Titel: The epigenetic link between early B-cells and Merkel cell carcinoma
ID: W8-002
Art: Invited talk
Redezeit: 15 min
Session: Workshop 8
(Epi-)Genomics and Cancer

Referent: Emil Chteinberg (Ulm/DE)

Abstract - Text


Merkel cell carcinoma (MCC) is an aggressive skin cancer, which mainly occurs in elderly patients. Intriguingly, the majority of MCC express markers usually associated with the B-lymphoid lineage. Among these, 89.5% (128/143) of MCCs express - the pivotal B-cell differentiation transcription factor (TF) - paired box gene 5 (PAX5). In hematopoietic cells PAX5 induces B-cell specific transcription by binding distinct sites located in enhancer and promoter elements. DNA methylation of CpG islands located in these PAX5 binding sites has been shown to inversely correlate with expression levels of PAX5. To shed light on the consequences of PAX5 expression in MCC, we compared genome-wide DNA methylation pattern of PAX5 binding sites in MCC to different B-cell populations.

We quantified DNA methylation of 13 MCC tissues obtained from the Laboratory of Translational Cell and Tissue Research, University of Leuven, Belgium, by using the Infinium Methylation EPIC arrays. For comparison, available and public DNA Infinium HM450k array methylation data from 46 lymphoid leukemia and lymphoma cell lines and 91 benign B-cell populations was mined. Moreover, we subjected the 13 MCC tissues and three MCC cell lines, to RNAseq with an average output of reads with 1.2 giga base pairs per sample. Protein expression of pivotal B-cell TFs was studied using immunohistochemistry.

We focused the analysis on 61043 CpGs localized within known PAX5 binding sites in promoter and enhancer elements in the lymphoblastoid cell line GM12878. Comparing benign B-cell subsets with MCC revealed 1425 of these loci to be differentially methylated. After excluding 245 CpGs associated unspecifically with tumorigenesis, we were left with 1180 CpGs located in regulatory elements of 271 genes. Of these, 168 genes were associated with hypermethylated CpGs and were not expressed in MCC. HOMER TF binding motif analysis revealed IRF and ETS-family transcription binding site association with the not expressed genes. This led us to study the RNA and protein expression of IRF and ETS-family transcription factors in MCC. By this, we could show absence of the key B-cell transcription factors IRF4 and SPI1 in MCC. As expression of these TFs inverse correlates with DNA methylation of their binding sites in B-cells, we postulate that the lack of their expression causes the differential DNA methylation in MCC as compared to B-cell and also the different programming of the MCC tumor cells as compared to B-cell neoplasms. Thus, this study not only sheds light into the pathogenesis of MCC but also indicates the importance of TF combinatoric binding to regulate differentiation programs.