Biology and Microenvironment
J. Vogt1, H. Kretzmer2, O. Ammerpohl1, L. Vallés Uriate3, H. G. Drexler4, R. Wagener1, C. López1, R. Siebert1
1Institute of Human Genetics, University Ulm and Ulm University Medical Center, Ulm, Germany,2Max-Planck-Institute of Molecular Genetics, Berlin, Germany,3Christian-Albrechts Universität zu Kiel, Kiel, Germany,4Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
Classical Hodgkin lymphoma (cHL) is an atypical germinal-center derived B-cell lymphoma, in which the tumor cells have lost parts of their B-cell identity and instead up-regulate expression of genes characteristic for other hematopoietic lineages. The nature of the transcription factors (TFs) initiating and maintaining Hodgkin-Reed-Sternberg-specific gene expression as well as the mechanisms of simultaneous down-regulation of many B-cell-specific genes remain poorly understood. In theory, gene silencing could be achieved by mutations, absence of TFs or by epigenetic silencing. Indeed, previous studies suggest that epigenetic -modifications could be involved in this cHL-associated B-cell reprogramming. The aim of the present study was therefore to investigate the DNA methylation patterns that are specific for cHL. As the tumor cell content in primary cHL biopsies is very low (∼1%), we performed our analyses on five well characterized cHL cell lines. We investigated the DNA methylation of these cHL cell lines using the Infinium HumanMethylation450 BeadChip (Illumina) and compared these findings to 38 non-Hodgkin lymphoma (NHL) and 6 lymphoblastoid cell lines with the aim to identify differences in DNA methylation that are specific for cHL. For selected cell lines we also performed whole genome bisulfite sequencing. After normalization of the array data we performed thorough filtering. Hence, 462,452 loci finally entered subsequent analyses. We compared the DNA methylation profiles of cHL cell lines versus NHL and lymphoblastoid cell lines in order to remove differences in DNA methylation that are cell line and normal B-cell specific. We identified 2617 cHL-specific loci that are differentially methylated, of which 2271 (86.8%) were hypermethylated. A significant enrichment of those hypermethylated loci was observed in enhancer and promoter regions, which might alter gene expression in cHL. Moreover, these hypermethylated loci were significantly enriched in binding sites of the TFs BCL11, EBF, ELF1, MEF2, MTA3, NFIC, PU.1, RUNX3 and PML (OR > 2) which might also contribute to the aberrant B-cell phenotype in cHL. This is in line with previous analyses showing that also the expression of the TFs PU.1 and EBF themselves is drastically reduced in cHL which correlated with the hypermethylation of the respective promoter. Our analyses, thus, further support the notion that epigenetic processes play a major role in B-cell-specific gene silencing in cHL.