E2A-PBX1 functions as a coactivator for RUNX1 in acute lymphoblastic leukemia

Blood. 2020 Jul 2;136(1):11-23. doi: 10.1182/blood.2019003312.


E2A, a basic helix-loop-helix transcription factor, plays a crucial role in determining tissue-specific cell fate, including differentiation of B-cell lineages. In 5% of childhood acute lymphoblastic leukemia (ALL), the t(1,19) chromosomal translocation specifically targets the E2A gene and produces an oncogenic E2A-PBX1 fusion protein. Although previous studies have shown the oncogenic functions of E2A-PBX1 in cell and animal models, the E2A-PBX1-enforced cistrome, the E2A-PBX1 interactome, and related mechanisms underlying leukemogenesis remain unclear. Here, by unbiased genomic profiling approaches, we identify the direct target sites of E2A-PBX1 in t(1,19)-positive pre-B ALL cells and show that, compared with normal E2A, E2A-PBX1 preferentially binds to a subset of gene loci cobound by RUNX1 and gene-activating machineries (p300, MED1, and H3K27 acetylation). Using biochemical analyses, we further document a direct interaction of E2A-PBX1, through a region spanning the PBX1 homeodomain, with RUNX1. Our results also show that E2A-PBX1 binding to gene enhancers is dependent on the RUNX1 interaction but not the DNA-binding activity harbored within the PBX1 homeodomain of E2A-PBX1. Transcriptome analyses and cell transformation assays further establish a significant RUNX1 requirement for E2A-PBX1-mediated target gene activation and leukemogenesis. Notably, the RUNX1 locus itself is also directly activated by E2A-PBX1, indicating a multilayered interplay between E2A-PBX1 and RUNX1. Collectively, our study provides the first unbiased profiling of the E2A-PBX1 cistrome in pre-B ALL cells and reveals a previously unappreciated pathway in which E2A-PBX1 acts in concert with RUNX1 to enforce transcriptome alterations for the development of pre-B ALL.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Cell Line, Tumor
  • Cell Transformation, Neoplastic / genetics
  • Core Binding Factor Alpha 2 Subunit / chemistry
  • Core Binding Factor Alpha 2 Subunit / genetics
  • Core Binding Factor Alpha 2 Subunit / physiology*
  • DNA / metabolism
  • Enhancer Elements, Genetic
  • Gene Expression Regulation, Leukemic / genetics*
  • Histone Code
  • Homeodomain Proteins / chemistry
  • Homeodomain Proteins / physiology*
  • Humans
  • Mediator Complex / metabolism
  • Neoplasm Proteins / metabolism*
  • Oncogene Proteins, Fusion / chemistry
  • Oncogene Proteins, Fusion / physiology*
  • Precursor B-Cell Lymphoblastic Leukemia-Lymphoma / genetics
  • Precursor B-Cell Lymphoblastic Leukemia-Lymphoma / pathology
  • Protein Domains
  • Protein Interaction Mapping
  • RNA, Messenger / biosynthesis
  • RNA, Messenger / genetics
  • RNA, Neoplasm / biosynthesis
  • RNA, Neoplasm / genetics
  • Structure-Activity Relationship
  • Transcriptome
  • p300-CBP Transcription Factors / metabolism


  • Core Binding Factor Alpha 2 Subunit
  • Homeodomain Proteins
  • Mediator Complex
  • Neoplasm Proteins
  • Oncogene Proteins, Fusion
  • RNA, Messenger
  • RNA, Neoplasm
  • RUNX1 protein, human
  • E2A-Pbx1 fusion protein
  • DNA
  • p300-CBP Transcription Factors