Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalization

  1. Andrew P. Feinberg2,7,9
  1. 1Department of Biostatistics,
  2. 2Center for Epigenetics,
  3. 3Institute of Genetic Medicine,
  4. 4Department of Pediatrics,
  5. 5Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21205, USA;
  6. 6Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, S-171 77 Stockholm, Sweden;
  7. 7Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
    1. 8 These authors contributed equally to this work.

    Abstract

    Altered DNA methylation occurs ubiquitously in human cancer from the earliest measurable stages. A cogent approach to understanding the mechanism and timing of altered DNA methylation is to analyze it in the context of carcinogenesis by a defined agent. Epstein-Barr virus (EBV) is a human oncogenic herpesvirus associated with lymphoma and nasopharyngeal carcinoma, but also used commonly in the laboratory to immortalize human B-cells in culture. Here we have performed whole-genome bisulfite sequencing of normal B-cells, activated B-cells, and EBV-immortalized B-cells from the same three individuals, in order to identify the impact of transformation on the methylome. Surprisingly, large-scale hypomethylated blocks comprising two-thirds of the genome were induced by EBV immortalization but not by B-cell activation per se. These regions largely corresponded to hypomethylated blocks that we have observed in human cancer, and they were associated with gene-expression hypervariability, similar to human cancer, and consistent with a model of epigenomic change promoting tumor cell heterogeneity. We also describe small-scale changes in DNA methylation near CpG islands. These results suggest that methylation disruption is an early and critical step in malignant transformation.

    Footnotes

    • 9 Corresponding author

      E-mail afeinberg{at}jhu.edu

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.157743.113.

      Freely available online through the Genome Research Open Access option.

    • Received March 15, 2013.
    • Accepted September 25, 2013.

    This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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