EWS-FLI1 target genes recovered from Ewing's sarcoma chromatin.
In all, 85% of Ewing's sarcoma family tumors (ESFT), a neoplasm of unknown histogenesis, express EWS-FLI1 transcription factor gene fusions. To characterize direct target genes avoiding artificial model systems, we cloned genomic DNA from ESFT chromatin precipitating with EWS-FLI1. We now present a comprehensive list of 99 putative transcription factor targets identified, for the first time, by a hypothesis-free approach based on physical interaction. Gene-derived chromatin fragments co-precipitating with EWS-FLI1 were nonrandomly distributed over the human genome and localized predominantly to the upstream region and the first two introns of the genes. At least 20% of putative direct EWS-FLI1 targets were neural genes. One-third of genes recovered showed a significant ESFT-specific expression pattern and were found to be altered upon RNAi-mediated knockdown of EWS-FLI1. Among them, MK-STYX, encoding a MAP kinase phosphatase-like protein, was consistently expressed in ESFT. EWS-FLI1 was found to drive MK-STYX expression by binding to a single ETS binding motif within the first gene intron. MK-STYX serves as precedence for successful recovery of direct EWS-FLI1 targets from the authentic ESFT cellular context, the most relevant system to study oncogenic mechanisms for the discovery of new therapeutic targets in this disease.
Siligan
Christine
C
Children's Cancer Research Institute (CCRI), St Anna Kinderspital, Kinderspitalgasse 6, Vienna A1090, Austria.
Ban
Jozef
J
Bachmaier
Radostina
R
Spahn
Laura
L
Kreppel
Michael
M
Schaefer
Karl-Ludwig
KL
Poremba
Christopher
C
Aryee
Dave N T
DN
Kovar
Heinrich
H
D001859:Bone Neoplasms / Q000235:genetics*; D002843:Chromatin / Q000235:genetics*; D004273:DNA, Neoplasm / Q000032:analysis; D004268:DNA-Binding Proteins / Q000235:genetics*; D020869:Gene Expression Profiling; D006801:Humans; D047468:Immunoprecipitation; D020411:Oligonucleotide Array Sequence Analysis; D017027:Protein Tyrosine Phosphatases / Q000235:genetics / Q000494:pharmacology*; D051789:Proto-Oncogene Protein c-fli-1; D034802:RNA-Binding Protein EWS / Q000235:genetics*; D012512:Sarcoma, Ewing / Q000235:genetics*; D015534:Trans-Activators / Q000235:genetics*
D002843:Chromatin; D004273:DNA, Neoplasm; D004268:DNA-Binding Proteins; C078433:FLI1 protein, human; D051789:Proto-Oncogene Protein c-fli-1; D034802:RNA-Binding Protein EWS; D015534:Trans-Activators; D017027:Protein Tyrosine Phosphatases