Open Access Research

The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion

Henar Hernando1, Claire Shannon-Lowe2, Abul B Islam3, Fatima Al-Shahrour4, Javier Rodríguez-Ubreva1, Virginia C Rodríguez-Cortez1, Biola M Javierre1, Cristina Mangas5, Agustín F Fernández5, Maribel Parra6, Henri-Jacques Delecluse7, Manel Esteller8, Eduardo López-Granados9, Mario F Fraga105, Nuria López-Bigas3 and Esteban Ballestar1*

Author Affiliations

1 Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avda. Gran Via 199-203, 08908 L'Hospitalet de Llobregat, Barcelona, Spain

2 CR-UK Institute for Cancer Studies, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK

3 Department of Experimental and Health Sciences, Barcelona Biomedical Research Park, Universitat Pompeu Fabra (UPF), c/Dr. Aiguader, 88, 08003 Barcelona, Spain

4 Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA and Hematology Division, Brigham and Women's Hospital, Harvard Medical School, One Blackfan Circle, Brookline, MA 02115, USA

5 Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), HUCA, Universidad de Oviedo, C/Dr. Emilio Rodríguez Vigil, s/n, 33006 Oviedo, Spain

6 Cellular Differentiation Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avda. Gran Via 199-203, 08908 L'Hospitalet de Llobregat, Barcelona, Spain

7 Department of Virus Associated Tumours, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany

8 Cancer Epigenetics Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avda. Gran Via 199-203, 08908 L'Hospitalet de Llobregat, Barcelona, Spain

9 Clinical Immunology Department, University Hospital La Paz, P° de la Castellana, 261, 28046 Madrid, Spain

10 Department of Immunology and Oncology, Centro Nacional de Biotecnología/CNB-CSIC, Cantoblanco, Darwin 3, 28049 Madrid, Spain

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Genome Biology 2013, 14:R3  doi:10.1186/gb-2013-14-1-r3

Published: 15 January 2013

Abstract

Background

Epstein-Barr virus (EBV) infection is a well characterized etiopathogenic factor for a variety of immune-related conditions, including lymphomas, lymphoproliferative disorders and autoimmune diseases. EBV-mediated transformation of resting B cells to proliferating lymphoblastoid cells occurs in early stages of infection and is an excellent model for investigating the mechanisms associated with acquisition of unlimited growth.

Results

We investigated the effects of experimental EBV infection of B cells on DNA methylation profiles by using high-throughput analysis. Remarkably, we observed hypomethylation of around 250 genes, but no hypermethylation. Hypomethylation did not occur at repetitive sequences, consistent with the absence of genomic instability in lymphoproliferative cells. Changes in methylation only occurred after cell divisions started, without the participation of the active demethylation machinery, and were concomitant with acquisition by B cells of the ability to proliferate. Gene Ontology analysis, expression profiling, and high-throughput analysis of the presence of transcription factor binding motifs and occupancy revealed that most genes undergoing hypomethylation are active and display the presence of NF-κB p65 and other B cell-specific transcription factors. Promoter hypomethylation was associated with upregulation of genes relevant for the phenotype of proliferating lymphoblasts. Interestingly, pharmacologically induced demethylation increased the efficiency of transformation of resting B cells to lymphoblastoid cells, consistent with productive cooperation between hypomethylation and lymphocyte proliferation.

Conclusions

Our data provide novel clues on the role of the B cell transcription program leading to DNA methylation changes, which we find to be key to the EBV-associated conversion of resting B cells to proliferating lymphoblasts.