Genome-Wide Mapping of Binding Sites and Networks of Potential Target Genes of the Fusion Oncogene ETV6/RUNX1 in Acute Lymphoblastic Leukemia in Childhood

Acute lymphoblastic leukemia (ALL) in childhood, a clinically and biologically heterogeneous disease, represents the most common malignant disease in childhood. Approximately 20-25% of B-cell precursor ALL (BCP-ALL) carry the cryptic chromosomal translocation t(12;21)(p13;q22), the most common reciprocal chromosomal translocation in childhood ALL. This translocation combines two transcription factors and essential regulators of normal hematopoiesis, ETV6 and RUNX1, into the fusion oncogene ETV6/RUNX1 (E/R; synonym TEL/AML1).

Recent studies in various animal models have strengthened the view that E/R positive cells give rise to preleukemic clones with a differentiation block in the pro/pre-B stage of B cell development that, after acquisition of additional mutations, may transform into full malignancy.

Regarding the molecular mechanism by which the chimeric fusion protein E/R causes gene expression changes, it is assumed that E/R binds with the runt homology domain of RUNX1 (RHD, DNA-binding domain) to RUNX1 target sequences of gene promoters and recruits corepressors and histone deacetylases through its ETV6 portion, leading to chromatin condensation and transcriptional repression. Thus, E/R appears to act mainly as an epigenetic repressor of genes that are normally activated by RUNX1. However, the precise mechanism of cellular transformation and the identity of E/R target genes are largely unknown.

Therefore, we used chromatin immunoprecipitation (ChIP), followed by next generation sequencing (ChIP-Seq) to identify E/R target genes in the E/R positive BCP-ALL cell lines REH and UoC-B6 as well as in primary patient material from children with relapsed E/R positive ALL. We were able to detect a core gene set of 335 candidate target genes common to all samples analyzed. Those genes could be assigned to 15 significantly overrepresented KEGG pathways (e.g. cell cycle, pathways in cancer, hematopoietic cell lineage and B cell receptor signaling pathway).

The results show, besides target genes already reported in the literature such as EPOR, MPO and IGLL1, numerous not previously described candidate E/R target genes, such as LEF1, E2F2, FLT3, FGFR1 and RUNX1 that are potentially important in the pathogenesis of E/R positive ALL and may lead to new treatment options.