title: Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray.
abstract: BACKGROUND
  The Epstein-Barr virus (EBV) is associated with lymphoid malignancies, including Burkitt's lymphoma (BL), and can transform human B cells in vitro. EBV-harboring cell lines are widely used to investigate lymphocyte transformation and oncogenesis. Qualitative EBV gene expression has been extensively described, but knowledge of quantitative transcription is lacking. We hypothesized that transcription levels of EBNA1, the gene essential for EBV persistence within an infected cell, are similar in BL cell lines.
  
  
  RESULTS
  To compare quantitative gene transcription in the BL cell lines Namalwa, Raji, Akata, Jijoye, and P3HR1, we developed an oligonucleotide microarray chip, including 17 housekeeping genes, six latent EBV genes (EBNA1, EBNA2, EBNA3A, EBNA3C, LMP1, LMP2), and four lytic EBV genes (BZLF1, BXLF2, BKRF2, BZLF2), and used the cell line B95.8 as a reference for EBV gene transcription. Quantitative polymerase chain reaction assays were used to validate microarray results. We found that transcription levels of housekeeping genes differed considerably among BL cell lines. Using a selection of housekeeping genes with similar quantitative transcription in the tested cell lines to normalize EBV gene transcription data, we showed that transcription levels of EBNA1 were quite similar in very different BL cell lines, in contrast to transcription levels of other EBV genes. As demonstrated with Akata cells, the chip allowed us to accurately measure EBV gene transcription changes triggered by treatment interventions.
  
  
  CONCLUSIONS
  Our results suggest uniform EBNA1 transcription levels in BL and that microarray profiling can reveal novel insights on quantitative EBV gene transcription and its impact on lymphocyte biology.
authors.affiliation: Division of Infectious Diseases, University Children's Hospital of Zurich, August Forel-Strasse 1, CH-8008 Zurich, Switzerland. michele.bernasconi@kispi.unizh.ch
authors.forename: Michele
authors.initials: M
authors.lastname: Bernasconi
authors.forename: Christoph
authors.initials: C
authors.lastname: Berger
authors.forename: Jürg A
authors.initials: JA
authors.lastname: Sigrist
authors.forename: Athos
authors.initials: A
authors.lastname: Bonanomi
authors.forename: Jens
authors.initials: J
authors.lastname: Sobek
authors.forename: Felix K
authors.initials: FK
authors.lastname: Niggli
authors.forename: David
authors.initials: D
authors.lastname: Nadal
mesh_terms: D002051:Burkitt Lymphoma / Q000821:virology*; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D015967:Gene Expression Regulation, Viral; D016679:Genome, Viral; D004854:Herpesvirus 4, Human / Q000235:genetics*; D006801:Humans; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D014158:Transcription, Genetic