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Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal.

Ptasinska A, Assi SA, Martinez-Soria N, Imperato MR, Piper J, Cauchy P, Pickin A, James SR, Hoogenkamp M, Williamson D, Wu M, Tenen DG, Ott S, Westhead DR, Cockerill PN, Heidenreich O, Bonifer C - Cell Rep (2014)

Bottom Line: 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.Our work demonstrates on a genome-wide level that the extent of impaired myeloid differentiation in t(8;21) is controlled by the dynamic balance between RUNX1/ETO and RUNX1 activities through the repression of transcription factors that drive differentiation.

View Article: PubMed Central - PubMed

Affiliation: School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.

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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.
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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.

Mentions: 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.


Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal.

Ptasinska A, Assi SA, Martinez-Soria N, Imperato MR, Piper J, Cauchy P, Pickin A, James SR, Hoogenkamp M, Williamson D, Wu M, Tenen DG, Ott S, Westhead DR, Cockerill PN, Heidenreich O, Bonifer C - Cell Rep (2014)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4487811&req=5

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.
Mentions: 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.

Bottom Line: 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.Our work demonstrates on a genome-wide level that the extent of impaired myeloid differentiation in t(8;21) is controlled by the dynamic balance between RUNX1/ETO and RUNX1 activities through the repression of transcription factors that drive differentiation.

View Article: PubMed Central - PubMed

Affiliation: School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.

Show MeSH