Characterization Of The Effects Of Mutated EZH2 On Expression and Epigenome In a Mouse Lymphoma Model

The histone methyl-transferase EZH2 is frequently affected by gain-of-function mutations in germinal-center lymphoma. To further test if these EZH2 mutations can be driver mutations in lymphomagenesis, we have previously generated and characterized a mouse line transgenic for EZH2^Y641F. This mouse model leads to an acceleration of lymphoma development in combination with Myc. We have now further investigated this model system and have used RNAseq and ChIPseq to characterize the effects of mutated EZH2 on gene expression and the epigenome.

We have previously shown that in contrast to lymphomas observed with Emu-Myc alone, all of the lymphomas observed in mice transgenic for both, Myc and EZH2^Y641F, present with a B220⁺IgM⁺phenotype. We have now characterized the accumulating B cell subset by performing in-depth immunophenotyping. This analysis showed that the cells are IgDlo, CD21-, CD23- and partially express AA4.1. This marker combination is consistent with the transitional stage (T1) of B cell development.

For the global gene expression and histone methylation analysis, splenic B cells (B220+) were isolated from one Eμ-Myc and one Eμ-Myc/EZH2Y641F mouse before the onset of disease symptoms. The samples were then processed for RNA sequencing and ChIP sequencing. ChIP was performed using validated antibodies for H3K4me3 and H3K27me3. Of the 22,137 genes studied we observed that 1,112 (412) genes were down-regulated and 788 (209) genes were up-regulated in Eμ-Myc/EZH2^Y641F mice with p-value<0.05 (FDR<0.1) when only genes with RPKM > 0.05 and a minimum number of reads of 30 were considered. An integrated analysis of the RNA sequencing data with the ChIP sequencing data for H3K27me3 and H3K4me3 was performed, and indicated that the altered epigenome of the Eμ-Myc/EZH2^Y641F mouse impacted protein-coding gene expression. This analysis showed that genes down-regulated in the Eμ-Myc/EZH2^Y641F mouse have increased H3K27me3 marks at their transcription start site indicative of a significant fraction of these genes being regulated by this mark. In contrast, genes up-regulated in the Eμ-Myc/EZH2^Y641Fmouse mainly exhibited increased H3K4Me3 marks at their transcription start site.

We then used DAVID/KEGG and the MGSA package to identify pathways associated with mutated EZH2 and identified GO terms that were enriched by the differentially expressed genes. Interestingly this analysis returned many important pathways in B cell regulation and immune function. The identified pathways include the B cell receptor signalling pathway and the JAK-STAT signaling pathway. We previously observed an increase in the proliferation rate of splenic B cells in Eμ-Myc/EZH2^Y641Fmice. While cell-cycle genes were not specifically enriched, there were several of these genes that were found deregulated (including e. g. CyclinD1).

In summary, we were able to identify several key pathways that may be contributing to the acceleration of lymphoma development observed with EZH2^Y641F and may also be important for the understanding of pathogenesis of EZH2 mutated lymphoma.