A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network.
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.
Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia Ashwin.unnikrishnan@unsw.edu.au.
Ashwin
A
Unnikrishnan
Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia.
Yi F
YF
Guan
Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia.
Yizhou
Y
Huang
Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia.|Center for Medical Genetics, Ghent University, De Pintelaan 185 9000 Ghent, Belgium.
Dominik
D
Beck
Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia.
Julie A I
JA
Thoms
Centre for Health Technologies and the School of Software, University of Technology, Sydney, 2007, Australia.
Sofie
S
Peirs
Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia.
Kathy
K
Knezevic
Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia.
Shiyong
S
Ma
Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185 9000 Ghent, Belgium.
Inge V
IV
de Walle
Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 00, Lund, Sweden.
Ineke
I
de Jong
Children's Cancer Institute Australia, Sydney, New South Wales, 2052 Australia.
Zara
Z
Ali
Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales 2052, Australia.
Ling
L
Zhong
Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales 2052, Australia.
Mark J
MJ
Raftery
Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185 9000 Ghent, Belgium.
Tom
T
Taghon
Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 00, Lund, Sweden.
Jonas
J
Larsson
Children's Cancer Institute Australia, Sydney, New South Wales, 2052 Australia.
Karen L
KL
MacKenzie
Centre for Health Technologies and the School of Software, University of Technology, Sydney, 2007, Australia.
Pieter
P
Van Vlierberghe
Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia Jason.wong@unsw.edu.au.
Jason W H
JW
Wong
Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia jpimanda@unsw.edu.au.|Department of Haematology, Prince of Wales Hospital, Sydney, 2031, Australia.
John E
JE
Pimanda
D001483:Base Sequence; D001665:Binding Sites; D045744:Cell Line, Tumor; D016384:Consensus Sequence; D004742:Enhancer Elements, Genetic; D015973:Gene Expression Regulation, Leukemic; D053263:Gene Regulatory Networks; D006801:Humans; D051740:Ikaros Transcription Factor / Q000502:physiology*; D053208:Kaplan-Meier Estimate; D015470:Leukemia, Myeloid, Acute / Q000235:genetics / Q000378:metabolism / Q000401:mortality; D011379:Prognosis; D016016:Proportional Hazards Models; D011485:Protein Binding; D020543:Proteome; D040901:Proteomics; D050783:Proto-Oncogene Proteins c-ets / Q000502:physiology*; D012097:Repressor Proteins / Q000502:physiology*; D014158:Transcription, Genetic; D000071230:Transcriptional Regulator ERG / Q000502:physiology; D000097764:ETS Translocation Variant 6 Protein
D051740:Ikaros Transcription Factor; D020543:Proteome; D050783:Proto-Oncogene Proteins c-ets; D012097:Repressor Proteins; D000071230:Transcriptional Regulator ERG; D000097764:ETS Translocation Variant 6 Protein; C072312:ERG protein, human; C497239:IKZF1 protein, human