title: Detection of doublecortin domain-containing 2 (DCDC2), a new candidate tumor suppressor gene of hepatocellular carcinoma, by triple combination array analysis.
abstract: BACKGROUND
  To detect genes correlated with hepatocellular carcinoma (HCC), we developed a triple combination array consisting of methylation array, gene expression array and single nucleotide polymorphism (SNP) array analysis.
  
  
  METHODS
  A surgical specimen obtained from a 68-year-old female HCC patient was analyzed by triple combination array, which identified doublecortin domain-containing 2 (DCDC2) as a candidate tumor suppressor gene of HCC. Subsequently, samples from 48 HCC patients were evaluated for their DCDC2 methylation and expression status using methylation specific PCR (MSP) and semi-quantitative reverse transcriptase (RT) PCR, respectively. Then, we investigated the relationship between clinicopathological factors and methylation status of DCDC2.
  
  
  RESULTS
  DCDC2 was revealed to be hypermethylated (methylation value 0.846, range 0-1.0) in cancer tissue, compared with adjacent normal tissue (0.212) by methylation array in the 68-year-old female patient. Expression array showed decreased expression of DCDC2 in cancerous tissue. SNP array showed that the copy number of chromosome 6p22.1, in which DCDC2 resides, was normal. MSP revealed hypermethylation of the promoter region of DCDC2 in 41 of the tumor samples. DCDC2 expression was significantly decreased in the cases with methylation (P = 0.048). Furthermore, the methylated cases revealed worse prognosis for overall survival than unmethylated cases (P = 0.048).
  
  
  CONCLUSIONS
  The present study indicates that triple combination array is an effective method to detect novel genes related to HCC. We propose that DCDC2 is a tumor suppressor gene of HCC.
authors.affiliation: Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Japan, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan. snomoto@med.nagoya-u.ac.jp.
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: Hiroyuki
authors.initials: H
authors.lastname: Sugimoto
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Fujii
authors.forename: Suguru
authors.initials: S
authors.lastname: Yamada
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Kodera
mesh_terms: D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D000089622:Doublecortin Domain Proteins; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D016147:Genes, Tumor Suppressor; D006801:Humans; D007150:Immunohistochemistry; D008113:Liver Neoplasms / Q000235:genetics* / Q000473:pathology; D008869:Microtubule-Associated Proteins / Q000235:genetics* / Q000378:metabolism; D009479:Neuropeptides / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D011379:Prognosis; D016019:Survival Analysis
chemical_list: D014408:Biomarkers, Tumor; D000089622:Doublecortin Domain Proteins; D008869:Microtubule-Associated Proteins; D009479:Neuropeptides
references.citation: Cancer J. 2004 Mar-Apr;10(2):97-103
references.pmid: 15130269
references.citation: Cancer. 2006 Aug 1;107(3):579-90
references.pmid: 16795071
references.citation: Ann Surg Oncol. 2010 Mar;17(3):923-32
references.pmid: 19898900
references.citation: Cancer. 2001 Jul 1;92(1):136-45
references.pmid: 11443619
references.citation: Trends Mol Med. 2006 Jul;12(7):333-41
references.pmid: 16781891
references.citation: J Clin Oncol. 2006 Sep 10;24(26):4293-300
references.pmid: 16908937
references.citation: Cancer Res. 1999 Jan 1;59(1):71-3
references.pmid: 9892188
references.citation: Nat Rev Genet. 2002 Jun;3(6):415-28
references.pmid: 12042769
references.citation: Cancer Genet Cytogenet. 2008 Jan 1;180(1):30-6
references.pmid: 18068530
references.citation: Br J Cancer. 2007 Nov 5;97(9):1260-5
references.pmid: 17968429
references.citation: Am J Pathol. 2003 Oct;163(4):1371-8
references.pmid: 14507645
references.citation: Gastroenterology. 2004 Nov;127(5 Suppl 1):S72-8
references.pmid: 15508106
references.citation: Biochim Biophys Acta. 2003 Jun 5;1653(1):1-24
references.pmid: 12781368
references.citation: Nat Genet. 1999 Feb;21(2):163-7
references.pmid: 9988266
references.citation: Mol Carcinog. 2011 Aug;50(8):571-9
references.pmid: 21268132
references.citation: Proc Natl Acad Sci U S A. 2005 Nov 22;102(47):17053-8
references.pmid: 16278297
references.citation: J Surg Oncol. 2012 Mar 15;105(4):381-6
references.pmid: 22052684
references.citation: Annu Rev Genomics Hum Genet. 2007;8:57-79
references.pmid: 17444811
references.citation: Cancer. 2006 Apr 15;106(8):1794-803
references.pmid: 16532500
references.citation: Cancer Lett. 2010 Mar 28;289(2):170-7
references.pmid: 19733004
references.citation: Biotechnol Bioeng. 2009 Nov 1;104(4):796-808
references.pmid: 19591186
references.citation: Tumour Biol. 2012 Apr;33(2):325-36
references.pmid: 22351518
references.citation: Radiology. 1999 Mar;210(3):655-61
references.pmid: 10207464
references.citation: Nat Genet. 2001 May;28(1):29-35
references.pmid: 11326271
references.citation: Blood. 2002 Oct 15;100(8):2957-64
references.pmid: 12351408
references.citation: N Engl J Med. 2003 Nov 20;349(21):2042-54
references.pmid: 14627790
references.citation: Oncogene. 2013 May 2;32(18):2315-24, 2324.e1-4
references.pmid: 22733135
references.citation: BMC Genomics. 2011 Dec 23;12 Suppl 5:S15
references.pmid: 22369656
references.citation: Int J Cancer. 2007 Sep 1;121(5):1028-35
references.pmid: 17443492
references.citation: In Silico Biol. 2003;3(3):235-40
references.pmid: 12954087
references.citation: Am J Pathol. 2003 Sep;163(3):1101-7
references.pmid: 12937151
references.citation: Cancer Lett. 2011 Dec 22;312(2):150-7
references.pmid: 21943823
references.citation: Gastroenterology. 2007 Jun;132(7):2557-76
references.pmid: 17570226
references.citation: Cell Res. 2007 Mar;17(3):195-211
references.pmid: 17325692
references.citation: Cancer Res. 2001 Mar 1;61(5):2129-37
references.pmid: 11280777
references.citation: Int J Oncol. 2009 Sep;35(3):477-83
references.pmid: 19639168
references.citation: Methods Mol Biol. 2009;507:149-63
references.pmid: 18987813
references.citation: BMC Genomics. 2006 Jul 26;7:188
references.pmid: 16869982
references.citation: Gastroenterology. 2006 Aug;131(2):461-9
references.pmid: 16890600
references.citation: PLoS One. 2011;6(6):e20580
references.pmid: 21698230
references.citation: Hepatobiliary Pancreat Dis Int. 2008 Jun;7(3):237-57
references.pmid: 18522878
references.citation: Am J Hum Genet. 2006 Jan;78(1):52-62
references.pmid: 16385449
references.citation: Ann Surg Oncol. 2011 Feb;18(2):572-9
references.pmid: 20734148
references.citation: Neuron. 1999 Jun;23(2):257-71
references.pmid: 10399933
references.citation: Lancet. 2003 Dec 6;362(9399):1907-17
references.pmid: 14667750