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

• Published in: Nucleic acids research Vol. 44; no. 22; pp. 10644 - 10661
• Main Authors: Unnikrishnan, Ashwin, Guan, Yi F, Huang, Yizhou, Beck, Dominik, Thoms, Julie A I, Peirs, Sofie, Knezevic, Kathy, Ma, Shiyong, de Walle, Inge V, de Jong, Ineke, Ali, Zara, Zhong, Ling, Raftery, Mark J, Taghon, Tom, Larsson, Jonas, MacKenzie, Karen L, Van Vlierberghe, Pieter, Wong, Jason W H, Pimanda, John E
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.12.2016
• Subjects: Base Sequence; Basic Medicine; Binding Sites; Cell Line, Tumor; Consensus Sequence; Enhancer Elements, Genetic; ETS Translocation Variant 6 Protein; Gene Expression Regulation, Leukemic; Gene regulation, Chromatin and Epigenetics; Gene Regulatory Networks; Humans; Ikaros Transcription Factor - physiology; Kaplan-Meier Estimate; Leukemia, Myeloid, Acute - genetics; Leukemia, Myeloid, Acute - metabolism; Leukemia, Myeloid, Acute - mortality; Medical and Health Sciences; Medical Genetics; Medicin och hälsovetenskap; Medicinsk genetik; Medicinska och farmaceutiska grundvetenskaper; Microbiology in the medical area; Mikrobiologi inom det medicinska området; Prognosis; Proportional Hazards Models; Protein Binding; Proteome; Proteomics; Proto-Oncogene Proteins c-ets - physiology; Repressor Proteins - physiology; Transcription, Genetic; Transcriptional Regulator ERG - physiology
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkw804

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.