Identification of leukemia-associated genes by MLL-EEN fusion protein through dysregulation of histone modification and DNA methylation

Abstract

Mixed lineage leukemia (MLL) gene undergoes chromosomal translocation with over 60 different fusion partner genes in human leukemias. The resultant MLL-fusion oncoproteins are profoundly implicated in leukemias with poor prognosis. Epigenetic dysregulations have been frequently reported in MLL-rearranged leukemogenesis. Our study aims to investigate the correlations between epigenetic alterations, including both histone modification and DNA methylation, and gene dysregulation in MLL-rearranged leukemia. My study focused on MLL-EEN fusion protein, which causes an onset of acute myeloid leukemia (AML). A novel Mll-Een expressing cell line, VLA33, was derived from the bone marrow of Mll-Een knockin mouse with AML phenotype. The cells were mainly myeloblast cells, possessing clonogenic ability and showed upregulation of Hoxa cluster genes. Previous study demonstrated that the protein arginine methyltransferase 1 (PRMT1) plays a significant role in MLL-EEN leukemogenesis through conferring H4R3 asymmetric dimethylation (H4R3me2a) mark on HoxA9 locus. Consistently, our ChIP analysis demonstrated enrichment of H4R3me2a at the Hoxa promoters while knockdown of Prmt1 attenuated the expression of Hoxa genes and reduced in vitro clonogenic potential of VLA33 cells. CD41, Runx1 and Tgm2 genes, which showed elevated expression in VLA33 cells, were identified as potential target genes of Mll-Een/Prmt1 complex. However, enrichment of active H4R3me2a was only observed at Runx1 promoters, but not at the regulatory regions of CD41 and Tgm2. Inhibition of Prmt1 by inhibitor AMI-1 reduced Runx1 and CD41 expression. Although Prmt1 knockdown reduced the enrichment of H4R3me2a at Runx1 promoter, it did not suppress the expression of Runx1. These data suggest the involvement of other regulatory mechanism and Prmt1 is not the sole factor causing gene dysregulation. CD41 is a marker of murine definitive hematopoietic progenitors. Interestingly, the CD41+ VLA33 cells demonstrated a trend of enhanced self-renewal ability in colony-forming assay as compared with CD41-/low cells. The CD41 expression was positively correlated with Mll-Een and Prmt1 expression. In addition, CD41+ cells expressed higher level of Hoxa9, Bmi-1, Runx1, Tal-1 and Lmo2 genes that are associated with HSC activities, suggesting reactivation of stem-cell regulatory program in CD41+ leukemia cells, which confer as leukemia stem cell population. The association between DNA methylation and MLL-EEN leukemogenesis was also investigated. The results demonstrated the establishment of stem cell Hox code, which was correlated with DNA hypomethylation status at Hox gene promoters in Mll-Een leukemia cells. Besides, Hox activation through DNA hypomethylation was independent of Prmt1-mediated histone modification, but was found associated with reduction of Bmi-1 binding at Hox loci. In conclusion, my study identified novel dysregulated genes in Mll-Een leukemogenesis. My findings provide insight into the reactivation of stem-cell program in leukemia cells through epigenetic dysregulation, which furthers our understanding of MLL-rearranged leukemogenesis.