Analysis of Epstein–Barr virus and cellular gene expression during the early phases of Epstein–Barr virus lytic induction Free

Abstract

In order to develop novel host/pathogen real-time PCR assays for routine diagnostic use, early gene expression patterns from both Epstein–Barr virus (EBV) and Raji cells were examined after inducing the lytic life cycle using 12--tetradecanoyl-13-phorbol ester and sodium butyrate. Real-time PCR identified several highly induced (>90-fold) EBV lytic genes over a 48 h time course during the lytic induction phase. Latent genes were induced at low levels during this phase. The cellular response to lytic viral replication is poorly understood. Whole human genome microarray analysis identified 113 cellular genes regulated twofold or more by EBV, including 63 upregulated and 46 downregulated genes, over a 24 h time course post-induction. The most upregulated gene was , a chitinase-3-like 1 protein (18.1-fold; <0.0084), and the most downregulated gene was , a thymidylate synthetase (−7.6-fold). Gene Ontology enrichment analysis using MetaCore software revealed cell cycle (core), cell cycle (role of anaphase-promoting complex) in cell cycle regulation) and lymphatic diseases as the most significantly represented biological network processes, canonical pathways and disease biomarkers, respectively. Chemotaxis, DNA damage and inflammation (IL-4 signalling) together with lymphoproliferative disorders and non-Hodgkin’s lymphoma were significantly represented biological processes and disease biomarkers.

Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.000352
2016-11-16
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/jmm/65/11/1243.html?itemId=/content/journal/jmm/10.1099/jmm.0.000352&mimeType=html&fmt=ahah

References

  1. Babcock G. J., Decker L. L., Volk M., Thorley-Lawson D. A. 1998; EBV persistence in memory B cells in vivo . Immunity 9:395–404 [View Article][PubMed]
    [Google Scholar]
  2. Baer R., Bankier A. T., Biggin M. D., Deininger P. L., Farrell P. J., Gibson T. J., Hatfull G., Hudson G. S., Satchwell S. C. et al. 1984; DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature 310:207–211 [View Article][PubMed]
    [Google Scholar]
  3. Bergbauer M., Kalla M., Schmeinck A., Göbel C., Rothbauer U., Eck S., Benet-Pagès A., Strom T. M., Hammerschmidt W. 2010; CpG-methylation regulates a class of Epstein-Barr virus promoters. PLoS Pathog 6: e1001114 [View Article][PubMed]
    [Google Scholar]
  4. Brink A. A., Dukers D. F., van den Brule A. J., Oudejans J. J., Middeldorp J. M., Meijer C. J., Jiwa M. 1997; Presence of Epstein-Barr virus latency type III at the single cell level in post-transplantation lymphoproliferative disorders and AIDS related lymphomas. J Clin Pathol 50:911–918 [View Article][PubMed]
    [Google Scholar]
  5. Brooks L. A., Lear A. L., Young L. S., Rickinson A. B. 1993; Transcripts from the Epstein-Barr virus BamHI A fragment are detectable in all three forms of virus latency. J Virol 67:3182–3190[PubMed]
    [Google Scholar]
  6. Cahir-McFarland E. D., Carter K., Rosenwald A., Giltnane J. M., Henrickson S. E., Staudt L. M., Kieff E. 2004; Role of NF-kappa B in cell survival and transcription of latent membrane protein 1-expressing or Epstein-Barr virus latency III-infected cells. J Virol 78:4108–4119 [View Article][PubMed]
    [Google Scholar]
  7. Cai Q., Chen K., Young K. H. 2015; Epstein-Barr virus-positive T/NK-cell lymphoproliferative disorders. Exp Mol Med 47:e133 [View Article][PubMed]
    [Google Scholar]
  8. Chang Y. H., Lee C. P., Su M. T., Wang J. T., Chen J. Y., Lin S. F., Tsai C. H., Hsieh M. J., Takada K., Chen M. R. 2012; Epstein-Barr virus BGLF4 kinase retards cellular S-phase progression and induces chromosomal abnormality. PLoS One 7:e39217 [View Article][PubMed]
    [Google Scholar]
  9. Chevallier-Greco A., Manet E., Chavrier P., Mosnier C., Daillie J., Sergeant A. 1986; Both Epstein-Barr virus (EBV)-encoded trans-acting factors, EB1 and EB2, are required to activate transcription from an EBV early promoter. EMBO J 5:3243–3249[PubMed]
    [Google Scholar]
  10. Concha M., Wang X., Cao S., Baddoo M., Fewell C., Lin Z., Hulme W., Hedges D., McBride J., Flemington E. K. 2012; Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq. J Virol 86:1458–1467 [View Article][PubMed]
    [Google Scholar]
  11. Crawford D. H. 2001; Biology and disease associations of Epstein-Barr virus. Philos Trans R Soc Lond B Biol Sci 356:461–473 [View Article][PubMed]
    [Google Scholar]
  12. Decaussin G., Leclerc V., Ooka T. 1995; The lytic cycle of Epstein-Barr virus in the nonproducer Raji line can be rescued by the expression of a 135-kilodalton protein encoded by the BALF2 open reading frame. J Virol 69:7309–7314[PubMed]
    [Google Scholar]
  13. Eurich K., Segawa M., Toei-Shimizu S., Mizoguchi E. 2009; Potential role of chitinase 3-like-1 in inflammation-associated carcinogenic changes of epithelial cells. World J Gastroenterol 15:5249–5259 [View Article][PubMed]
    [Google Scholar]
  14. Fields B. N., Knipe D. M., Howley P. M. 2007 Fields' Virology, 5th edn. Philadelphia, PA: Wolters Kluwer Health/Lippincott Williams & Wilkins;
    [Google Scholar]
  15. Forte E., Luftig M. A. 2011; The role of microRNAs in Epstein-Barr virus latency and lytic reactivation. Microbes Infect 13:1156–1167 [View Article][PubMed]
    [Google Scholar]
  16. Gonnella R., Farina A., Santarelli R., Raffa S., Feederle R., Bei R., Granato M., Modesti A., Frati L. et al. 2005; Characterization and intracellular localization of the Epstein-Barr virus protein BFLF2: interactions with BFRF1 and with the nuclear lamina. J Virol 79:3713–3727 [View Article][PubMed]
    [Google Scholar]
  17. Gruffat H., Kadjouf F., Mariamé B., Manet E. 2012; The Epstein-Barr virus BcRF1 gene product is a TBP-like protein with an essential role in late gene expression. J Virol 86:6023–6032 [View Article][PubMed]
    [Google Scholar]
  18. Guo Q., Qian L., Guo L., Shi M., Chen C., Lv X., Yu M., Hu M., Jiang G. et al. 2010a; Transactivators Zta and Rta of Epstein-Barr virus promote G0/G1 to S transition in Raji cells: a novel relationship between lytic virus and cell cycle. Mol Immunol 47:1783–1792 [View Article][PubMed]
    [Google Scholar]
  19. Guo Y., Zhang X., Yang M., Miao X., Shi Y., Yao J., Tan W., Sun T., Zhao D. et al. 2010b; Functional evaluation of missense variations in the human MAD1L1 and MAD2L1 genes and their impact on susceptibility to lung cancer. J Med Genet 47:616–622 [View Article][PubMed]
    [Google Scholar]
  20. Hatfull G., Bankier A. T., Barrell B. G., Farrell P. J. 1988; Sequence analysis of Raji Epstein-Barr virus DNA. Virology 164:334–340 [View Article][PubMed]
    [Google Scholar]
  21. Hertle M. L., Popp C., Petermann S., Maier S., Kremmer E., Lang R., Mages J., Kempkes B. 2009; Differential gene expression patterns of EBV infected EBNA-3A positive and negative human B lymphocytes. PLoS Pathog 5: e1000506 [View Article][PubMed]
    [Google Scholar]
  22. Hong G. K., Gulley M. L., Feng W. H., Delecluse H. J., Holley-Guthrie E., Kenney S. C. 2005; Epstein-Barr virus lytic infection contributes to lymphoproliferative disease in a SCID mouse model. J Virol 79:13993–14003 [View Article][PubMed]
    [Google Scholar]
  23. Hopwood P. A., Brooks L., Parratt R., Hunt B. J., Bokhari M., Thomas J. A., Yacoub M., Crawford D. H., Maria B. et al. 2002; Persistent Epstein-Barr virus infection: unrestricted latent and lytic viral gene expression in healthy immunosuppressed transplant recipients. Transplantation 74:194–202 [View Article][PubMed]
    [Google Scholar]
  24. Kallakury B., Sheehan C. E., Ambros R. A., Fisher H. A., Kaufman R. P., Ross J. S. 1997; The prognostic significance of p34cdc2 and cyclin D1 protein expression in prostate adenocarcinoma. Cancer 80:753–763 [View Article][PubMed]
    [Google Scholar]
  25. Kristiansen H., Gad H. H., Eskildsen-Larsen S., Despres P., Hartmann R. 2011; The oligoadenylate synthetase family: an ancient protein family with multiple antiviral activities. J Interferon Cytokine Res 31:41–47 [View Article][PubMed]
    [Google Scholar]
  26. Kudoh A., Fujita M., Kiyono T., Kuzushima K., Sugaya Y., Izuta S., Nishiyama Y., Tsurumi T. 2003; Reactivation of lytic replication from B cells latently infected with Epstein-Barr virus occurs with high S-phase cyclin-dependent kinase activity while inhibiting cellular DNA replication. J Virol 77:851–861 [View Article][PubMed]
    [Google Scholar]
  27. Kudoh A., Fujita M., Zhang L., Shirata N., Daikoku T., Sugaya Y., Isomura H., Nishiyama Y., Tsurumi T. 2005; Epstein-Barr virus lytic replication elicits ATM checkpoint signal transduction while providing an S-phase-like cellular environment. J Biol Chem 280:8156–8163 [View Article][PubMed]
    [Google Scholar]
  28. Küppers R. 2003; B cells under influence: transformation of B cells by Epstein-Barr virus. Nat Rev Immunol 3:801–812 [View Article][PubMed]
    [Google Scholar]
  29. Laux G., Freese U. K., Fischer R., Polack A., Kofler E., Bornkamm G. W. 1988; TPA-inducible Epstein-Barr virus genes in Raji cells and their regulation. Virology 162:503–507 [View Article][PubMed]
    [Google Scholar]
  30. Lee K. H., Choi E. Y., Kim M. K., Lee S. H., Jang B., Kim T. N., Kim S. W., Kim S. W., Song S. K. et al. 2010; Hepatoma-derived growth factor regulates the bad-mediated apoptotic pathway and induction of vascular endothelial growth factor in stomach cancer cells. Oncol Res 19:67–76 [View Article][PubMed]
    [Google Scholar]
  31. Liu Z., Falo L. D., You Z. 2011; Knockdown of HMGB1 in tumor cells attenuates their ability to induce regulatory T cells and uncovers naturally acquired CD8 T cell-dependent antitumor immunity. J Immunol 187:118–125 [View Article][PubMed]
    [Google Scholar]
  32. Livak K. J., Schmittgen T. D. 2001; Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔC T method. Methods 25:402–408 [View Article][PubMed]
    [Google Scholar]
  33. Lu F., Wikramasinghe P., Norseen J., Tsai K., Wang P., Showe L., Davuluri R. V., Lieberman P. M. 2010; Genome-wide analysis of host-chromosome binding sites for Epstein-Barr virus nuclear antigen 1 (EBNA1). Virol J 7:262 [View Article][PubMed]
    [Google Scholar]
  34. Lucchesi W., Brady G., Dittrich-Breiholz O., Kracht M., Russ R., Farrell P. J. 2008; Differential gene regulation by Epstein-Barr virus type 1 and type 2 EBNA2. J Virol 82:7456–7466 [View Article][PubMed]
    [Google Scholar]
  35. Malkas L. H., Herbert B. S., Abdel-Aziz W., Dobrolecki L. E., Liu Y., Agarwal B., Hoelz D., Badve S., Schnaper L. et al. 2006; A cancer-associated PCNA expressed in breast cancer has implications as a potential biomarker. Proc Natl Acad Sci U S A 103:19472–19477 [View Article][PubMed]
    [Google Scholar]
  36. Manenti G., Galbiati F., Pettinicchio A., Spinola M., Piconese S., Leoni V. P., Conti B., Ravagnani F., Incarbone M. et al. 2006; A V141L polymorphism of the human LRMP gene is associated with survival of lung cancer patients. Carcinogenesis 27:1386–1390 [View Article][PubMed]
    [Google Scholar]
  37. Minarovits J., Hu L. F., Marcsek Z., Minarovits-Kormuta S., Klein G., Ernberg I. 1992; RNA polymerase III-transcribed EBER 1 and 2 transcription units are expressed and hypomethylated in the major Epstein-Barr virus-carrying cell types. J Gen Virol 73:1687–1692 [View Article][PubMed]
    [Google Scholar]
  38. Myung D. S., Park Y. L., Kim N., Chung C. Y., Park H. C., Kim J. S., Cho S. B., Lee W. S., Lee J. H. et al. 2014; Expression of early growth response-1 in colorectal cancer and its relation to tumor cell proliferation and apoptosis. Oncol Rep 31:788–794 [View Article][PubMed]
    [Google Scholar]
  39. Nakayama T., Hieshima K., Nagakubo D., Sato E., Nakayama M., Kawa K., Yoshie O. 2004; Selective induction of Th2-attracting chemokines CCL17 and CCL22 in human B cells by latent membrane protein 1 of Epstein-Barr virus. J Virol 78:1665–1674 [View Article][PubMed]
    [Google Scholar]
  40. Neuhierl B., Delecluse H. J. 2006; The Epstein-Barr virus BMRF1 gene is essential for lytic virus replication. J Virol 80:5078–5081 [View Article][PubMed]
    [Google Scholar]
  41. Nutter L. M., Grill S. P., Li J. S., Tan R. S., Cheng Y. C. 1987; Induction of virus enzymes by phorbol esters and n-butyrate in Epstein-Barr virus genome-carrying Raji cells. Cancer Res 47:4407–4412[PubMed]
    [Google Scholar]
  42. Pan Y. R., Fang C. Y., Chang Y. S., Chang H. Y. 2005; Analysis of Epstein-Barr virus gene expression upon phorbol ester and hydroxyurea treatment by real-time quantitative PCR. Arch Virol 150:755–770 [View Article][PubMed]
    [Google Scholar]
  43. Parkhitko A., Myachina F., Morrison T. A., Hindi K. M., Auricchio N., Karbowniczek M., Wu J. J., Finkel T., Kwiatkowski D. J. et al. 2011; Tumorigenesis in tuberous sclerosis complex is autophagy and p62/sequestosome 1 (SQSTM1)-dependent. Proc Natl Acad Sci U S A 108:12455–12460 [View Article][PubMed]
    [Google Scholar]
  44. Peng L., Yanjiao M., Ai-guo W., Pengtao G., Jianhua L., Ju Y., Hongsheng O., Xichen Z. 2011; A fine balance between CCNL1 and TIMP1 contributes to the development of breast cancer cells. Biochem Biophys Res Commun 409:344–349 [View Article][PubMed]
    [Google Scholar]
  45. Rea D., Delecluse H.-J., Hamilton-Dutoit S. J., Marelle L., Joab I., Edelman L., Finet J.-F., Raphael M. French Study Group of Pathology for HIV-associated Tumors 1994a; Epstein-Barr virus latent and replicative gene expression in post-transplant lymphoproliferative disorders and AIDS-related non-Hodgkin's lymphomas. Ann Oncol 5:S113–S116 [View Article]
    [Google Scholar]
  46. Rea D., Fourcade C., Leblond V., Rowe M., Joab I., Edelman L., Bitker M. O., Gandjbakhch I., Suberbielle C. et al. 1994b; Patterns of Epstein-Barr virus latent and replicative gene expression in Epstein-Barr virus B cell lymphoproliferative disorders after organ transplantation. Transplantation 58:317–324 [CrossRef]
    [Google Scholar]
  47. Rodig S. J., Abramson J. S., Pinkus G. S., Treon S. P., Dorfman D. M., Dong H. Y., Shipp M. A., Kutok J. L. 2006; Heterogeneous CD52 expression among hematologic neoplasms: implications for the use of alemtuzumab (CAMPATH-1H). Clin Cancer Res 12:7174–7179 [View Article][PubMed]
    [Google Scholar]
  48. Salvant B. S., Fortunato E. A., Spector D. H. 1998; Cell cycle dysregulation by human cytomegalovirus: influence of the cell cycle phase at the time of infection and effects on cyclin transcription. J Virol 72:3729–3741[PubMed]
    [Google Scholar]
  49. Shin S. H., Park S. Y., Kang G. H. 2013; Down-regulation of dual-specificity phosphatase 5 in gastric cancer by promoter CpG island hypermethylation and its potential role in carcinogenesis. Am J Pathol 182:1275–1285 [View Article][PubMed]
    [Google Scholar]
  50. Smith P. R., de Jesus O., Turner D., Hollyoake M., Karstegl C. E., Griffin B. E., Karran L., Wang Y., Hayward S. D., Farrell P. J. 2000; Structure and coding content of CST (BART) family RNAs of Epstein-Barr virus. J Virol 74:3082–3092 [View Article][PubMed]
    [Google Scholar]
  51. Spender L. C., Lucchesi W., Bodelon G., Bilancio A., Karstegl C. E., Asano T., Dittrich-Breiholz O., Kracht M., Vanhaesebroeck B., Farrell P. J. 2006; Cell target genes of Epstein-Barr virus transcription factor EBNA-2: induction of the p55alpha regulatory subunit of PI3-kinase and its role in survival of EREB2.5 cells. J Gen Virol 87:2859–2867 [View Article][PubMed]
    [Google Scholar]
  52. Tejpar S., Bertagnolli M., Bosman F., Lenz H. J., Garraway L., Waldman F., Warren R., Bild A., Collins-Brennan D. et al. 2010; Prognostic and predictive biomarkers in resected colon cancer: current status and future perspectives for integrating genomics into biomarker discovery. Oncologist 15:390–404 [View Article][PubMed]
    [Google Scholar]
  53. Tsukamoto Y., Uchida T., Karnan S., Noguchi T., Nguyen L. T., Tanigawa M., Takeuchi I., Matsuura K., Hijiya N. et al. 2008; Genome-wide analysis of DNA copy number alterations and gene expression in gastric cancer. J Pathol 216:471–482 [View Article][PubMed]
    [Google Scholar]
  54. Tsurumi T. 2001; EBV replication enzymes. Curr Top Microbiol Immunol 258:65–87[PubMed]
    [Google Scholar]
  55. Uchihara J. N., Krensky A. M., Matsuda T., Kawakami H., Okudaira T., Masuda M., Ohta T., Takasu N., Mori N. 2005; Transactivation of the CCL5/RANTES gene by Epstein-Barr virus latent membrane protein 1. Int J Cancer 114:747–755 [View Article][PubMed]
    [Google Scholar]
  56. Vockerodt M., Pinkert D., Smola-Hess S., Michels A., Ransohoff R. M., Tesch H., Kube D. 2005; The Epstein-Barr virus oncoprotein latent membrane protein 1 induces expression of the chemokine IP-10: importance of mRNA half-life regulation. Int J Cancer 114:598–605 [View Article][PubMed]
    [Google Scholar]
  57. Young L. S., Rickinson A. B. 2004; Epstein-Barr virus: 40 years on. Nat Rev Cancer 4:757–768 [View Article][PubMed]
    [Google Scholar]
  58. Yuan J., Cahir-McFarland E., Zhao B., Kieff E. 2006; Virus and cell RNAs expressed during Epstein-Barr virus replication. J Virol 80:2548–2565 [View Article][PubMed]
    [Google Scholar]
  59. Zhao B., Maruo S., Cooper A., Chase M. R., Johannsen E., Kieff E., Cahir-McFarland E. 2006; RNAs induced by Epstein-Barr virus nuclear antigen 2 in lymphoblastoid cell lines. Proc Natl Acad Sci U S A 103:1900–1905 [View Article][PubMed]
    [Google Scholar]
  60. Zhao B., Keerthivasan G., Mei Y., Yang J., McElherne J., Wong P., Doench J. G., Feng G., Root D. E., Ji P. 2014; Targeted shRNA screening identified critical roles of pleckstrin-2 in erythropoiesis. Haematologica 99:1157–1167 [View Article][PubMed]
    [Google Scholar]
  61. de Jesus O., Smith P. R., Spender L. C., Elgueta Karstegl C., Niller H. H., Huang D., Farrell P. J. 2003; Updated Epstein-Barr virus (EBV) DNA sequence and analysis of a promoter for the BART (CST, BARF0) RNAs of EBV. J Gen Virol 84:1443–1450 [View Article][PubMed]
    [Google Scholar]
  62. van Beek J., Brink A. A., Vervoort M. B., van Zijp M. J., Meijer C. J., van den Brule A. J., Middeldorp J. M. 2003; In vivo transcription of the Epstein-Barr virus (EBV) BamHI-A region without associated in vivo BARF0 protein expression in multiple EBV-associated disorders. J Gen Virol 84:2647–2659 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.000352
Loading
/content/journal/jmm/10.1099/jmm.0.000352
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed