title: Frequent methylation of HOXA9 gene in tumor tissues and plasma samples from human hepatocellular carcinomas.
abstract: BACKGROUND
  Aberrant DNA methylation is associated with the development of hepatocellular carcinoma (HCC), suggesting that gene methylation could be a potential biomarker for detection of HCC. The aim of this study is to identify potential biomarkers in HCC.
  
  
  METHODS
  We used the Infinium methylation array and a DNA-pooling strategy to analyze the genome-wide methylation profile in HCC. Quantitative methylation-specific PCR (Q-MSP) was used to validate homeobox A9 (HOXA9) methylation in 29 normal controls, 100 HCC samples and adjacent non-tumor tissues and in 74 plasma samples, including 40 patients with HCC.
  
  
  RESULTS
  Ten genes (HOXA9, NEUROG1, TNFRSF10C, IRAK3, GFPT2, ZNF177, DPYSL4, ELOVL4, FSD1, and CACNA1G) showed differences in methylation between controls and HCCs. Of these, HOXA9 was significantly hypermethylated in HCCs (76.7%; 23/30) compared with controls (3.4%; 1/29). In addition, combination analysis of two- and three-gene sets for HCC detection showed greater sensitivity (90%-96.7%) and comparable specificity (93.1%-96.6%) to each individual gene (33.3%-76.7% and 55.2%-100.0%). HOXA9 methylation was further validated by Q-MSP in two independent set of clinical samples including 100 HCC and paired non-tumor tissues. Further, HOXA9 methylation could be detected in plasma from HCC patients (n=40) but not in normal plasma (n=34) (p<0.0005). Combined testing (either parameter positive) for α-fetoprotein (AFP, a plasma protein biomarker) and HOXA9 methylation showed greater sensitivity (94.6%) for detection of HCC than AFP alone (75.7%).
  
  
  CONCLUSIONS
  These data suggest that methylation of HOXA9 could be a helpful biomarker to assist in HCC detection.
authors.forename: Chih-Chi
authors.initials: CC
authors.lastname: Kuo
authors.forename: Ching-Yu
authors.initials: CY
authors.lastname: Lin
authors.forename: Yu-Lueng
authors.initials: YL
authors.lastname: Shih
authors.forename: Chung-Bao
authors.initials: CB
authors.lastname: Hsieh
authors.forename: Pei-Yu
authors.initials: PY
authors.lastname: Lin
authors.forename: Shuh-Bing
authors.initials: SB
authors.lastname: Guan
authors.forename: Ming-Song
authors.initials: MS
authors.lastname: Hsieh
authors.forename: Hung-Cheng
authors.initials: HC
authors.lastname: Lai
authors.forename: Chien-Jen
authors.initials: CJ
authors.lastname: Chen
authors.forename: Ya-Wen
authors.initials: YW
authors.lastname: Lin
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000097:blood / Q000235:genetics* / Q000473:pathology; D002460:Cell Line; D045744:Cell Line, Tumor; D019175:DNA Methylation; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D008113:Liver Neoplasms / Q000097:blood / Q000235:genetics* / Q000473:pathology; D008297:Male; D011401:Promoter Regions, Genetic
chemical_list: D018398:Homeodomain Proteins; C097899:homeobox protein HOXA9