A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network

Nucleic Acids Res. 2016 Dec 15;44(22):10644-10661. doi: 10.1093/nar/gkw804. Epub 2016 Sep 6.

Abstract

Aberrant stem cell-like gene regulatory networks are a feature of leukaemogenesis. The ETS-related gene (ERG), an important regulator of normal haematopoiesis, is also highly expressed in T-ALL and acute myeloid leukaemia (AML). However, the transcriptional regulation of ERG in leukaemic cells remains poorly understood. In order to discover transcriptional regulators of ERG, we employed a quantitative mass spectrometry-based method to identify factors binding the 321 bp ERG +85 stem cell enhancer region in MOLT-4 T-ALL and KG-1 AML cells. Using this approach, we identified a number of known binders of the +85 enhancer in leukaemic cells along with previously unknown binders, including ETV6 and IKZF1. We confirmed that ETV6 and IKZF1 were also bound at the +85 enhancer in both leukaemic cells and in healthy human CD34+ haematopoietic stem and progenitor cells. Knockdown experiments confirmed that ETV6 and IKZF1 are transcriptional regulators not just of ERG, but also of a number of genes regulated by a densely interconnected network of seven transcription factors. At last, we show that ETV6 and IKZF1 expression levels are positively correlated with expression of a number of heptad genes in AML and high expression of all nine genes confers poorer overall prognosis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • Cell Line, Tumor
  • Consensus Sequence
  • Enhancer Elements, Genetic
  • Gene Expression Regulation, Leukemic
  • Gene Regulatory Networks
  • Humans
  • Ikaros Transcription Factor / physiology*
  • Kaplan-Meier Estimate
  • Leukemia, Myeloid, Acute / genetics
  • Leukemia, Myeloid, Acute / metabolism
  • Leukemia, Myeloid, Acute / mortality
  • Prognosis
  • Proportional Hazards Models
  • Protein Binding
  • Proteome
  • Proteomics
  • Proto-Oncogene Proteins c-ets / physiology*
  • Repressor Proteins / physiology*
  • Transcription, Genetic*
  • Transcriptional Regulator ERG / physiology

Substances

  • ERG protein, human
  • ETS translocation variant 6 protein
  • IKZF1 protein, human
  • Proteome
  • Proto-Oncogene Proteins c-ets
  • Repressor Proteins
  • Transcriptional Regulator ERG
  • Ikaros Transcription Factor