title: Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.
abstract: BACKGROUND
  Activating mutations in one allele of an oncogene (heterozygous mutations) are widely believed to be sufficient for tumorigenesis. However, mutant allele specific imbalance (MASI) has been observed in tumors and cell lines harboring mutations of oncogenes.
  
  
  RESULTS
  We determined 1) mutational status, 2) copy number gains (CNGs) and 3) relative ratio between mutant and wild type alleles of KRAS, BRAF, PIK3CA and EGFR genes by direct sequencing and quantitative PCR assay in over 400 human tumors, cell lines, and xenografts of lung, colorectal, and pancreatic cancers. Examination of a public database indicated that homozygous mutations of five oncogenes were frequent (20%) in 833 cell lines of 12 tumor types. Our data indicated two major forms of MASI: 1) MASI with CNG, either complete or partial; and 2) MASI without CNG (uniparental disomy; UPD), due to complete loss of wild type allele. MASI was a frequent event in mutant EGFR (75%) and was due mainly to CNGs, while MASI, also frequent in mutant KRAS (58%), was mainly due to UPD. Mutant: wild type allelic ratios at the genomic level were precisely maintained after transcription. KRAS mutations or CNGs were significantly associated with increased ras GTPase activity, as measured by ELISA, and the two molecular changes were synergistic. Of 237 lung adenocarcinoma tumors, the small number with both KRAS mutation and CNG were associated with shortened survival.
  
  
  CONCLUSIONS
  MASI is frequently present in mutant EGFR and KRAS tumor cells, and is associated with increased mutant allele transcription and gene activity. The frequent finding of mutations, CNGs and MASI occurring together in tumor cells indicates that these three genetic alterations, acting together, may have a greater role in the development or maintenance of the malignant phenotype than any individual alteration.
authors.affiliation: Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.
authors.forename: Junichi
authors.initials: J
authors.lastname: Soh
authors.forename: Naoki
authors.initials: N
authors.lastname: Okumura
authors.forename: William W
authors.initials: WW
authors.lastname: Lockwood
authors.forename: Hiromasa
authors.initials: H
authors.lastname: Yamamoto
authors.forename: Hisayuki
authors.initials: H
authors.lastname: Shigematsu
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.forename: Raj
authors.initials: R
authors.lastname: Chari
authors.forename: David S
authors.initials: DS
authors.lastname: Shames
authors.forename: Ximing
authors.initials: X
authors.lastname: Tang
authors.forename: Calum
authors.initials: C
authors.lastname: MacAulay
authors.forename: Marileila
authors.initials: M
authors.lastname: Varella-Garcia
authors.forename: Tõnu
authors.initials: T
authors.lastname: Vooder
authors.forename: Ignacio I
authors.initials: II
authors.lastname: Wistuba
authors.forename: Stephen
authors.initials: S
authors.lastname: Lam
authors.forename: Rolf
authors.initials: R
authors.lastname: Brekken
authors.forename: Shinichi
authors.initials: S
authors.lastname: Toyooka
authors.forename: John D
authors.initials: JD
authors.lastname: Minna
authors.forename: Wan L
authors.initials: WL
authors.lastname: Lam
authors.forename: Adi F
authors.initials: AF
authors.lastname: Gazdar
mesh_terms: D000483:Alleles; D045744:Cell Line, Tumor; D003001:Cloning, Molecular; D004252:DNA Mutational Analysis; D015972:Gene Expression Regulation, Neoplastic; D006579:Heterozygote; D006801:Humans; D008957:Models, Genetic; D009154:Mutation; D009369:Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D009857:Oncogenes; D010641:Phenotype; D010957:Plasmids / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D016896:Treatment Outcome