title: Dynamin 3: a new candidate tumor suppressor gene in hepatocellular carcinoma detected by triple combination array analysis.
abstract: BACKGROUND
  To identify genes associated with hepatocellular carcinoma (HCC) pathogenesis, we developed a triple combination array strategy comprising methylation, gene expression, and single nucleotide polymorphism (SNP) array analysis.
  
  
  METHODS
  Surgical specimens obtained from a 68-year-old female HCC patient were analyzed by triple combination array, and identified Dynamin 3 (DNM3) as a candidate tumor suppressor gene in HCC. Subsequently, samples from 48 HCC patients were evaluated for DNM3 methylation and expression status using methylation specific polymerase chain reaction (PCR; MSP) and semi-quantitative reverse transcriptase (RT)-PCR, respectively. The relationship between clinicopathological factors and DNM3 methylation status was also investigated.
  
  
  RESULTS
  DNM3 was shown to be hypermethylated (methylation value 0.879, range 0-1.0) in cancer tissue compared with adjacent normal tissue (0.213) by methylation array in the 68-year-old female patient. Expression arrays revealed decreased expression of DNM3 in cancerous tissue. SNP arrays revealed that the copy number of chromosome 1q24.3, in which DNM3 resides, was normal. MSP revealed hypermethylation of the DNM3 promoter region in 33 of 48 tumor samples. A trend toward decreased DNM3 expression was observed in patients with DNM3 promoter methylation (P = 0.189). Furthermore, patients with reduced expression of DNM3 in tumor tissues exhibited worse prognosis with decreased disease specific survival compared to patients without decreased expression (P = 0.014).
  
  
  CONCLUSIONS
  The present study indicates that a triple combination array strategy is an effective method to detect novel genes related to HCC. We propose that DNM3 is a tumor suppressor gene in HCC.
authors.affiliation: Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya Japan.
authors.forename: Yoshikuni
authors.initials: Y
authors.lastname: Inokawa
authors.forename: Shuji
authors.initials: S
authors.lastname: Nomoto
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Hishida
authors.forename: Masamichi
authors.initials: M
authors.lastname: Hayashi
authors.forename: Mitsuro
authors.initials: M
authors.lastname: Kanda
authors.forename: Yoko
authors.initials: Y
authors.lastname: Nishikawa
authors.forename: Shin
authors.initials: S
authors.lastname: Takeda
authors.forename: Michitaka
authors.initials: M
authors.lastname: Fujiwara
authors.forename: Masahiko
authors.initials: M
authors.lastname: Koike
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Sugimoto
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Fujii
authors.forename: Goro
authors.initials: G
authors.lastname: Nakayama
authors.forename: Suguru
authors.initials: S
authors.lastname: Yamada
authors.forename: Chie
authors.initials: C
authors.lastname: Tanaka
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kobayashi
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Kodera
keywords: DNM3; hepatocellular carcinoma; methylation; triple combination array