title: Protein tyrosine kinase 7: a hepatocellular carcinoma-related gene detected by triple-combination array.
abstract: BACKGROUND
  Hepatocellular carcinoma (HCC) is one of the top five causes of cancer-related deaths worldwide. We developed a novel technique to identify cancer-related genes of HCC as follows: triple-combination array analysis, which combines gene expression profiles, single nucleotide polymorphism arrays, and methylation arrays.
  
  
  METHODS
  Triple-combination array analysis was performed on one HCC sample from a 68-y-old female patient, and one candidate cancer-related gene was selected. Subsequently, we analyzed the identified gene by quantitative real-time reverse-transcriptase polymerase chain reaction (PCR) and methylation-specific PCR in nine HCC cell lines and in samples from 48 HCC patients. Additionally, we evaluated gene expression by immunohistochemistry and Western blotting.
  
  
  RESULTS
  Using this method, protein tyrosine kinase 7 (PTK7) was detected as a candidate cancer-related gene. PTK7 was revealed to be hypermethylated (methylation value 0.826, range 0-1.0) in cancer tissue, compared with that of adjacent noncancerous tissues (0.047) by methylation array. Of the 48 clinical samples, 30 HCC samples (62.5%) showed PTK7 promoter hypermethylation. Downregulation of PTK7 (expressions in tumor tissues decreased by ≥ 50% compared with the noncancerous tissues) was significantly associated with age >60 y (P = 0.030) and elevation in serum protein induced by vitamin K absence or antagonists-II (P = 0.033). Moreover, patients with downregulation were significantly inferior in overall survival (P < 0.001) than the others.
  
  
  CONCLUSIONS
  Our data imply that PTK7 acts as a cancer-related gene and may be a potent prognostic marker for HCC. Triple-combination array analysis was once again found to be useful in identifying cancer-related genes.
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Mitsuhiro
authors: M
authors: Hishida
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Yoshikuni
authors: Y
authors: Inokawa
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Nao
authors: N
authors: Takano
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Yoko
authors: Y
authors: Nishikawa
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Naoki
authors: N
authors: Iwata
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Mitsuro
authors: M
authors: Kanda
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Chie
authors: C
authors: Tanaka
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Daisuke
authors: D
authors: Kobayashi
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Suguru
authors: S
authors: Yamada
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Goro
authors: G
authors: Nakayama
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Tsutomu
authors: T
authors: Fujii
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Hiroyuki
authors: H
authors: Sugimoto
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Masahiko
authors: M
authors: Koike
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Michitaka
authors: M
authors: Fujiwara
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan.
authors: Yasuhiro
authors: Y
authors: Kodera
authors: Gastroenterological Surgery (Department of Surgery II), Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya, Japan; Department of Surgery, Aichi-Gakuin University School of Dentistry, Chikusa-ku, Nagoya, Japan. Electronic address: snomoto@med.nagoya-u.ac.jp.
authors: Shuji
authors: S
authors: Nomoto
mesh_terms: D000328:Adult; D000368:Aged; D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D015815:Cell Adhesion Molecules / Q000032:analysis / Q000235:genetics* / Q000502:physiology; D019175:DNA Methylation; D005260:Female; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction; D020794:Receptor Protein-Tyrosine Kinases / Q000032:analysis / Q000235:genetics* / Q000502:physiology
chemical_list: D015815:Cell Adhesion Molecules; C096905:PTK7 protein, human; D020794:Receptor Protein-Tyrosine Kinases
keywords: Array analysis; Cancer-related genes; Hepatocellular carcinoma; Methylation; Protein tyrosine kinase 7