Inhibition of the SET/MLL Histone Methyltransferase Complex as a Novel Epigenetic Targeted Therapy in Mixed Lineage Leukemia

Abstract

Aggressive acute leukemias in children, adolescents, and adults arise due to a chromosomal translocation and subsequent fusion that occurs at chromosome 11q23 to the mixed-linage leukemia-1 (MLL1) gene. MLL-rearranged leukemias comprise 10% of all human leukemias, and comparatively, have poor therapeutic outcomes compared to non-MLL hematologic malignancies. MLL1 encodes the large, interchangeable catalytic subunit of the SET/MLL histone methyltransferase complex. Under normal physiologic conditions, it regulates a tightly controlled mechanism and specific pattern of Histone 3, Lysine 4 methylation (H3K4me). In contrast, when the SET/MLL complex is activated through fusion partners with MLL1, it causes epigenetic dysregulation promoting tumorigenic pathways such as oncogenic MYC expression. MYC dysregulation is one of the most common features across solid and hematologic malignancies. Historically, MYC has been difficult to target therapeutically due to its intrinsically disordered structure and conserved binding interfaces. Due to recent success in targeting MYC through global epigenetic modulation, we propose that targeting the DPY30 subunit of the SET/MLL complex has the potential to combat both aberrant H3K4 histone methylation patterns and downstream oncogenic MYC and MYC target gene expression. Here, we designed a high throughput screen to identify small molecules that specifically inhibit the DPY30-ASH2L protein interaction. Through biochemical and in vitro characterization, we have validated the on-target affinity of multiple compounds, which significantly inhibit downstream H3K4me3 and MYC expression across multiple cell lines. Additionally, we have identified a compound that abolishes MLL-rearranged leukemic cell proliferation in vitro and significantly decreased MLL tumor burden in vivo. Through these proof-of-concept studies, we have identified a first-in-class novel therapeutic target in MLL-rearranged leukemias through inhibition of the DPY30-ASH2L interaction of the histone SET/MLL complex.