, Mallick AB, Brooks JSJ, Rosenbaum JN, Zhang PJ. TERT gene rearrangement in chordomas and comparison to other TERT-rearranged solid tumors. Cancer Genet 2021; 258-259:74-79. [PMID: 34583232 DOI: 10.1016/j.cancergen.2021.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/25/2021] [Accepted: 09/16/2021] [Indexed: 11/27/2022]
Abstract
Chordomas are rare, slow-growing neoplasms thought to arise from the foetal notochord remnant. A limited number of studies that examined the mutational profiles in chordomas identified potential driver mutations, including duplication in the TBXT gene (encoding brachyury), mutations in the PI3K/AKT signaling pathway, and loss of the CDKN2A gene. Most chordomas remain without clear driver mutations, and no fusion genes have been identified thus far. We discovered a novel TERT in-frame fusion involving RPH3AL (exon 5) and TERT (exon 2) in the index chordoma case. We screened a discovery cohort of 18 additional chordoma cases for TERT gene rearrangement by FISH, in which TERT rearrangement was identified in one additional case. In our independent, validation cohort of 36 chordomas, no TERT rearrangement was observed by FISH. Immunohistochemistry optimized for nuclear TERT expression showed at least focal TERT expression in 40/55 (72.7%) chordomas. Selected cases underwent molecular genetic profiling, which showed low tumor mutational burdens (TMBs) without obvious driver oncogenic mutations. We next examined a cohort of 1,913 solid tumor patients for TERT rearrangements, and TERT fusions involving exon 2 were observed in 7/1,913 (0.4%) cases. The seven tumors comprised five glial tumors, and two poorly differentiated carcinomas. In contrast to chordomas, the other TERT-rearranged tumors were notable for higher TMBs, frequent TP53 mutations (6/7) and presence of other driver oncogenic mutations, including a concurrent fusion (TRIM24-MET). In conclusion, TERT gene rearrangements are seen in a small subset (2/55, 3.6%) of chordomas. In contrast to other TERT-rearranged tumors, where the TERT rearrangements are likely passenger events, the possibility that TERT protein overexpression representing a key event in chordoma tumorigenesis is left open.
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Affiliation(s)
- Ju-Yoon Yoon
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States; Department of Laboratory Medicine, St. Michael's Hospital/Unity Health Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Wei Jiang
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, United States
| | - Christopher R Orr
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Chase Rushton
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Stacey Gargano
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, United States
| | - Sharon J Song
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Mitul Modi
- Department of Pathology, Pennsylvania Hospital, Philadelphia, Pennsylvania, United States
| | - Bryan Hozack
- Rothman Orthopedic Institute, Philadelphia, Pennsylvania, United States
| | - John Abraham
- Rothman Orthopedic Institute, Philadelphia, Pennsylvania, United States; Division of Sarcoma and Bone Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States
| | - Atrayee Basu Mallick
- Department of Medical Oncology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, United States
| | - John S J Brooks
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States; Department of Pathology, Pennsylvania Hospital, Philadelphia, Pennsylvania, United States
| | - Jason N Rosenbaum
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States; Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Paul J Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States.
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12
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Zhang L, Chen L, Xiao M, Xie X, Wang F. Locally advanced undifferentiated sarcomatoid carcinoma of the right maxillary sinus with PDCD6-TERT fusion: A rare case report. Oral Oncol 2021; 124:105466. [PMID: 34348839 DOI: 10.1016/j.oraloncology.2021.105466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 02/05/2023]
Abstract
Sarcomatoid carcinoma of maxillary sinus tumor is extremely rare in head and neck tumors and has poor prognosis and frequently occurs to relapse locally after surgery. We first reported a case of locally advanced undifferentiated sarcomatoid carcinoma of right maxillary sinus with PDCD6-TERT fusion gene. The patient with a previous history of moderate alcohol drinking and smoking. The patient underwent surgical treatment. The tumor tissue using NGS analysis, no other driver gene mutations, and the PD-L1 IHC was negative. He received TPF regimen induction chemotherapy combined with anti-PD1 inhibitor and radiotherapy. The effect of treatment was good.
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Affiliation(s)
- Li Zhang
- Department of Medical Oncology, Cancer Center, West China Hospital, West China Medical School, Sichuan University, Sichuan, China
| | - Lin Chen
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing 210002, China
| | - Mingzhe Xiao
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing 210002, China
| | - Xiaoqi Xie
- Department of Critical Care Medicine, West China Hospital, Sichuan University, Chendu, Sichuan Province, China
| | - Feng Wang
- Department of Medical Oncology, Cancer Center, West China Hospital, West China Medical School, Sichuan University, Sichuan, China.
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13
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Ohki K, Kiyokawa N, Watanabe S, Iwafuchi H, Nakazawa A, Ishiwata K, Ogata-Kawata H, Nakabayashi K, Okamura K, Tanaka F, Fukano R, Hata K, Mori T, Moriya Saito A, Hayashi Y, Taga T, Sekimizu M, Kobayashi R. Characteristics of genetic alterations of peripheral T-cell lymphoma in childhood including identification of novel fusion genes: the Japan Children's Cancer Group (JCCG). Br J Haematol 2021; 194:718-729. [PMID: 34258755 DOI: 10.1111/bjh.17639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/16/2021] [Accepted: 05/21/2021] [Indexed: 12/12/2022]
Abstract
Peripheral T-cell lymphoma (PTCL) is a group of heterogeneous non-Hodgkin lymphomas showing a mature T-cell or natural killer cell phenotype, but its molecular abnormalities in paediatric patients remain unclear. By employing next-generation sequencing and multiplex ligation-dependent probe amplification of tumour samples from 26 patients, we identified somatic alterations in paediatric PTCL including Epstein-Barr virus (EBV)-negative (EBV- ) and EBV-positive (EBV+ ) patients. As recurrent mutational targets for PTCL, we identified several previously unreported genes, including TNS1, ZFHX3, LRP2, NCOA2 and HOXA1, as well as genes previously reported in adult patients, e.g. TET2, CDKN2A, STAT3 and TP53. However, for other reported mutations, VAV1-related abnormalities were absent and mutations of NRAS, GATA3 and JAK3 showed a low frequency in our cohort. Concerning the association of EBV infection, two novel fusion genes: STAG2-AFF2 and ITPR2-FSTL4, and deletion and alteration of CDKN2A/2B, LMO1 and HOXA1 were identified in EBV- PTCL, but not in EBV+ PTCL. Conversely, alterations of PCDHGA4, ADAR, CUL9 and TP53 were identified only in EBV+ PTCL. Our observations suggest a clear difference in the molecular mechanism of onset between paediatric and adult PTCL and a difference in the characteristics of genetic alterations between EBV- and EBV+ paediatric PTCL.
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Affiliation(s)
- Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Satoru Watanabe
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hideto Iwafuchi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pathology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Astuko Nakazawa
- Department of Clinical Research, Saitama Children's Medical Center, Saitama, Japan
| | - Keisuke Ishiwata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hiroko Ogata-Kawata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Fumiko Tanaka
- Department of Pediatrics, Saiseikai Yokohamashi Nanbu Hospital, Kanagawa, Japan
| | - Reiji Fukano
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tetsuya Mori
- Department of Pediatrics, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Akiko Moriya Saito
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yasuhide Hayashi
- Institute of Physiology and Medicine, Jobu University, Takasaki, Japan
| | - Takashi Taga
- Department of Pediatrics, Shiga University of Medical Science, Shiga, Japan
| | - Masahiro Sekimizu
- Department of Pediatrics, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Ryoji Kobayashi
- Department of Hematology/Oncology for Children and Adolescents, Sapporo Hokuyu Hospital, Hokkaido, Japan
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14
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Hildebrand KM, Singla AK, McNeil R, Marritt KL, Hildebrand KN, Zemp F, Rajwani J, Itani D, Bose P, Mahoney DJ, Jirik FR, Monument MJ. The KrasG12D;Trp53fl/fl murine model of undifferentiated pleomorphic sarcoma is macrophage dense, lymphocyte poor, and resistant to immune checkpoint blockade. PLoS One 2021; 16:e0253864. [PMID: 34242269 PMCID: PMC8270133 DOI: 10.1371/journal.pone.0253864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/15/2021] [Indexed: 11/19/2022] Open
Abstract
Sarcomas are rare, difficult to treat, mesenchymal lineage tumours that affect children and adults. Immunologically-based therapies have improved outcomes for numerous adult cancers, however, these therapeutic strategies have been minimally effective in sarcoma so far. Clinically relevant, immunologically-competent, and transplantable pre-clinical sarcoma models are essential to advance sarcoma immunology research. Herein we show that Cre-mediated activation of KrasG12D, and deletion of Trp53, in the hindlimb muscles of C57Bl/6 mice results in the highly penetrant, rapid onset undifferentiated pleomorphic sarcomas (UPS), one of the most common human sarcoma subtypes. Cell lines derived from spontaneous UPS tumours can be reproducibly transplanted into the hindlimbs or lungs of naïve, immune competent syngeneic mice. Immunological characterization of both spontaneous and transplanted UPS tumours demonstrates an immunologically-‘quiescent’ microenvironment, characterized by a paucity of lymphocytes, limited spontaneous adaptive immune pathways, and dense macrophage infiltrates. Macrophages are the dominant immune population in both spontaneous and transplanted UPS tumours, although compared to spontaneous tumours, transplanted tumours demonstrate increased spontaneous lymphocytic infiltrates. The growth of transplanted UPS tumours is unaffected by host lymphocyte deficiency, and despite strong expression of PD-1 on tumour infiltrating lymphocytes, tumours are resistant to immunological checkpoint blockade. This spontaneous and transplantable immune competent UPS model will be an important experimental tool in the pre-clinical development and evaluation of novel immunotherapeutic approaches for immunologically cold soft tissue sarcomas.
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Affiliation(s)
- Karys M. Hildebrand
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Arvind K. Singla
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Reid McNeil
- Arnie Charbonneau Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kayla L. Marritt
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kurt N. Hildebrand
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Franz Zemp
- Arnie Charbonneau Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Jahanara Rajwani
- Arnie Charbonneau Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Doha Itani
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Pinaki Bose
- Arnie Charbonneau Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Douglas J. Mahoney
- Arnie Charbonneau Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Frank R. Jirik
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Michael J. Monument
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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15
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Watson S. [New data on the molecular biology of soft tissue sarcoma]. Bull Cancer 2021; 108:654-667. [PMID: 33985762 DOI: 10.1016/j.bulcan.2021.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/15/2022]
Abstract
Sarcoma consists in a group of rare malignant tumours of mesenchymal origin characterized by their vast clinical, pathological and biological heterogeneity. The pathological diagnosis of sarcoma relies classically of the differentiation features of tumour cells, with dozens of different tumour subtypes described in the last international classifications. Over the last decades, the advances in the development of new techniques of molecular biology have led to a major complexification of sarcoma classification, with the identification of multiple and specific molecular alterations that have led to significant changes for patients diagnostic, prognostic and therapeutic management. This review aims at giving an overview on the current knowledge of the molecular biology of soft tissue sarcoma, and emphasizes on their consequences for the daily management of patients.
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Affiliation(s)
- Sarah Watson
- Institut Curie, département d'oncologie médicale, Inserm U830, 26, rue d'Ulm, 75005 Paris, France.
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16
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Germinal GLT8D1, GATAD2A and SLC25A39 mutations in a patient with a glomangiopericytal tumor and five different sarcomas over a 10-year period. Sci Rep 2021; 11:9765. [PMID: 33963205 PMCID: PMC8105326 DOI: 10.1038/s41598-021-88671-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/15/2021] [Indexed: 11/26/2022] Open
Abstract
Soft tissue sarcoma represents about 1% of all adult cancers. Occurrence of multiple sarcomas in a same individual cannot be fortuitous. A 72-year-old patient had between 2007 and 2016 a glomangiopericytal tumor of the right forearm and a succession of sarcomas of the extremities: a leiomyosarcoma of the left buttock, a myxofibrosarcoma (MFS) of the right forearm, a MFS of the left scapula, a left latero-thoracic MFS and two undifferentiated sarcomas on the left forearm. Pathological examination of the six locations was not in favor of disease with local/distant recurrences but could not confirm different diseases. An extensive molecular analysis including DNA-array, RNA-sequencing and DNA-Sanger-sequencing, was thus performed to determine the link between them. The genomic profile of the glomangiopericytal tumor and the six sarcomas revealed that five sarcomas were different diseases and one was the local recurrence of the glomangiopericytal tumor. While the chromosomal alterations in the six tumors were different, a common somatic CDKN2A/CDKN2B deletion was identified. RNA-sequencing of five tumors identified mutations in GLT8D1, GATAD2A and SLC25A39 in all samples. The germline origin of these mutations was confirmed by Sanger-sequencing. Innovative molecular analysis methods have made possible a better understanding of the complex tumorigenesis of multiple sarcomas.
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17
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Chen R, Wu J, Lu C, Yan T, Qian Y, Shen H, Zhao Y, Wang J, Kong P, Zhang X. Systematic Transcriptome Analysis Reveals the Inhibitory Function of Cinnamaldehyde in Non-Small Cell Lung Cancer. Front Pharmacol 2021; 11:611060. [PMID: 33633568 PMCID: PMC7900626 DOI: 10.3389/fphar.2020.611060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/29/2020] [Indexed: 12/19/2022] Open
Abstract
Cinnamaldehyde (CA) is the main component extracted from the traditional Chinese medicine cinnamon. Recent studies revealed that CA has antiviral and anti-tumor effects. However, the effect and mechanism of CA on non-small cell lung cancer (NSCLC) through whole transcriptome sequencing integrated analysis have not been systematically investigated. In this study, whole transcriptome sequencing was used to identify differentially expressed messenger RNAs (mRNAs), micro RNAs (miRNAs), and long non-coding RNAs (lncRNAs) that were influenced by CA and screen regulatory pathways. The results showed that CA significantly inhibited proliferation, invasion, and migration, whereas it induced the apoptosis of NSCLC cells. CA inhibited tumor growth in vivo. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis revealed that these differentially expressed mRNAs were potentially implicated in the CA-suppressing malignant phenotypes of NSCLC. According to the competing endogenous RNA (ceRNA) hypothesis, a ceRNA network was constructed, including 13 mRNAs, 6 miRNAs, and 11 lncRNAs. Kyoto Encyclopedia of Genes and Genomes analysis of the 13 mRNAs in the ceRNA network showed that suppressors of cytokine signaling 1 (SOCS1), BTG anti-proliferation factor 2 (BTG2), and Bruton tyrosine kinase (BTK) were significantly enriched in the JAK/STAT signaling pathway, RNA degradation, and nuclear factor-κB (NF-κB) signaling pathway related to cancer. These findings indicated that SOCS1, BTG2, and BTK play an essential role in CA against NSCLC. Meanwhile, based on the ceRNA network, three lncRNAs (long intergenic non-protein coding RNA 1504 [LINC01504], LINC01783, and THUMPD3 antisense RNA 1 [THUMPD3-AS1]) and three miRNAs (has-miR-155-5p, has-miR-7-5p, and has-miR-425-5p) associated with SOCS1, BTG2, and BTK may be important in CA against NSCLC. Taken together, the present study demonstrated the activity of CA against lung cancer and its potential use as a therapeutic agent.
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Affiliation(s)
- Ru Chen
- Department of Respiratory and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Juan Wu
- Department of Respiratory and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Chang Lu
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Ting Yan
- Department of Pathology and Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, China
| | - Yu Qian
- Department of Pathology and Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, China
| | - Huiqing Shen
- Department of Respiratory and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yujing Zhao
- Department of Respiratory and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Jianzhen Wang
- Department of Respiratory and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Pengzhou Kong
- Department of Pathology and Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, China
| | - Xinri Zhang
- Department of Respiratory and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
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18
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Cell-cell fusion of mesenchymal cells with distinct differentiations triggers genomic and transcriptomic remodelling toward tumour aggressiveness. Sci Rep 2020; 10:21634. [PMID: 33303824 PMCID: PMC7729932 DOI: 10.1038/s41598-020-78502-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Cell–cell fusion is a physiological process that is hijacked during oncogenesis and promotes tumour evolution. The main known impact of cell fusion is to promote the formation of metastatic hybrid cells following fusion between mobile leucocytes and proliferating tumour cells. We show here that cell fusion between immortalized myoblasts and transformed fibroblasts, through genomic instability and expression of a specific transcriptomic profile, leads to emergence of hybrid cells acquiring dissemination properties. This is associated with acquisition of clonogenic ability by fused cells. In addition, by inheriting parental properties, hybrid tumours were found to mimic the histological characteristics of a specific histotype of sarcomas: undifferentiated pleomorphic sarcomas with incomplete muscular differentiation. This finding suggests that cell fusion, as macroevolution event, favours specific sarcoma development according to the differentiation lineage of parent cells.
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19
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Deng J, Zeng W, Kong W, Shi Y, Mou X. The Study of Sarcoma Microenvironment Heterogeneity Associated With Prognosis Based on an Immunogenomic Landscape Analysis. Front Bioeng Biotechnol 2020; 8:1003. [PMID: 32974322 PMCID: PMC7471631 DOI: 10.3389/fbioe.2020.01003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
Microenvironment-driven tumor heterogeneity causes the limitation of immunotherapy of sarcomas. Nonetheless, systematical studies of various molecular levels can enhance the understanding of tumor microenvironment (TME) related to prognosis and provide novel insights of precision immunotherapy. Three prognostic-related TME phenotypes were identified by consensus clustering of the relative infiltration of 22 immune cells from 869 samples of sarcomas. Additionally, integrative immunogenomic analysis is applied to explore the characteristics of different TME groups. The results revealed that most of the immune cell infiltration is higher in the better prognostic group, which are more affected by lower DNA methylation levels and fewer copy number variations in the worse prognostic group. The signaling pathway crosstalk analysis suggested that the changes in the TME will cause considerable variation in the flow of information between pathways, especially when the degree of relative infiltration of immune cells is low, patient’s endocrine system may also be significantly affected. Also, the endogenous competitive network analysis indicated that several differentially expressed long non-coding RNAs (lncRNAs) associated with the prognosis or tumor recurrence of sarcoma patients affected the regulatory relationship between miRNAs and different genes when the sarcoma microenvironment changes. In summary, the significant relationship between genetic alterations and prognostic-related TME characteristics in sarcomas were determined in this study. These findings may provide new clues for the treatment of sarcomas.
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Affiliation(s)
- Jin Deng
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Weiming Zeng
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Wei Kong
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Yuhu Shi
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Xiaoyang Mou
- Department of Biochemistry, Rowan University and Guava Medicine, Glassboro, NJ, United States
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20
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Han C, Sun LY, Wang WT, Sun YM, Chen YQ. Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications. J Mol Cell Biol 2020; 11:886-898. [PMID: 31361891 PMCID: PMC6884712 DOI: 10.1093/jmcb/mjz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 12/25/2022] Open
Abstract
Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.
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Affiliation(s)
- Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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21
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Occidental M, Shen G, Feng X, Zhu K, Kelly K, Nie Q, Reddi HV, Lakiotaki E, Viniou NA, Korkolopoulou P, Linos K, Jour G. Novel CTNND2-TERT fusion in a spindle cell liposarcoma. Genes Chromosomes Cancer 2020; 59:544-548. [PMID: 32352179 DOI: 10.1002/gcc.22856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Soft tissue tumors can be categorized molecularly into two categories: tumors which are known to have recurrent molecular alterations and tumors which do not have consistent recurrent molecular alterations or translocations. These "nontranslocation" associated sarcomas are clinically more aggressive than their more stable counterparts. However, recent advances in RNA sequencing have discovered recurrent novel fusions within the latter group, namely TERT-TRIO fusions. Furthermore, a recent report discovered this fusion in a spindle cell liposarcoma. Our case describes a novel fusion of CTNND2, a neighbor gene of TRIO, and TERT in a spindle cell liposarcoma, and provides further evidence that spindle cell liposarcoma should be a distinct entity from dedifferentiated liposarcoma.
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Affiliation(s)
- Michael Occidental
- Department of Pathology, New York University Langone Health, New York, New York, USA
| | - Guomiao Shen
- Department of Pathology, New York University Langone Health, New York, New York, USA
| | - Xiaojun Feng
- Department of Pathology, New York University Langone Health, New York, New York, USA
| | - Kelsey Zhu
- Department of Pathology, New York University Langone Health, New York, New York, USA
| | - Kevin Kelly
- The Jackson Laboratory, Farmington, Connecticut, USA
| | - Qian Nie
- The Jackson Laboratory, Farmington, Connecticut, USA
| | - Honey V Reddi
- The Jackson Laboratory, Farmington, Connecticut, USA
| | - Eleftheria Lakiotaki
- First Department of Pathology, National and Kapodistrian University of Athens, Athens, Greece
| | - Nora Athina Viniou
- First Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Penelope Korkolopoulou
- First Department of Pathology, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Linos
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA.,Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - George Jour
- Department of Pathology, New York University Langone Health, New York, New York, USA.,Department of Dermatology, New York University Langone Health, New York, New York, USA
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22
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Chen L, Oke T, Siegel N, Cojocaru G, Tam AJ, Blosser RL, Swailes J, Ligon JA, Lebid A, Morris C, Levin A, Rhee DS, Johnston FM, Greer JB, Meyer CF, Ladle BH, Thompson ED, Montgomery EA, Choi W, McConkey DJ, Anders RA, Pardoll DM, Llosa NJ. The Immunosuppressive Niche of Soft-Tissue Sarcomas is Sustained by Tumor-Associated Macrophages and Characterized by Intratumoral Tertiary Lymphoid Structures. Clin Cancer Res 2020; 26:4018-4030. [PMID: 32332015 DOI: 10.1158/1078-0432.ccr-19-3416] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/01/2020] [Accepted: 04/20/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Clinical trials with immune checkpoint inhibition in sarcomas have demonstrated minimal response. Here, we interrogated the tumor microenvironment (TME) of two contrasting soft-tissue sarcomas (STS), rhabdomyosarcomas and undifferentiated pleomorphic sarcomas (UPS), with differing genetic underpinnings and responses to immune checkpoint inhibition to understand the mechanisms that lead to response. EXPERIMENTAL DESIGN Utilizing fresh and formalin-fixed, paraffin-embedded tissue from patients diagnosed with UPS and rhabdomyosarcomas, we dissected the TME by using IHC, flow cytometry, and comparative transcriptomic studies. RESULTS Our results demonstrated both STS subtypes to be dominated by tumor-associated macrophages and infiltrated with immune cells that localized near the tumor vasculature. Both subtypes had similar T-cell densities, however, their in situ distribution diverged. UPS specimens demonstrated diffuse intratumoral infiltration of T cells, while rhabdomyosarcomas samples revealed intratumoral T cells that clustered with B cells near perivascular beds, forming tertiary lymphoid structures (TLS). T cells in UPS specimens were comprised of abundant CD8+ T cells exhibiting high PD-1 expression, which might represent the tumor reactive repertoire. In rhabdomyosarcomas, T cells were limited to TLS, but expressed immune checkpoints and immunomodulatory molecules which, if appropriately targeted, could help unleash T cells into the rest of the tumor tissue. CONCLUSIONS Our work in STS revealed an immunosuppressive TME dominated by myeloid cells, which may be overcome with activation of T cells that traffic into the tumor. In rhabdomyosarcomas, targeting T cells found within TLS may be key to achieve antitumor response.
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Affiliation(s)
- Lingling Chen
- Departement of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Teniola Oke
- Departement of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | | | - Gady Cojocaru
- Discovery Research, Computational Research & Development, Compugen Ltd
| | - Ada J Tam
- Departement of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Richard L Blosser
- Departement of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Jessica Swailes
- Departement of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - John A Ligon
- Departement of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Andriana Lebid
- Division of Immunology and Hematopoiesis, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Carol Morris
- Department of Orthopaedic Surgery and Oncology, Johns Hopkins University, Baltimore, MD
| | - Adam Levin
- Department of Orthopaedic Surgery and Oncology, Johns Hopkins University, Baltimore, MD
| | - Daniel S Rhee
- Department of Pediatric Surgery, Johns Hopkins University, Baltimore, MD
| | - Fabian M Johnston
- Department of Surgical Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jonathan B Greer
- Department of Surgical Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christian F Meyer
- Department of Medical Oncology, The Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Brian H Ladle
- Departement of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Elizabeth D Thompson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Elizabeth A Montgomery
- Department of Gastrointestinal and Liver Pathology, Johns Hopkins University, Baltimore, MD
| | - Woonyoung Choi
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - David J McConkey
- The Greenberg Bladder Cancer Institute, Johns Hopkins School of Medicine, Baltimore, MD
| | - Robert A Anders
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Drew M Pardoll
- Division of Immunology and Hematopoiesis, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nicolas J Llosa
- Departement of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD.
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23
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Zheng B, Zhang S, Cai W, Wang J, Wang T, Tang N, Shi Y, Luo X, Yan W. Identification of Novel Fusion Transcripts in Undifferentiated Pleomorphic Sarcomas by Transcriptome Sequencing. Cancer Genomics Proteomics 2020; 16:399-408. [PMID: 31467233 DOI: 10.21873/cgp.20144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/03/2019] [Accepted: 07/04/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND/AIM Undifferentiated pleomorphic sarcoma (UPS) is an aggressive mesenchymal neoplasm characterized by chromosomal instability. The aim of this study was to identify fusion events involved in UPS. MATERIALS AND METHODS Transcriptome sequencing was performed to search for new fusion genes in 19 UPS samples, including two paired recurrent (R) and re-recurrent (RR) samples. RESULTS A total of 66 fusion genes were detected. Among them, 10 novel fusion genes were further confirmed by reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing. Retinoblastoma (RB1) fusions (2 cases) were the most recurrent fusion genes. The gene fusions RB1-RNASEH2B, RB1-FGF14-AS1, and E2F6-FKBP4 were correlated with the Rb/E2F pathway. Pseudogenes were involved in the formation of the gene fusions CIC-DUX4L8 and EIF2AK4-ANXA2P2. Importantly, targetable gene fusions (PDGFRA-MACROD2 and NCOR1-MAP2K1) were detected in UPS. CONCLUSION Screening for the presence of fusion transcripts will provide vital clues to the understanding of genetic alterations and the finding of new targeted therapies for UPS.
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Affiliation(s)
- Biqiang Zheng
- Department of Musculoskeletal Cancer Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | | | - Weiluo Cai
- Department of Musculoskeletal Cancer Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Jian Wang
- Department of Musculoskeletal Cancer Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Ting Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Ning Tang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Yingqiang Shi
- Department of Musculoskeletal Cancer Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Xiaoying Luo
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Wangjun Yan
- Department of Musculoskeletal Cancer Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, P.R. China
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24
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Lesluyes T, Baud J, Pérot G, Charon-Barra C, You A, Valo I, Bazille C, Mishellany F, Leroux A, Renard-Oldrini S, Terrier P, Le Cesne A, Laé M, Piperno-Neumann S, Bonvalot S, Neuville A, Collin F, Maingon P, Coindre JM, Chibon F. Genomic and transcriptomic comparison of post-radiation versus sporadic sarcomas. Mod Pathol 2019; 32:1786-1794. [PMID: 31243333 DOI: 10.1038/s41379-019-0300-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 01/16/2023]
Abstract
Post-radiation sarcomas are rare secondary cancers arising from radiation therapies. To date, few genetic specificities have been described for such malignancies and the oncogenesis of sarcomas with complex genetics (both sporadic and post-radiation) remains largely misunderstood. We performed genomic and transcriptomic analyses on 77 post-radiation sarcomas using DNA-array and RNA sequencing. Consequently, we were able to investigate changes in copy number variations, transcriptome profiling, fusion gene expression, and mutational landscapes. We compare these data to a reference cohort of 93 sporadic sarcomas. At genomic level, similar chromosomal complexity was observed both in post-radiation and sporadic sarcomas with complex genetics. We found more frequent CDKN2A and CDKN2B (coding for p14/p16 and p15 proteins, respectively; at 9p21.3) losses in post-radiation (71%) than in sporadic tumors (39%; P = 6.92e-3). Among all detected fusion genes and punctual variations, few specificities were observed between these groups and such alterations are not able to drive a strong and specific oncogenesis. Recurrent MYC amplifications (96%) and KDR variants (8%) were detected in post-radiation angiosarcomas, in agreement with the literature. Transcriptomic analysis of such angiosarcomas revealed two distinct groups harboring different genomic imbalances (in particular gains of 17q24.2-17qter) with different clinical courses according to patient's vital status. Differential gene expression analysis permitted to focus on the immune response as a potential actor to tumor aggressiveness. Histochemistry validated a lower inflammation and lower immune infiltrate at tumor periphery for highly aggressive angiosarcomas. Our results provide new genomic and transcriptomic information about post-radiation sarcomas. The techniques we used (RNA-seq and DNA-arrays) did not highlight major differences in sarcomas with complex genetics depending on the radiation context, revealing similar patterns of transcriptomic profiles and chromosomal copy number variations. Additional characterizations, particularly whole genome sequencing, could measure changes in DNA following radiation therapy in such malignancies and may precise their oncogenesis.
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Affiliation(s)
- Tom Lesluyes
- Inserm U1218, Institut Bergonié, Bordeaux, France.,University of Bordeaux, F-33000, Bordeaux, France.,Inserm UMR1037, Cancer Research Center of Toulouse, Toulouse, France.,Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | - Jessica Baud
- Inserm U1218, Institut Bergonié, Bordeaux, France.,University of Bordeaux, F-33000, Bordeaux, France
| | - Gaëlle Pérot
- Inserm U1218, Institut Bergonié, Bordeaux, France.,Department of Pathology, Institut Bergonié, Bordeaux, France
| | | | - Axel You
- Inserm U1218, Institut Bergonié, Bordeaux, France.,University of Nantes, F-44000, Nantes, France
| | - Isabelle Valo
- Department of Pathology, Institut de cancérologie de l'Ouest site Paul Papin, Angers, France
| | - Céline Bazille
- Department of Pathology, University Hospital, Caen, France
| | | | - Agnès Leroux
- Department of Pathology, Centre Alexis Vautrin, Vandoeuvre-lès-Nancy, France
| | - Sophie Renard-Oldrini
- Department of Radiation Therapy, Centre Alexis Vautrin, Vandoeuvre-lès-Nancy, France
| | - Philippe Terrier
- Department of Pathology, Institut Gustave Roussy, Villejuif, France
| | - Axel Le Cesne
- Department of Medical Oncology, Institut Gustave Roussy, Villejuif, France
| | - Marick Laé
- Department of Pathology, Institut Curie, Paris, France.,Department of Pathology, Centre Henri Becquerel, Inserm U1245, UniRouen Normandy University, Rouen, France
| | | | | | - Agnès Neuville
- Department of Pathology, Institut Bergonié, Bordeaux, France.,Contades Office of Pathological Anatomy and Cytology, Strasbourg, France
| | - Françoise Collin
- Department of Pathology, Centre Georges-François Leclerc, Dijon, France
| | - Philippe Maingon
- Department of Radiation Oncology, Hôpital La Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - Jean-Michel Coindre
- University of Bordeaux, F-33000, Bordeaux, France.,Department of Pathology, Institut Bergonié, Bordeaux, France
| | - Frédéric Chibon
- Inserm UMR1037, Cancer Research Center of Toulouse, Toulouse, France. .,Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France.
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25
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26
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Yakirevich E, Madison R, Fridman E, Mangray S, Carneiro BA, Lu S, Cooke M, Bratslavsky G, Webster J, Ross JS, Ali SM. Comprehensive Genomic Profiling of Adult Renal Sarcomas Provides Insight into Disease Biology and Opportunities for Targeted Therapies. Eur Urol Oncol 2019; 4:282-288. [PMID: 31412008 DOI: 10.1016/j.euo.2019.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/12/2019] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Primary adult renal sarcomas (RSs) are rare aggressive neoplasms. Clinical outcomes are extremely poor, and optimal treatment remains challenging. OBJECTIVE To identify genomic alterations (GAs) in patients with RSs. DESIGN, SETTING, AND PARTICIPANTS Comprehensive genomic profiling (CGP) was conducted on DNA/RNA extracted from formalin-fixed paraffin-embedded tissue using the FoundationOne Heme/Sarcoma assay in 13 adult, locally advanced or metastatic RSs of various histologic types. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS All classes of GAs, including base substitutions, small indels, rearrangements, copy number alterations, tumor mutational burden (TMB), and microsatellite instability (MSI), were analyzed. RESULTS AND LIMITATIONS CGP revealed 55 GAs (4.2 per tumor), 29 of which were clinically relevant genomic alterations (CRGAs; 2.2 per tumor). At least one CRGA was detected in nine (69%) cases. High-level amplifications (more than six copies) involving 4q12 amplicon of the KIT and PDGFRA genes were identified in four (31%) cases (two undifferentiated pleomorphic sarcomas [UPSs], one sarcomatoid renal cell carcinoma, and one myxofibrosarcoma). Both UPSs also had KDR gene amplification in addition to KIT and PDGFRA. Additional CRGAs were found in CDKN2A/B (23%), NF1 (23%), and MET (8%). All RSs were MSI stable, the mean TMB was 3.5 mutations/megabase (Mb), and none (0%) featured TMB >10 mutations/Mb. Limitations include the small sample size. CONCLUSIONS RSs are characterized by diverse histology and genomic profiles including 31% of cases with 4q12 amplification harboring the KIT/PDGFRA/KDR genes. Of the tumors, 69% carry CRGAs, which could lead to potential benefit from targeted therapies; however, a low TMB also suggests that these cases are unlikely to respond to checkpoint inhibitors. PATIENT SUMMARY This study provides insights into molecular biology of renal sarcoma, a rare aggressive subtype of kidney tumors. We demonstrated that renal sarcomas harbor unique, recurrent, clinically relevant molecular abnormalities that provide new opportunities for targeted therapies.
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Affiliation(s)
- Evgeny Yakirevich
- Department of Pathology, Rhode Island Hospital, Providence, RI, USA; Alpert Medical School at Brown University, Providence, RI, USA.
| | | | - Eduard Fridman
- Department of Pathology, Sheba Medical Center, Tel-Aviv, Israel
| | - Shamlal Mangray
- Department of Pathology, Rhode Island Hospital, Providence, RI, USA; Alpert Medical School at Brown University, Providence, RI, USA
| | - Benedito A Carneiro
- Alpert Medical School at Brown University, Providence, RI, USA; Hematology/Oncology Division, Lifespan Cancer Institute, Department of Internal Medicine, Rhode Island Hospital, Providence, RI, USA
| | - Shaolei Lu
- Department of Pathology, Rhode Island Hospital, Providence, RI, USA; Alpert Medical School at Brown University, Providence, RI, USA
| | | | | | | | | | - Siraj M Ali
- Foundation Medicine Inc., Cambridge, MA, USA
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27
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Carvalho SD, Pissaloux D, Crombé A, Coindre JM, Le Loarer F. Pleomorphic Sarcomas: The State of the Art. Surg Pathol Clin 2019; 12:63-105. [PMID: 30709449 DOI: 10.1016/j.path.2018.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This article focuses on pleomorphic sarcomas, which are malignant mesenchymal tumors with complex genetic background at the root of their morphologic pleomorphism. They are poorly differentiated tumors that may retain different lines of differentiation, sometimes correlating with clinicopathological or prognostic features. Accurate diagnosis in this group of tumors relies on adequate sampling due to their heterogeneity and assessment with both microscopy and large panels of immunohistochemistry. Molecular analyses have a limited role in their diagnosis as opposed to translocation-related sarcomas but may provide theranostic and important prognostic information in the future.
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Affiliation(s)
- Sofia Daniela Carvalho
- Department of Pathology, Hospital de Braga, Sete Fontes-Sao Victor, 4710-243 Braga, Portugal; Department of Pathology, Institut Bergonié, 276 cours de l'Argonne, 33000, Bordeaux, France
| | - Daniel Pissaloux
- Department of Pathology, Centre Leon Berard, Promenade Lea Bullukian, 69376 Lyon, France
| | - Amandine Crombé
- Department of Radiology, Institut Bergonié, 276 cours de l'Argonne, 33000, Bordeaux, France
| | - Jean-Michel Coindre
- Department of Pathology, Institut Bergonié, 276 cours de l'Argonne, 33000, Bordeaux, France; University of Bordeaux, Talence, France
| | - François Le Loarer
- Department of Pathology, Hospital de Braga, Sete Fontes-Sao Victor, 4710-243 Braga, Portugal; University of Bordeaux, Talence, France.
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Suster DI, Deshpande V, Chebib I, Taylor MS, Mullen J, Bredella MA, Nielsen GP. Spindle cell liposarcoma with a TRIO-TERT fusion transcript. Virchows Arch 2019; 475:391-394. [DOI: 10.1007/s00428-019-02545-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 01/07/2023]
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29
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Integrated genetic and epigenetic analysis of myxofibrosarcoma. Nat Commun 2018; 9:2765. [PMID: 30018380 PMCID: PMC6050269 DOI: 10.1038/s41467-018-03891-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 03/20/2018] [Indexed: 12/27/2022] Open
Abstract
Myxofibrosarcoma (MFS) is a common adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high local recurrence rate. Here we report the genetic and epigenetic landscape of MFS based on the results of whole-exome sequencing (N = 41), RNA sequencing (N = 29), and methylation analysis (N = 41), using 41 MFSs as a discovery set, and subsequent targeted sequencing of 140 genes in the entire cohort of 99 MFSs and 17 MFSs' data from TCGA. Fourteen driver genes are identified, including potentially actionable therapeutic targets seen in 37% of cases. There are frequent alterations in p53 signaling (51%) and cell cycle checkpoint genes (43%). Other conceivably actionable driver genes including ATRX, JAK1, NF1, NTRK1, and novel oncogenic BRAF fusion gene are identified. Methylation patterns cluster into three subtypes associated with unique combinations of driver mutations, clinical outcomes, and immune cell compositions. Our results provide a valuable genomic resource to enable the design of precision medicine for MFS. Myxofibrosarcoma occurs in adults and is associated with high local relapse. Here, based on exome/transcriptome sequencing and DNA methylation analysis, the authors identify driver genes and methylation clusters associated with unique combinations of mutations, outcomes, and immune cell compositions.
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Widemann BC, Italiano A. Biology and Management of Undifferentiated Pleomorphic Sarcoma, Myxofibrosarcoma, and Malignant Peripheral Nerve Sheath Tumors: State of the Art and Perspectives. J Clin Oncol 2017; 36:160-167. [PMID: 29220302 DOI: 10.1200/jco.2017.75.3467] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Undifferentiated pleomorphic sarcomas, myxofibrosarcomas, and malignant peripheral nerve sheath tumors are characterized by complex genomic characteristics and aggressive clinical behavior. Recent advances in the understanding of the pathogenesis of these tumors may allow for the development of more-effective innovative therapeutic strategies, including immunotherapies. This review describes the current knowledge of the epidemiology, clinical presentation, treatment, and pathogenesis of these tumors and highlights ongoing and future research.
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Affiliation(s)
- Brigitte C Widemann
- Brigitte C. Widemann, National Cancer Institute, Bethesda, MD; and Antoine Italiano, Institut Bergonié and University of Bordeaux, Bordeaux, France
| | - Antoine Italiano
- Brigitte C. Widemann, National Cancer Institute, Bethesda, MD; and Antoine Italiano, Institut Bergonié and University of Bordeaux, Bordeaux, France
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Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell 2017; 171:950-965.e28. [PMID: 29100075 DOI: 10.1016/j.cell.2017.10.014] [Citation(s) in RCA: 640] [Impact Index Per Article: 91.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/07/2017] [Accepted: 10/05/2017] [Indexed: 12/26/2022]
Abstract
Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (TP53, ATRX, RB1) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types.
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