Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal.
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.
- Leukemia, Myeloid, Acute/metabolism/pathology*
- Translocation, Genetic*
- Adaptor Proteins, Signal Transducing/metabolism
- CCAAT-Enhancer-Binding Protein-alpha/genetics/metabolism
- Cell Line, Tumor
- Chromatin Immunoprecipitation
- Chromosome Mapping
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Core Binding Factor Alpha 2 Subunit/metabolism
- Gene Regulatory Networks
- LIM Domain Proteins/metabolism
- Protein Binding
- Proto-Oncogene Proteins/metabolism
- RNA Interference
- RNA, Messenger/metabolism
- RNA, Small Interfering
- Sequence Analysis, RNA
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Figure 1: Transcription-Factor Occupancy Patterns Are Similar between RUNX1/ETO-Expressing Cell Lines and Patient Cells(A) UCSC genome browser screenshot showing the binding patterns of RUNX1/ETO, RUNX1, HEB, LMO2, C/EBPα, PU.1, DHS, H3K9Ac, and RNA-Polymerase II (POLII), as well as input reads and conservation among vertebrates at the LMO2 locus as aligned reads.(B) UCSC genome browser screenshot of ChIP-seq and DHS data aligned with digital footprints at the NFE2 locus within a DHS shared between two t(8;21) patients and purified normal CD34+ cells (top). It also shows the binding pattern of RUNX1 in CD34+ cells and RUNX1/ETO, RUNX1, HEB, LMO2, and PU.1 in Kasumi-1 cells as determined by ChIP. Footprint probabilities as calculated by Wellington are indicated as gray columns below the lines. The bottom indicates the location of occupied RUNX, ETS, and C/EBP motifs.(C) Occupied RUNX, E box, and ETS motifs in patient cells cluster within DHS sites that colocalize with RUNX1/ETO binding in Kasumi-1 cells. The heatmap shows hierarchical clustering of footprinted motif co-occurrences by Z score within RUNX1/ETO peaks, indicating transcription factor co-occupancy. Footprint probabilities within RUNX1/ETO-bound peaks were calculated using DNaseI-seq data from t(8;21) patient 1. The motif search was done within RUNX1/ETO footprint coordinates. Red and blue colors indicate statistically over- and underrepresented motif co-occurrences, respectively. For a more detailed explanation, see the legend of Figure S1 and the Supplemental Experimental Procedures.
RUNX1/ETO exists as a complex with other transcription factors (Sun et al., 2013). Consistent with these findings, we observed a colocalization of RUNX1/ETO, RUNX1, HEB, LMO2, C/EBPα, and/or PU.1 binding at many DHSs in Kasumi-1 cells, as exemplified by the LMO2 locus (Figure 1A). Closer examination of the genome-wide occupancy patterns of LMO2 and HEB revealed that a substantial overlap existed among LMO2, HEB, and RUNX1/ETO binding sites (Figure S1A). Although there was some overlap with the other factors, the PU.1 and C/EBPα binding sites did not closely cluster as a group with those for the RUNX1/ETO complexes in Kasumi-1.