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Open Access Research article

Array-based DNA methylation profiling of primary lymphomas of the central nervous system

Julia Richter1, Ole Ammerpohl1, José I Martín-Subero1, Manuel Montesinos-Rongen2, Marina Bibikova3, Eliza Wickham-Garcia3, Otmar D Wiestler4, Martina Deckert2 and Reiner Siebert1*

Author Affiliations

1 Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany

2 Department of Neuropathology, University of Cologne, Cologne, Germany

3 Illumina Inc., San Diego, CA, USA

4 Molecular Neuro-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany

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BMC Cancer 2009, 9:455  doi:10.1186/1471-2407-9-455

Published: 21 December 2009

Abstract

Background

Although primary lymphomas of the central nervous system (PCNSL) and extracerebral diffuse large B-cell lymphoma (DLBCL) cannot be distinguished histologically, it is still a matter of debate whether PCNSL differ from systemic DLBCL with respect to their molecular features and pathogenesis. Analysis of the DNA methylation pattern might provide further data distinguishing these entities at a molecular level.

Methods

Using an array-based technology we have assessed the DNA methylation status of 1,505 individual CpG loci in five PCNSL and compared the results to DNA methylation profiles of 49 DLBCL and ten hematopoietic controls.

Results

We identified 194 genes differentially methylated between PCNSL and normal controls. Interestingly, Polycomb target genes and genes with promoters showing a high CpG content were significantly enriched in the group of genes hypermethylated in PCNSL. However, PCNSL and systemic DLBCL did not differ in their methylation pattern.

Conclusions

Based on the data presented here, PCNSL and DLBCL do not differ in their DNA methylation pattern. Thus, DNA methylation analysis does not support a separation of PCNSL and DLBCL into individual entities. However, PCNSL and DLBCL differ in their DNA methylation pattern from non- malignant controls.