title: Integrated analyses of DNA methylation and hydroxymethylation reveal tumor suppressive roles of ECM1, ATF5, and EOMES in human hepatocellular carcinoma.
abstract: BACKGROUND
  Differences in 5-hydroxymethylcytosine, 5hmC, distributions may complicate previous observations of abnormal cytosine methylation statuses that are used for the identification of new tumor suppressor gene candidates that are relevant to human hepatocarcinogenesis. The simultaneous detection of 5-methylcytosine and 5-hydroxymethylcytosine is likely to stimulate the discovery of aberrantly methylated genes with increased accuracy in human hepatocellular carcinoma.
  
  
  RESULTS
  Here, we performed ultra-performance liquid chromatography/tandem mass spectrometry and single-base high-throughput sequencing, Hydroxymethylation and Methylation Sensitive Tag sequencing, HMST-seq, to synchronously measure these two modifications in human hepatocellular carcinoma samples. After identification of differentially methylated and hydroxymethylated genes in human hepatocellular carcinoma, we integrate DNA copy-number alterations, as determined using array-based comparative genomic hybridization data, with gene expression to identify genes that are potentially silenced by promoter hypermethylation.
  
  
  CONCLUSIONS
  We report a high enrichment of genes with epigenetic aberrations in cancer signaling pathways. Six genes were selected as tumor suppressor gene candidates, among which, ECM1, ATF5 and EOMES are confirmed via siRNA experiments to have potential anti-cancer functions.
authors.forename: Fei
authors.initials: F
authors.lastname: Gao
authors.forename: Yudong
authors.initials: Y
authors.lastname: Xia
authors.forename: Junwen
authors.initials: J
authors.lastname: Wang
authors.forename: Zhilong
authors.initials: Z
authors.lastname: Lin
authors.forename: Ying
authors.initials: Y
authors.lastname: Ou
authors.forename: Xing
authors.initials: X
authors.lastname: Liu
authors.forename: Weilong
authors.initials: W
authors.lastname: Liu
authors.forename: Boping
authors.initials: B
authors.lastname: Zhou
authors.forename: Huijuan
authors.initials: H
authors.lastname: Luo
authors.forename: Baojin
authors.initials: B
authors.lastname: Zhou
authors.forename: Bo
authors.initials: B
authors.lastname: Wen
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
authors.forename: Jian
authors.initials: J
authors.lastname: Huang
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism / Q000031:analogs & derivatives; D051696:Activating Transcription Factors / Q000235:genetics*; D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D045744:Cell Line, Tumor; D055028:Comparative Genomic Hybridization; D003596:Cytosine / Q000031:analogs & derivatives / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D016326:Extracellular Matrix Proteins / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic; D020022:Genetic Predisposition to Disease; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods; D020825:T-Box Domain Proteins / Q000235:genetics*
chemical_list: C507532:ATF5 protein, human; D051696:Activating Transcription Factors; C490607:ECM1 protein, human; C491199:EOMES protein, human; D016326:Extracellular Matrix Proteins; D020825:T-Box Domain Proteins; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine