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

BMC Cancer. 2009 Dec 21;9:455. doi: 10.1186/1471-2407-9-455.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Central Nervous System Neoplasms / genetics*
  • Central Nervous System Neoplasms / metabolism
  • Central Nervous System Neoplasms / pathology
  • Cluster Analysis
  • CpG Islands / genetics
  • DNA Methylation*
  • Embryonic Stem Cells / metabolism
  • Female
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Neoplastic
  • Hematopoiesis / genetics
  • Humans
  • Lymphoma / genetics*
  • Oligonucleotide Array Sequence Analysis* / methods
  • Polycomb-Group Proteins
  • Repressor Proteins / metabolism
  • Repressor Proteins / physiology


  • Polycomb-Group Proteins
  • Repressor Proteins