title: Deep Sequencing in Conjunction with Expression and Functional Analyses Reveals Activation of FGFR1 in Ewing Sarcoma.
abstract: OBJECTIVE
  A low mutation rate seems to be a general feature of pediatric cancers, in particular in oncofusion gene-driven tumors. Genetically, Ewing sarcoma is defined by balanced chromosomal EWS/ETS translocations, which give rise to oncogenic chimeric proteins (EWS-ETS). Other contributing somatic mutations involved in disease development have only been observed at low frequency.
  
  
  METHODS
  Tumor samples of 116 Ewing sarcoma patients were analyzed here. Whole-genome sequencing was performed on two patients with normal, primary, and relapsed tissue. Whole-exome sequencing was performed on 50 Ewing sarcoma and 22 matched normal tissues. A discovery dataset of 14 of these tumor/normal pairs identified 232 somatic mutations. Recurrent nonsynonymous mutations were validated in the 36 remaining exomes. Transcriptome analysis was performed in a subset of 14 of 50 Ewing sarcomas and DNA copy number gain and expression of FGFR1 in 63 of 116 Ewing sarcomas.
  
  
  RESULTS
  Relapsed tumors consistently showed a 2- to 3-fold increased number of mutations. We identified several recurrently mutated genes at low frequency (ANKRD30A, CCDC19, KIAA0319, KIAA1522, LAMB4, SLFN11, STAG2, TP53, UNC80, ZNF98). An oncogenic fibroblast growth factor receptor 1 (FGFR1) mutation (N546K) was detected, and the FGFR1 locus frequently showed copy number gain (31.7%) in primary tumors. Furthermore, high-level FGFR1 expression was noted as a characteristic feature of Ewing sarcoma. RNA interference of FGFR1 expression in Ewing sarcoma lines blocked proliferation and completely suppressed xenograft tumor growth. FGFR1 tyrosine kinase inhibitor (TKI) therapy in a patient with Ewing sarcoma relapse significantly reduced 18-FDG-PET activity.
  
  
  CONCLUSIONS
  FGFR1 may constitute a promising target for novel therapeutic approaches in Ewing sarcoma.
authors.affiliation: Department of Medicine A, Hematology, and Oncology, University Hospital of Muenster, Muenster, Germany.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Agelopoulos
authors.affiliation: Children's Cancer Research Center and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München and Comprehensive Cancer Center Munich (CCCM), Munich, Germany, together with the German Cancer Consortium (DKTK), Germany. carsten.mueller-tidow@uk-halle.de guenther.richter@lrz.tum.de.
authors.forename: Günther H S
authors.initials: GH
authors.lastname: Richter
authors.affiliation: Department of Medicine A, Hematology, and Oncology, University Hospital of Muenster, Muenster, Germany.
authors.forename: Eva
authors.initials: E
authors.lastname: Schmidt
authors.affiliation: Department of Pediatric Oncology and Hematology, University Children's Hospital Muenster, Muenster, Germany.
authors.forename: Uta
authors.initials: U
authors.lastname: Dirksen
authors.affiliation: Children's Cancer Research Center and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München and Comprehensive Cancer Center Munich (CCCM), Munich, Germany, together with the German Cancer Consortium (DKTK), Germany.
authors.forename: Kristina
authors.initials: K
authors.lastname: von Heyking
authors.affiliation: Department of Medicine A, Hematology, and Oncology, University Hospital of Muenster, Muenster, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Moser
authors.affiliation: Institute of Medical Informatics, University of Muenster, Muenster, Germany.
authors.forename: Hans-Ulrich
authors.initials: HU
authors.lastname: Klein
authors.affiliation: Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
authors.forename: Udo
authors.initials: U
authors.lastname: Kontny
authors.affiliation: Institute of Medical Informatics, University of Muenster, Muenster, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Dugas
authors.affiliation: Institute of Bioinformatics, University Hospital of Muenster, Muenster, Germany.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Poos
authors.affiliation: Institute of Bioinformatics, University Hospital of Muenster, Muenster, Germany.
authors.forename: Eberhard
authors.initials: E
authors.lastname: Korsching
authors.affiliation: Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany. Institute of Laboratory Animal Science, University of Zurich, Zurich, Switzerland.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Buch
authors.affiliation: Department of Nuclear Medicine, University of Muenster, Muenster, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Weckesser
authors.affiliation: Department of Medicine A, Hematology, and Oncology, University Hospital of Muenster, Muenster, Germany. Department of Medicine IV, Hematology and Oncology, State Center for Cell and Gene Therapy, University Hospital Halle, Halle (Saale), Germany.
authors.forename: Isabell
authors.initials: I
authors.lastname: Schulze
authors.affiliation: Institute of Human Genetics, University of Muenster, Muenster, Germany.
authors.forename: Regina
authors.initials: R
authors.lastname: Besoke
authors.affiliation: Institute of Human Genetics, Genetic Epidemiology, University of Muenster, Muenster, Germany.
authors.forename: Anika
authors.initials: A
authors.lastname: Witten
authors.affiliation: Institute of Human Genetics, Genetic Epidemiology, University of Muenster, Muenster, Germany.
authors.forename: Monika
authors.initials: M
authors.lastname: Stoll
authors.affiliation: Institute of Pathology, Klinikum Fulda, Fulda, Germany.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Köhler
authors.affiliation: Department of Pathology, University of Muenster, Muenster, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Hartmann
authors.affiliation: Department of Pathology, University of Muenster, Muenster, Germany.
authors.forename: Eva
authors.initials: E
authors.lastname: Wardelmann
authors.affiliation: Department of Pediatric Oncology and Hematology, University Children's Hospital Muenster, Muenster, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Rossig
authors.affiliation: Bone Tumor Reference Center at the Institute of Pathology, University Hospital Basel, Basel, Switzerland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Baumhoer
authors.affiliation: Department of Pediatric Oncology and Hematology, University Children's Hospital Muenster, Muenster, Germany.
authors.forename: Heribert
authors.initials: H
authors.lastname: Jürgens
authors.affiliation: Children's Cancer Research Center and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München and Comprehensive Cancer Center Munich (CCCM), Munich, Germany, together with the German Cancer Consortium (DKTK), Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Burdach
authors.affiliation: Department of Medicine A, Hematology, and Oncology, University Hospital of Muenster, Muenster, Germany.
authors.forename: Wolfgang E
authors.initials: WE
authors.lastname: Berdel
authors.affiliation: Department of Medicine A, Hematology, and Oncology, University Hospital of Muenster, Muenster, Germany. Department of Medicine IV, Hematology and Oncology, State Center for Cell and Gene Therapy, University Hospital Halle, Halle (Saale), Germany. carsten.mueller-tidow@uk-halle.de guenther.richter@lrz.tum.de.
authors.forename: Carsten
authors.initials: C
authors.lastname: Müller-Tidow
mesh_terms: D000293:Adolescent; D000328:Adult; D000818:Animals; D045744:Cell Line, Tumor; D002648:Child; D056915:DNA Copy Number Variations; D004195:Disease Models, Animal; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D005787:Gene Frequency; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D018345:Mice, Knockout; D009154:Mutation; D009364:Neoplasm Recurrence, Local; D009367:Neoplasm Staging; D051496:Receptor, Fibroblast Growth Factor, Type 1 / Q000235:genetics* / Q000378:metabolism*; D012512:Sarcoma, Ewing / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D015398:Signal Transduction; D055815:Young Adult
chemical_list: D051496:Receptor, Fibroblast Growth Factor, Type 1