@article{b36f862dbc1f4106b95742414239158f,
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",
keywords = "DNA methylation, HCC biomarker, HOXA9, methylation array",
author = "Kuo, \{Chih Chi\} and Lin, \{Ching Yu\} and Shih, \{Yu Lueng\} and Hsieh, \{Chung Bao\} and Lin, \{Pei Yu\} and Guan, \{Shuh Bing\} and Hsieh, \{Ming Song\} and Lai, \{Hung Cheng\} and Chen, \{Chien Jen\} and Lin, \{Ya Wen\}",
note = "Funding Information: Acknowledgments: We would like to thank TLCN for providing tissue samples and related clinical data (all are anonymous) for our research work. This network currently includes five major medical centers (National Taiwan University Hospital, Chang-Gung Memorial Hospital-Linko, Veteran General Hospital-Taichung, Chang-Gung Memorial Hospital-Kaohsiung, and Veteran General Hospital -Kaohsiung). TLCN is supported by grants from National Science Council since 2005 till now (NSC 100-2325-B-182-006) and National Health Research Institutes, Taiwan. The authors are grateful to Mr. Chia-Hsin Lin, Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan, ROC, for the assistance on Q-MSP and Dr. Yu-Ching Chou, School of Public Health, National Defense Medical Center, Taipei, Funding Information: The TLCN is funded by the National Science Council to provide researchers in Taiwan with primary liver cancer tissue specimens and their associated clinical information. The use of clinical samples in this study was approved by our Institutional Review Board and the TLCN User Committee. A normal liver cell line (THLE-3) and 9 HCC cell lines (HepG2, Hep3B, SK-HEP1, TONG, Mahlavu, PLC/PRF/5, HuH6, HuH7, and HA22T) were used in this study. THLE-3, HepG2, Hep3B, and SK-HEP1 cells were purchased from American type culture collection (ATCC). TONG, Mahlavu, PLC/PRF/5, HuH6, HuH7, and HA22T cells were obtained from Professor K.H. Lin (Chuang-Gung University, Taiwan). For 5-aza-2′-deoxycytidine (5DAC) treatment, HCC cells were prepared as previously described and harvested directly for DNA and RNA extraction [19]. For microarray analysis, five specimens of normal liver from hemangiomas and 15 pairs of HCC and adjacent non-tumor tissue samples obtained from patients with HCC of different viral etiologies were obtained from TLCN and selected as the subjects (more details are described below).",
year = "2014",
month = aug,
day = "1",
doi = "10.1515/cclm-2013-0780",
language = "English",
volume = "52",
pages = "1235--1245",
journal = "Clinical Chemistry and Laboratory Medicine",
issn = "1434-6621",
publisher = "Walter de Gruyter GmbH",
number = "8",
}
