Genome-wide analysis of Epstein-Barr virus (EBV) isolated from EBV-associated gastric carcinoma (EBVaGC)

Oncotarget

Volumn 7, Issue 4, 2016, Pages 4903-4914

  Liu, Ying ^a   Yang, Wenjun ^b   Pan, Yaqi ^a   Ji, Jiafu ^a   Lu, Zheming ^a   Ke, Yang ^a  

^a PEKING UNIVERSITY CANCER HOSPITAL AND INSTITUTE   (China)

^b NINGXIA MEDICAL UNIVERSITY   (China)

Author keywords

EBVaGC; Epstein Barr virus; Gastric carcinoma; Next generation sequencing

Indexed keywords

DNA; VIRAL PROTEIN;

ADULT; AGED; ARTICLE; EBNA1 GENE; EPSTEIN BARR VIRUS; EPSTEIN BARR VIRUS ASSOCIATED GASTRIC CARCINOMA; FEMALE; GENE; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; IN SITU HYBRIDIZATION; LMP2A GENE; MAJOR CLINICAL STUDY; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PREVALENCE; SINGLE NUCLEOTIDE POLYMORPHISM; STOMACH CARCINOMA; TUMOR BIOPSY; VERY ELDERLY; VIRUS GENOME; VIRUS ISOLATION; VIRUS STRAIN; WILD TYPE; CHINA; COMPLICATION; EPSTEIN BARR VIRUS INFECTION; FOLLOW UP; GENETIC POLYMORPHISM; GENETICS; MIDDLE AGED; PATHOGENICITY; STOMACH NEOPLASMS; VIROLOGY;

ADULT; AGED; AGED, 80 AND OVER; CHINA; EPSTEIN-BARR VIRUS INFECTIONS; FEMALE; FOLLOW-UP STUDIES; GENOME, VIRAL; HERPESVIRUS 4, HUMAN; HUMANS; IN SITU HYBRIDIZATION; MALE; MIDDLE AGED; PHYLOGENY; POLYMORPHISM, GENETIC; STOMACH NEOPLASMS; VIRAL PROTEINS;

EID: 84958012652     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.6751     Document Type: Article

References (47)

1. Shibata D, Weiss LM. Epstein-Barr virus-associated gastric adenocarcinoma. Am J Pathol. 1992; 140:769-774.
2. Tokunaga M, Land CE, Uemura Y, Tokudome T, Tanaka S, Sato E. Epstein-Barr virus in gastric carcinoma. Am J Pathol. 1993; 143:1250-1254.
3. Takada K. Epstein-Barr virus and gastric carcinoma. Mol Pathol. 2000; 53:255-261.
4. Murphy G, Pfeiffer R, Camargo MC, Rabkin CS. Metaanalysis shows that prevalence of Epstein-Barr viruspositive gastric cancer differs based on sex and anatomic location. Gastroenterology. 2009; 137:824-833.
5. Akiba S, Koriyama C, Herrera-Goepfert R, Eizuru Y. Epstein-Barr virus associated gastric carcinoma: epidemiological and clinicopathological features. Cancer Sci. 2008; 99:195-201.
6. Farrell PJ. Epstein-Barr virus. The B95-8 strain map. Methods Mol Biol. 2001; 174:3-12.
7. de Jesus O, Smith PR, Spender LC, Elgueta Karstegl C, Niller HH, Huang D, Farrell PJ. Updated Epstein-Barr virus (EBV) DNA sequence and analysis of a promoter for the BART (CST, BARF0) RNAs of EBV. J Gen Virol. 2003; 84:1443-1450.
8. Dolan A, Addison C, Gatherer D, Davison AJ, McGeoch DJ. The genome of Epstein-Barr virus type 2 strain AG876. Virology. 2006; 350:164-170.
9. Lin Z, Wang X, Strong MJ, Concha M, Baddoo M, Xu G, Baribault C, Fewell C, Hulme W, Hedges D, Taylor CM, Flemington EK. Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains. J Virol. 2013; 87:1172-1182.
10. Lei H, Li T, Hung GC, Li B, Tsai S, Lo SC. Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology. BMC genomics. 2013; 14:804.
11. Cheung ST, Huang DP, Hui AB, Lo KW, Ko CW, Tsang YS, Wong N, Whitney BM, Lee JC. Nasopharyngeal carcinoma cell line (C666-1) consistently harbouring Epstein-Barr virus. Int J Cancer. 1999; 83:121-126.
12. Tso KK, Yip KY, Mak CK, Chung GT, Lee SD, Cheung ST, To KF, Lo KW. Complete genomic sequence of Epstein-Barr virus in nasopharyngeal carcinoma cell line C666-1. Infect Agent Cancer. 2013; 8:29.
13. Zeng MS, Li DJ, Liu QL, Song LB, Li MZ, Zhang RH, Yu XJ, Wang HM, Ernberg I, Zeng YX. Genomic sequence analysis of Epstein-Barr virus strain GD1 from a nasopharyngeal carcinoma patient. J Virol. 2005; 79: 15323-15330.
14. Liu P, Fang X, Feng Z, Guo YM, Peng RJ, Liu T, Huang Z, Feng Y, Sun X, Xiong Z, Guo X, Pang SS, Wang B, et al. Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology. J Virol. 2011; 85:11291-11299.
15. Kwok H, Tong AH, Lin CH, Lok S, Farrell PJ, Kwong DL, Chiang AK. Genomic sequencing and comparative analysis of Epstein-Barr virus genome isolated from primary nasopharyngeal carcinoma biopsy. PLoS One. 2012; 7:e36939.
16. Kwok H, Wu CW, Palser AL, Kellam P, Sham PC, Kwong DL, Chiang AK. Genomic diversity of Epstein-Barr virus genomes isolated from primary nasopharyngeal carcinoma biopsy samples. J Virol. 2014; 88:10662-10672.
17. Tarbouriech N, Buisson M, Geoui T, Daenke S, Cusack S, Burmeister WP. Structural genomics of the Epstein-Barr virus. Acta crystallographica Section D, Biological crystallography. 2006; 62(Pt 10):1276-1285.
18. Bhatia K, Raj A, Guitierrez MI, Judde JG, Spangler G, Venkatesh H, Magrath IT. Variation in the sequence of Epstein Barr virus nuclear antigen 1 in normal peripheral blood lymphocytes and in Burkitt's lymphomas. Oncogene. 1996; 13:177-181.
19. Gutierrez MI, Raj A, Spangler G, Sharma A, Hussain A, Judde JG, Tsao SW, Yuen PW, Joab I, Magrath IT, Bhatia K. Sequence variations in EBNA-1 may dictate restriction of tissue distribution of Epstein-Barr virus in normal and tumour cells. J Gen Virol. 1997; 78:1663-1670.
20. Chen JN, Ding YG, Feng ZY, Li HG, He D, Du H, Wu B, Shao CK. Association of distinctive Epstein-Barr virus variants with gastric carcinoma in Guangzhou, southern China. J Med Virol. 2010; 82:658-667.
21. Sugiura M, Imai S, Tokunaga M, Koizumi S, Uchizawa M, Okamoto K, Osato T. Transcriptional analysis of Epstein-Barr virus gene expression in EBV-positive gastric carcinoma: unique viral latency in the tumour cells. Br J Cancer. 1996; 74:625-631.
22. Luo B, Wang Y, Wang XF, Liang H, Yan LP, Huang BH, Zhao P. Expression of Epstein-Barr virus genes in EBVassociated gastric carcinomas. World J Gastroenterol. 2005; 11:629-633.
23. Long HM, Leese AM, Chagoury OL, Connerty SR, Quarcoopome J, Quinn LL, Shannon-Lowe C, Rickinson AB. Cytotoxic CD4+ T cell responses to EBV contrast with CD8 responses in breadth of lytic cycle antigen choice and in lytic cycle recognition. J Immunol. 2011; 187:92-101.
24. Sitompul LS, Widodo N, Djati MS, Utomo DH. Epitope mapping of gp350/220 conserved domain of Epstein Barr virus to develop nasopharyngeal carcinoma (npc) vaccine. Bioinformation. 2012; 8:479-482.
25. Hislop AD, Taylor GS, Sauce D, Rickinson AB. Cellular responses to viral infection in humans: lessons from Epstein-Barr virus. Annual review of immunology. 2007; 25:587-617.
26. Herrera-Goepfert R, Akiba S, Koriyama C, Ding S, Reyes E, Itoh T, Minakami Y, Eizuru Y. Epstein-Barr virus-associated gastric carcinoma: Evidence of age-dependence among a Mexican population. World J Gastroenterol. 2005; 11: 6096-6103.
27. Trimeche M, Ksiaa F, Ziadi S, Mestiri S, Hachana M, Gacem RB, Sriha B, Korbi S. Prevalence and characteristics of Epstein-Barr virus-associated gastric carcinomas in Tunisia. Eur J Gastroenterol Hepatol. 2009; 21:1001-1007.
28. BenAyed-Guerfali D, Ayadi W, Miladi-Abdennadher I, Khabir A, Sellami-Boudawara T, Gargouri A, Mokdad-Gargouri R. Characteristics of epstein barr virus variants associated with gastric carcinoma in Southern Tunisia. Virol J. 2011; 8:500.
29. Uozaki H, Fukayama M. Epstein-Barr virus and gastric carcinoma-viral carcinogenesis through epigenetic mechanisms. International journal of clinical and experimental pathology. 2008; 1:198-216.
30. Alipov G, Nakayama T, Nakashima M, Wen CY, Niino D, Kondo H, Pruglo Y, Sekine I. Epstein-Barr virus-associated gastric carcinoma in Kazakhstan. World J Gastroenterol. 2005; 11:27-30.
31. Chang MS, Lee HS, Kim CW, Kim YI, Kim WH. Clinicopathologic characteristics of Epstein-Barr virusincorporated gastric cancers in Korea. Pathology, research and practice. 2001; 197:395-400.
32. Galetsky SA, Tsvetnov VV, Land CE, Afanasieva TA, Petrovichev NN, Gurtsevitch VE, Tokunaga M. Epstein Barr-virus-associated gastric cancer in Russia. Int J Cancer. 1997; 73:786-789.
33. Camargo MC, Murphy G, Koriyama C, Pfeiffer RM, Kim WH, Herrera-Goepfert R, Corvalan AH, Carrascal E, Abdirad A, Anwar M, Hao Z, Kattoor J, Yoshiwara-Wakabayashi E, et al. Determinants of Epstein-Barr virus-positive gastric cancer: an international pooled analysis. Br J Cancer. 2011; 105:38-43.
34. Fukayama M, Ushiku T. Epstein-Barr virus-associated gastric carcinoma. Pathology, research and practice. 2011; 207:529-537.
35. Young LS, Murray PG. Epstein-Barr virus and oncogenesis: from latent genes to tumours. Oncogene. 2003; 22:5108-5121.
36. Chang KL, Chen YY, Chen WG, Hayashi K, Bacchi C, Bacchi M, Weiss LM. EBNA-1 gene sequences in Brazilian and American patients with Hodgkin's disease. Blood. 1999; 94:244-250.
37. Chen YY, Chang KL, Chen WG, Shibata D, Hayashi K, Weiss LM. Epstein-Barr virus-associated nuclear antigen-1 carboxy-terminal gene sequences in Japanese and American patients with gastric carcinoma. Laboratory investigation; a journal of technical methods and pathology. 1998; 78: 877-882.
38. Fassone L, Cingolani A, Martini M, Migliaretti G, Oreste PL, Capello D, Gloghini A, Vivenza D, Dolcetti R, Carbone A, Antinori A, Gaidano G, Larocca LM. Characterization of Epstein-Barr virus genotype in AIDS-related non-Hodgkin's lymphoma. AIDS research and human retroviruses. 2002; 18:19-26.
39. Greiner TC, Abou-Elella AA, Smir BN, Orazi A, Hinrichs S, Anderson J, Gross T, Bierman P, Hauke R. Molecular epidemiology of EBNA-1 substrains of Epstein-Barr virus in posttransplant lymphoproliferative disorders which have infrequent p53 mutations. Leukemia & lymphoma. 2000; 38:563-576.
40. Gutierrez MI, Spangler G, Kingma D, Raffeld M, Guerrero I, Misad O, Jaffe ES, Magrath IT, Bhatia K. Epstein-Barr virus in nasal lymphomas contains multiple ongoing mutations in the EBNA-1 gene. Blood. 1998; 92:600-606.
41. Habeshaw G, Yao QY, Bell AI, Morton D, Rickinson AB. Epstein-barr virus nuclear antigen 1 sequences in endemic and sporadic Burkitt's lymphoma reflect virus strains prevalent in different geographic areas. J Virol. 1999; 73:965-975.
42. MacKenzie J, Gray D, Pinto-Paes R, Barrezueta LF, Armstrong AA, Alexander FA, McGeoch DJ, Jarrett RF. Analysis of Epstein-Barr virus (EBV) nuclear antigen 1 subtypes in EBV-associated lymphomas from Brazil and the United Kingdom. J Gen Virol. 1999; 80:2741-2745.
43. Sandvej K, Zhou XG, Hamilton-Dutoit S. EBNA-1 sequence variation in Danish and Chinese EBV-associated tumours: evidence for geographical polymorphism but not for tumour-specific subtype restriction. J Pathol. 2000; 191:127-131.
44. Wang Y, Liu X, Xing X, Cui Y, Zhao C, Luo B. Variations of Epstein-Barr virus nuclear antigen 1 gene in gastric carcinomas and nasopharyngeal carcinomas from Northern China. Virus Res. 2010; 147:258-264.
45. Rooney CM, Leen AM, Vera JF, Heslop HE. T lymphocytes targeting native receptors. Immunological reviews. 2014; 257:39-55.
46. Bell MJ, Brennan R, Miles JJ, Moss DJ, Burrows JM, Burrows SR. Widespread sequence variation in Epstein-Barr virus nuclear antigen 1 influences the antiviral T cell response. J Infect Dis. 2008; 197:1594-1597.
47. Icheva V, Kayser S, Wolff D, Tuve S, Kyzirakos C, Bethge W, Greil J, Albert MH, Schwinger W, Nathrath M, Schumm M, Stevanovic S, Handgretinger R, et al. Adoptive transfer of epstein-barr virus (EBV) nuclear antigen 1-specific t cells as treatment for EBV reactivation and lymphoproliferative disorders after allogeneic stem-cell transplantation. J Clin Oncol. 2013; 31:39-48.