title: Integrative identification of Epstein-Barr virus-associated mutations and epigenetic alterations in gastric cancer.
abstract: OBJECTIVE
  The mechanisms by which Epstein-Barr virus (EBV) contributes to the development of gastric cancer are unclear. We investigated EBV-associated genomic and epigenomic variations in gastric cancer cells and tumors.
  
  
  METHODS
  We performed whole-genome, transcriptome, and epigenome sequence analyses of a gastric adenocarcinoma cell line (AGS cells), before and after EBV infection. We then looked for alterations in gastric tumor samples, with (n = 34) or without (n = 100) EBV infection, collected from patients at the Prince of Wales Hospital, Chinese University of Hong Kong (from 1998 through 2004), or the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (from 1999 through 2006).
  
  
  RESULTS
  Transcriptome analysis showed that infected cells expressed 9 EBV genes previously detected in EBV-associated gastric tumors and 71 EBV genes not previously reported in gastric tumors. Ten viral genes that had not been reported previously in gastric cancer but were expressed most highly in EBV-infected cells also were expressed in primary EBV-positive gastric tumors. Whole-genome sequence analysis identified 45 EBV-associated nonsynonymous mutations. These mutations, in genes such as AKT2, CCNA1, MAP3K4, and TGFBR1, were associated significantly with EBV-positive gastric tumors, compared with EBV-negative tumors. An activating mutation in AKT2 was associated with reduced survival times of patients with EBV-positive gastric cancer (P = .006); this mutation was found to dysregulate mitogen-activated protein kinase signaling. Integrated epigenome and transcriptome analyses identified 216 genes transcriptionally down-regulated by EBV-associated hypermethylation; methylation of ACSS1, FAM3B, IHH, and TRABD increased significantly in EBV-positive tumors. Overexpression of Indian hedgehog (IHH) and TraB domain containing (TRABD) increased proliferation and colony formation of gastric cancer cells, whereas knockdown of these genes reduced these activities. We found 5 signaling pathways (axon guidance, focal adhesion formation, interactions among cytokines and receptors, mitogen-activated protein kinase signaling, and actin cytoskeleton regulation) to be affected commonly by EBV-associated genomic and epigenomic alterations.
  
  
  CONCLUSIONS
  By using genomic, transcriptome, and epigenomic comparisons of EBV infected vs noninfected gastric cancer cells and tumor samples, we identified alterations in genes, gene expression, and methylation that affect different signaling networks. These might be involved in EBV-associated gastric carcinogenesis.
authors.affiliation: Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China; The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
authors.forename: Qiaoyi
authors.initials: Q
authors.lastname: Liang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xiaotian
authors.initials: X
authors.lastname: Yao
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Senwei
authors.initials: S
authors.lastname: Tang
authors.affiliation: Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China; The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
authors.forename: Jingwan
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China; The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
authors.forename: Tung On
authors.initials: TO
authors.lastname: Yau
authors.affiliation: Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China; The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
authors.forename: Xiaoxing
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Pharmacology, University of Oxford, Oxford, United Kingdom.
authors.forename: Ceen-Ming
authors.initials: CM
authors.lastname: Tang
authors.affiliation: Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Kang
authors.affiliation: Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Raymond W M
authors.initials: RW
authors.lastname: Lung
authors.affiliation: School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Jing Woei
authors.initials: JW
authors.lastname: Li
authors.affiliation: School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Ting Fung
authors.initials: TF
authors.lastname: Chan
authors.affiliation: Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, Beijing, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Xing
authors.affiliation: Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, Beijing, China.
authors.forename: Youyong
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Kwok Wai
authors.initials: KW
authors.lastname: Lo
authors.affiliation: Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Wong
authors.affiliation: Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Ka Fai
authors.initials: KF
authors.lastname: To
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Chang
authors.initials: C
authors.lastname: Yu
authors.affiliation: Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China; The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
authors.forename: Francis K L
authors.initials: FK
authors.lastname: Chan
authors.affiliation: Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China; The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
authors.forename: Joseph J Y
authors.initials: JJ
authors.lastname: Sung
authors.affiliation: Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China; The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China. Electronic address: junyu@cuhk.edu.hk.
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000821:virology; D045744:Cell Line, Tumor; D056750:Cyclin A1 / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D044127:Epigenesis, Genetic / Q000235:genetics; D020031:Epstein-Barr Virus Infections / Q000235:genetics* / Q000821:virology; D015972:Gene Expression Regulation, Neoplastic; D015967:Gene Expression Regulation, Viral; D005814:Genes, Viral; D055106:Genome-Wide Association Study; D004854:Herpesvirus 4, Human / Q000235:genetics*; D006801:Humans; D048768:MAP Kinase Kinase Kinase 4 / Q000235:genetics; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D051057:Proto-Oncogene Proteins c-akt / Q000235:genetics; D000077293:Receptor, Transforming Growth Factor-beta Type I; D018125:Receptors, Transforming Growth Factor beta / Q000235:genetics; D013274:Stomach Neoplasms / Q000235:genetics* / Q000821:virology; D059467:Transcriptome
chemical_list: C503745:CCNA1 protein, human; D056750:Cyclin A1; D018125:Receptors, Transforming Growth Factor beta; C494921:AKT2 protein, human; D017346:Protein Serine-Threonine Kinases; D051057:Proto-Oncogene Proteins c-akt; D048768:MAP Kinase Kinase Kinase 4; C482779:MAP3K4 protein, human; D000077293:Receptor, Transforming Growth Factor-beta Type I; C000625841:TGFBR1 protein, human
keywords: AKT2; Genome Sequencing; Methylation; Transcriptome