title: Relatively Small Contribution of Methylation and Genomic Copy Number Aberration to the Aberrant Expression of Inflammation-Related Genes in HBV-Related Hepatocellular Carcinoma.
abstract: BACKGROUND
  It is well known that chronic inflammation plays a pivotal role in the development of hepatitis B virus (HBV) related hepatocellular carcinoma (HCC). However, the causes behind aberrant expression of inflammation-related genes occurred in HCC remain unclear.
  
  
  METHODS
  We performed array-based analyses to comprehensively investigate the contributions of DNA methylation and somatic copy number aberration (SCNA) to the aberrant expression of 1,027 inflammation-related genes in 30 HCCs and paired non-tumor tissues. The results were validated in public datasets and an additional sample set of 47 paired HCCs and non-tumor tissues.
  
  
  RESULTS
  We identified 252 differentially expressed, 125 aberrantly methylated and 287 copy number changed inflammation-related genes. Despite reasonable statistical power, among them, only 11 genes and 56 genes whose aberrant expression was associated with DNA methylation or SCNA, respectively. DNA methylation and SCNA together contributed to less than 30% aberrant expression of inflammation-related genes.
  
  
  CONCLUSIONS
  These results suggest that molecular mechanisms other than DNA methylation and SCNA might play major role in the regulation of aberrant expression of inflammation-related gene in HBV-related HCCs.
authors.affiliation: State Key Laboratory of Molecular Oncology and Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Dianke
authors.initials: D
authors.lastname: Yu
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America; Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America.
authors.forename: Guosheng
authors.initials: G
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Molecular Oncology and Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Xudong
authors.initials: X
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Molecular Oncology and Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Molecular Oncology and Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Tan
authors.affiliation: State Key Laboratory of Molecular Oncology and Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Qiao
authors.affiliation: State Key Laboratory of Molecular Oncology and Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Chang
authors.affiliation: Department of Abdominal Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Department of Abdominal Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Xinyu
authors.initials: X
authors.lastname: Bi
authors.affiliation: Department of Abdominal Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Jianqiang
authors.initials: J
authors.lastname: Cai
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America; Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America.
authors.forename: Yun
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Molecular Oncology and Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors.forename: Dongxin
authors.initials: D
authors.lastname: Lin
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000276:immunology / Q000821:virology; D019175:DNA Methylation; D030541:Databases, Genetic; D018628:Gene Dosage; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006509:Hepatitis B / Q000150:complications* / Q000235:genetics; D006801:Humans; D007249:Inflammation / Q000235:genetics* / Q000821:virology; D008113:Liver Neoplasms / Q000235:genetics* / Q000276:immunology / Q000821:virology; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic