Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal.
Bottom Line: Here, we use digital footprinting and chromatin immunoprecipitation sequencing (ChIP-seq) to identify the core RUNX1/ETO-responsive transcriptional network of t(8;21) cells.We show that the transcriptional program underlying leukemic propagation is regulated by a dynamic equilibrium between RUNX1/ETO and RUNX1 complexes, which bind to identical DNA sites in a mutually exclusive fashion.Perturbation of this equilibrium in t(8;21) cells by RUNX1/ETO depletion leads to a global redistribution of transcription factor complexes within preexisting open chromatin, resulting in the formation of a transcriptional network that drives myeloid differentiation.
Affiliation: School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.Show MeSH
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Mentions: We next analyzed our ChIP-seq data sets to identify the core transcriptional network that characterizes the cellular identity of t(8;21) cells by determining overrepresented combinatorial binding patterns for the transcription factors RUNX1/ETO, C/EBPα, HEB, LMO2, PU.1, and RUNX1 (Tijssen et al., 2011). ChIP sequences in RUNX1/ETO-positive cells were enriched for just 11 of the 63 possible different binding patterns, which included six significantly enriched combinatorial patterns containing RUNX1/ETO and five patterns that did not (Figure 4A, marked by asterisks). Two possible binding patterns (111010 and 110011) were not observed. We then associated such elements with the nearest genes and performed a gene set enrichment analysis (GSEA) using gene-expression data sets derived from a time course of RUNX1/ETO knockdown in two different t(8;21) cell lines (Figures S4A and S4B; Ptasinska et al., 2012). In addition, we compared these gene signatures with a RNA-seq-based gene-expression data set derived from a 4-day RUNX1/ETO knockdown in Kasumi-1 cells (Figures 4B and S4C). This analysis demonstrated that all overrepresented RUNX1/ETO-containing binding patterns were associated with the upregulation of gene expression upon knockdown (Figure 4B, red asterisks), whereas loci that do not bind RUNX1/ETO were enriched in genes that were downregulated after RUNX1/ETO knockdown (green asterisks). The very same genes behaved similarly when assayed after knockdown of RUNX1/ETO in patient cells, confirming the similarity between cell lines and primary cells (Figure 4C).
Affiliation: School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.