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: To test whether increased expression of C/EBPα was crucially involved in shifting the transcriptional network after RUNX1/ETO depletion, we defined overrepresented binding patterns for C/EBPα, PU.1, RUNX1, and LMO2 after RUNX1/ETO knockdown. Loss of RUNX1/ETO resulted in the formation of a transcriptional network dominated by C/EBPα-containing binding patterns, all of which were predominantly associated with upregulated genes in RUNX1/ETO-depleted Kasumi-1 and patient cells (Figures 6A–6C, S6A, and S6B; Table S3). Different patterns were again indicative of different classes of genes in terms of both GO and pathway analyses, with differentiation and signal transduction pathways being prominently featured (Figures S6C, S6D, and S7A). However, increased C/EBPα binding was also observed with a subset of genes that were downregulated (Figure 6D). Previous studies have shown that in addition to C/EBPα’s role in driving myeloid differentiation, low levels of C/EBPα are required for stem cell maintenance, as upregulation of C/EBPα represses genes required for stem-cell self-renewal (Zhang et al., 2004, 2013). Therefore, we identified genes that (1) were downregulated after RUNX1/ETO knockdown and (2) showed increased C/EBPα binding (a total of 145 genes met the latter criterion; Figure 6D). This category included stem cell genes such as ERG and CD34 (Figures S6F and S6G), as well as a large number of genes encoding for signaling molecules that are involved in regulating proliferation and differentiation, such as DUSP6 or PTK2 (Figure S6G).
Affiliation: School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.