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

Unnikrishnan, Ashwin ; Guan, Yi F ; Huang, Yizhou ; Beck, Dominik ; Thoms, Julie A I ; Peirs, Sofie ; Knezevic, Kathy ; Ma, Shiyong ; de Walle, Inge V and de Jong, Ineke LU , et al. (2016) In Nucleic Acids Research 44(22). p.10644-10661
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... (More)

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.

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keywords
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, Prognosis, Proportional Hazards Models, Protein Binding, Proteome, Proteomics, Proto-Oncogene Proteins c-ets/physiology, Repressor Proteins/physiology, Transcription, Genetic, Transcriptional Regulator ERG/physiology
in
Nucleic Acids Research
volume
44
issue
22
pages
10644 - 10661
publisher
Oxford University Press
external identifiers
  • scopus:85009994524
  • pmid:27604872
ISSN
1362-4962
DOI
10.1093/nar/gkw804
language
English
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yes
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© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
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72afdccf-8ed2-422b-a5d0-34b3c146db47
date added to LUP
2020-04-06 16:05:53
date last changed
2020-04-12 06:15:35
@article{72afdccf-8ed2-422b-a5d0-34b3c146db47,
  abstract     = {<p>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.</p>},
  author       = {Unnikrishnan, Ashwin and Guan, Yi F and Huang, Yizhou and Beck, Dominik and Thoms, Julie A I and Peirs, Sofie and Knezevic, Kathy and Ma, Shiyong and de Walle, Inge V and de Jong, Ineke and Ali, Zara and Zhong, Ling and Raftery, Mark J and Taghon, Tom and Larsson, Jonas and MacKenzie, Karen L and Van Vlierberghe, Pieter and Wong, Jason W H and Pimanda, John E},
  issn         = {1362-4962},
  language     = {eng},
  month        = {12},
  number       = {22},
  pages        = {10644--10661},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network},
  url          = {http://dx.doi.org/10.1093/nar/gkw804},
  doi          = {10.1093/nar/gkw804},
  volume       = {44},
  year         = {2016},
}