title: Somatic loss of function mutations in neurofibromin 1 and MYC associated factor X genes identified by exome-wide sequencing in a wild-type GIST case.
abstract: BACKGROUND
  Approximately 10-15 % of gastrointestinal stromal tumors (GISTs) lack gain of function mutations in the KIT and platelet-derived growth factor receptor alpha (PDGFRA) genes. An alternate mechanism of oncogenesis through loss of function of the succinate-dehydrogenase (SDH) enzyme complex has been identified for a subset of these "wild type" GISTs.
  
  
  METHODS
  Paired tumor and normal DNA from an SDH-intact wild-type GIST case was subjected to whole exome sequencing to identify the pathogenic mechanism(s) in this tumor. Selected findings were further investigated in panels of GIST tumors through Sanger DNA sequencing, quantitative real-time PCR, and immunohistochemical approaches.
  
  
  RESULTS
  A hemizygous frameshift mutation (p.His2261Leufs*4), in the neurofibromin 1 (NF1) gene was identified in the patient's GIST; however, no germline NF1 mutation was found. A somatic frameshift mutation (p.Lys54Argfs*31) in the MYC associated factor X (MAX) gene was also identified. Immunohistochemical analysis for MAX on a large panel of GISTs identified loss of MAX expression in the MAX-mutated GIST and in a subset of mainly KIT-mutated tumors.
  
  
  CONCLUSIONS
  This study suggests that inactivating NF1 mutations outside the context of neurofibromatosis may be the oncogenic mechanism for a subset of sporadic GIST. In addition, loss of function mutation of the MAX gene was identified for the first time in GIST, and a broader role for MAX in GIST progression was suggested.
authors.affiliation: Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111-2497, USA. martin.belinsky@fccc.edu.
authors.forename: Martin G
authors.initials: MG
authors.lastname: Belinsky
authors.affiliation: Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111-2497, USA. lori.rink@fccc.edu.
authors.forename: Lori
authors.initials: L
authors.lastname: Rink
authors.affiliation: Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA. qi.cai@fccc.edu.
authors.forename: Kathy Q
authors.initials: KQ
authors.lastname: Cai
authors.affiliation: Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111-2497, USA. scapuzzi@gmail.com.|Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC, USA. scapuzzi@gmail.com.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Capuzzi
authors.affiliation: Department of Bioinformatics and Biosystems Technology, University of Applied Sciences Wildau, Wildau, Germany. yhoang.thw@gmail.com.|Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA. yhoang.thw@gmail.com.
authors.forename: Yen
authors.initials: Y
authors.lastname: Hoang
authors.affiliation: Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA. jchien@kumc.edu.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Chien
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA. agodwin@kumc.edu.
authors.forename: Andrew K
authors.initials: AK
authors.lastname: Godwin
authors.affiliation: Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111-2497, USA. margaret.vonMehren@fccc.edu.
authors.forename: Margaret
authors.initials: M
authors.lastname: von Mehren
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D050976:Basic-Leucine Zipper Transcription Factors / Q000235:genetics*; D059472:Exome / Q000235:genetics; D005260:Female; D016368:Frameshift Mutation; D046152:Gastrointestinal Stromal Tumors / Q000235:genetics* / Q000473:pathology; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D025542:Neurofibromin 1 / Q000235:genetics*; D019009:Proto-Oncogene Proteins c-kit / Q000235:genetics; D020796:Receptor, Platelet-Derived Growth Factor alpha / Q000235:genetics; D013385:Succinate Dehydrogenase / Q000235:genetics
chemical_list: D050976:Basic-Leucine Zipper Transcription Factors; C067850:Myc associated factor X; D025542:Neurofibromin 1; D013385:Succinate Dehydrogenase; D019009:Proto-Oncogene Proteins c-kit; D020796:Receptor, Platelet-Derived Growth Factor alpha