Genetic regulators of myelopoiesis and leukemic signaling identified by gene profiling and linear modeling

Anna L. Brown^*^,^,^,1, Christopher R. Wilkinson^*^,^,^,^,1, Scott R. Waterman^¶, Chung H. Kok^*^,^,, Diana G. Salerno^*^,^,, Sonya M. Diakiw^*^,^,, Brenton Reynolds^*^,^,, Hamish S. Scott^||, Anna Tsykin^,¶, Gary F. Glonek, Gregory J. Goodall^¶^,**, Patty J. Solomon, Thomas J. Gonda and Richard J. D’Andrea^*^,^,^,2

^* Haematology and Oncology Program, Child Health Research Institute, North Adelaide, South Australia;
The Queen Elizabeth Hospital, Woodville, South Australia; Departments of
Paediatrics and
^** Medicine and
School of Mathematical Sciences, University of Adelaide, South Australia;
^¶ The Division of Human Immunology and Hanson Institute, Institute of Medical and Veterinary Sciences, Adelaide, South Australia;
^|| The Genetics and Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; and
Cancer Biology Program, Centre for Immunology and Cancer Research, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia

²Correspondence: Child Health Research Institute, 7th Floor, Clarence Rieger Building, 72 King William Road, North Adelaide, South Australia 5006, Australia. E-mail: Richard.dandrea{at}adelaide.edu.au

Mechanisms controlling the balance between proliferation andself-renewal versus growth suppression and differentiation duringnormal and leukemic myelopoiesis are not understood. We haveused the bi-potent FDB1 myeloid cell line model, which is responsiveto myelopoietic cytokines and activated mutants of the granulocytemacrophage-colony stimulating factor (GM-CSF) receptor, havingdifferential signaling and leukemogenic activity. This modelis suited to large-scale gene-profiling, and we have used afactorial time-course design to generate a substantial and powerfuldata set. Linear modeling was used to identify gene-expressionchanges associated with continued proliferation, differentiation,or leukemic receptor signaling. We focused on the changing transcriptionfactor profile, defined a set of novel genes with potentialto regulate myeloid growth and differentiation, and demonstratedthat the FDB1 cell line model is responsive to forced expressionof oncogenes identified in this study. We also identified gene-expressionchanges associated specifically with the leukemic GM-CSF receptormutant, V449E. Signaling from this receptor mutant down-regulatesCCAAT/enhancer-binding protein ${alpha}$ (C/EBP ${alpha}$ ) target genes and generateschanges characteristic of a specific acute myeloid leukemiasignature, defined previously by gene-expression profiling andassociated with C/EBP ${alpha}$ mutations.

Key Words: myeloid • transcription factor • myeloid leukemia • microarray • gene expression