Integrative analysis of RUNX1 downstream pathways and target genes.
BACKGROUND
The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible for a familial platelet disorder with predisposition to acute myeloid leukemia (FPD-AML). The disruption of the largely unknown biological pathways controlled by RUNX1 is likely to be responsible for the development of leukemia. We have used multiple microarray platforms and bioinformatic techniques to help identify these biological pathways to aid in the understanding of why RUNX1 mutations lead to leukemia.


RESULTS
Here we report genes regulated either directly or indirectly by RUNX1 based on the study of gene expression profiles generated from 3 different human and mouse platforms. The platforms used were global gene expression profiling of: 1) cell lines with RUNX1 mutations from FPD-AML patients, 2) over-expression of RUNX1 and CBFbeta, and 3) Runx1 knockout mouse embryos using either cDNA or Affymetrix microarrays. We observe that our datasets (lists of differentially expressed genes) significantly correlate with published microarray data from sporadic AML patients with mutations in either RUNX1 or its cofactor, CBFbeta. A number of biological processes were identified among the differentially expressed genes and functional assays suggest that heterozygous RUNX1 point mutations in patients with FPD-AML impair cell proliferation, microtubule dynamics and possibly genetic stability. In addition, analysis of the regulatory regions of the differentially expressed genes has for the first time systematically identified numerous potential novel RUNX1 target genes.


CONCLUSIONS
This work is the first large-scale study attempting to identify the genetic networks regulated by RUNX1, a master regulator in the development of the hematopoietic system and leukemia. The biological pathways and target genes controlled by RUNX1 will have considerable importance in disease progression in both familial and sporadic leukemia as well as therapeutic implications.
Michaud
Joëlle
J
Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3050, Victoria, Australia. Joelle.Michaud@unil.ch
Simpson
Ken M
KM
Escher
Robert
R
Buchet-Poyau
Karine
K
Beissbarth
Tim
T
Carmichael
Catherine
C
Ritchie
Matthew E
ME
Schütz
Frédéric
F
Cannon
Ping
P
Liu
Marjorie
M
Shen
Xiaofeng
X
Ito
Yoshiaki
Y
Raskind
Wendy H
WH
Horwitz
Marshall S
MS
Osato
Motomi
M
Turner
David R
DR
Speed
Terence P
TP
Kavallaris
Maria
M
Smyth
Gordon K
GK
Scott
Hamish S
HS
D000818:Animals; D001791:Blood Platelet Disorders / Q000235:genetics; D002461:Cell Line, Transformed; D019295:Computational Biology; D050676:Core Binding Factor Alpha 2 Subunit / Q000235:genetics*; D050658:Core Binding Factor beta Subunit / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease; D006367:HeLa Cells; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics; D051379:Mice; D008807:Mice, Inbred BALB C; D020411:Oligonucleotide Array Sequence Analysis; D017354:Point Mutation
C493692:CBFB protein, human; D050676:Core Binding Factor Alpha 2 Subunit; D050658:Core Binding Factor beta Subunit; C493728:RUNX1 protein, human; C493726:Runx1 protein, mouse