title: Integrative epigenomic and genomic filtering for methylation markers in hepatocellular carcinomas.
abstract: BACKGROUND
  Epigenome-wide studies in hepatocellular carcinoma (HCC) have identified numerous genes with aberrant DNA methylation. However, methods for triaging functional candidate genes as useful biomarkers for epidemiological study have not yet been developed.
  
  
  METHODS
  We conducted targeted next-generation bisulfite sequencing (bis-seq) to investigate associations of DNA methylation and mRNA expression in HCC. Integrative analyses of epigenetic profiles with DNA copy number analysis were used to pinpoint functional genes regulated mainly by altered DNA methylation.
  
  
  RESULTS
  Significant differences between HCC tumor and adjacent non-tumor tissue were observed for 28 bis-seq amplicons, with methylation differences varying from 12% to 43%. Available mRNA expression data in Oncomine were evaluated. Two candidate genes (GRASP and TSPYL5) were significantly under-expressed in HCC tumors in comparison with precursor and normal liver tissues. The expression levels in tumor tissues were, respectively, 1.828 and - 0.148, significantly lower than those in both precursor and normal liver tissue. Validations in an additional 42 paired tissues showed consistent under-expression in tumor tissue for GRASP (-7.49) and TSPYL5 (-9.71). A highly consistent DNA hypermethylation and mRNA repression pattern was obtained for both GRASP (69%) and TSPYL5 (73%), suggesting that their biological function is regulated by DNA methylation. Another two genes (RGS17 and NR2E1) at Chr6q showed significantly decreased DNA methylation in tumors with loss of DNA copy number compared to those without, suggesting alternative roles of DNA copy number losses and hypermethylation in the regulation of RGS17 and NR2E1.
  
  
  CONCLUSIONS
  These results suggest that integrative analyses of epigenomic and genomic data provide an efficient way to filter functional biomarkers for future epidemiological studies in human cancers.
authors.affiliation: Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, 10032, USA. js2182@cumc.columbia.edu.
authors.forename: Jing
authors.initials: J
authors.lastname: Shen
authors.affiliation: Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA. clarelefavephd@gmail.com.
authors.forename: Clare
authors.initials: C
authors.lastname: LeFave
authors.affiliation: Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, 10032, USA. is2043@cumc.columbia.edu.
authors.forename: Iryna
authors.initials: I
authors.lastname: Sirosh
authors.affiliation: Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA. aas54@columbia.edu.
authors.forename: Abby B
authors.initials: AB
authors.lastname: Siegel
authors.affiliation: Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA. bt12@columbia.edu.|Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA. bt12@columbia.edu.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Tycko
authors.affiliation: Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, 10032, USA. rps1@cumc.columbia.edu.
authors.forename: Regina M
authors.initials: RM
authors.lastname: Santella
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics; D019175:DNA Methylation; D057890:Epigenomics / Q000379:methods*; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D006801:Humans; D008099:Liver / Q000378:metabolism; D008113:Liver Neoplasms / Q000235:genetics*; D008297:Male; D008565:Membrane Proteins / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics; D008875:Middle Aged; D009687:Nuclear Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
chemical_list: D014408:Biomarkers, Tumor; D002352:Carrier Proteins; D008565:Membrane Proteins; D035683:MicroRNAs; D009687:Nuclear Proteins; D012333:RNA, Messenger; C527859:TSPYL5 protein, human; C410230:tamalin protein, human