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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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Knockdown of RUNX1/ETO Leads to a Reorganization of Transcription-Factor Assemblies within Preexisting Open Chromatin Regions(A) Three-way Venn diagrams showing the overlap between RUNX1/ETO and RUNX1 (top left), CEBPα (top right), LMO2 (bottom left), and PU.1 (bottom right) in Kasumi-1 cells treated for 48 hr with control (siMM) and with RUNX1/ETO siRNA (siRE).(B) UCSC genome browser screenshot showing the binding pattern of the indicated factors at the CEBPE locus in Kasumi-1 cells treated for 48 hr with control siRNA (siMM) and with RUNX1/ETO siRNA (siRE).(C) Binding of de novo (siRE unique), common, and lost (siMM unique) transcription factors (C/EBPα (top) and RUNX1 (bottom) to regions of increased (DHS up), unchanged (DHS invariant), or reduced DNaseI hypersensitivity.See also Figure S5.
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Figure 5: Knockdown of RUNX1/ETO Leads to a Reorganization of Transcription-Factor Assemblies within Preexisting Open Chromatin Regions(A) Three-way Venn diagrams showing the overlap between RUNX1/ETO and RUNX1 (top left), CEBPα (top right), LMO2 (bottom left), and PU.1 (bottom right) in Kasumi-1 cells treated for 48 hr with control (siMM) and with RUNX1/ETO siRNA (siRE).(B) UCSC genome browser screenshot showing the binding pattern of the indicated factors at the CEBPE locus in Kasumi-1 cells treated for 48 hr with control siRNA (siMM) and with RUNX1/ETO siRNA (siRE).(C) Binding of de novo (siRE unique), common, and lost (siMM unique) transcription factors (C/EBPα (top) and RUNX1 (bottom) to regions of increased (DHS up), unchanged (DHS invariant), or reduced DNaseI hypersensitivity.See also Figure S5.

Mentions: We next examined how the t(8;21) core transcriptional network changed 2 days after RUNX1/ETO depletion. Depletion had no immediate influence on the expression levels of any of the other factors studied above, with the notable exception of C/EBPα (Figure 3A). Nevertheless, loss of RUNX1/ETO had a profound effect on the binding of these transcription factors (Figure S5A). As exemplified by the CEBPE locus, depletion led to increased RUNX1 occupancy at several thousand sites, confirming that RUNX1/ETO and RUNX1 binding are in equilibrium (Figures 5A, top left, 5B, S5B, and S5C). Furthermore, increased RUNX1 occupancy, including RUNX1 sites that were not previously bound by RUNX1/ETO, was associated with a strong increase in p300 binding (Figure 3D). In contrast, more than 3,000 LMO2 binding sites were lost, mainly outside the regions bound by RUNX1/ ETO and RUNX1 (Figures 5A, bottom-right panel, and S5C). Furthermore, whereas 80% of all PU.1 binding sites remained unchanged, the number of sites bound by C/EBPα increased 4-fold. Interestingly, 65% of all C/EBPα de novo sites colocalized with PU.1 (Figures 5A, top left, S5B, and S5D). In agreement with these results, C/EBPα binding sites clustered more strongly with both RUNX1 and PU.1 sites upon depletion of RUNX1/ETO (Figure S5E).


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)

Knockdown of RUNX1/ETO Leads to a Reorganization of Transcription-Factor Assemblies within Preexisting Open Chromatin Regions(A) Three-way Venn diagrams showing the overlap between RUNX1/ETO and RUNX1 (top left), CEBPα (top right), LMO2 (bottom left), and PU.1 (bottom right) in Kasumi-1 cells treated for 48 hr with control (siMM) and with RUNX1/ETO siRNA (siRE).(B) UCSC genome browser screenshot showing the binding pattern of the indicated factors at the CEBPE locus in Kasumi-1 cells treated for 48 hr with control siRNA (siMM) and with RUNX1/ETO siRNA (siRE).(C) Binding of de novo (siRE unique), common, and lost (siMM unique) transcription factors (C/EBPα (top) and RUNX1 (bottom) to regions of increased (DHS up), unchanged (DHS invariant), or reduced DNaseI hypersensitivity.See also Figure S5.
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Related In: Results  -  Collection

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Figure 5: Knockdown of RUNX1/ETO Leads to a Reorganization of Transcription-Factor Assemblies within Preexisting Open Chromatin Regions(A) Three-way Venn diagrams showing the overlap between RUNX1/ETO and RUNX1 (top left), CEBPα (top right), LMO2 (bottom left), and PU.1 (bottom right) in Kasumi-1 cells treated for 48 hr with control (siMM) and with RUNX1/ETO siRNA (siRE).(B) UCSC genome browser screenshot showing the binding pattern of the indicated factors at the CEBPE locus in Kasumi-1 cells treated for 48 hr with control siRNA (siMM) and with RUNX1/ETO siRNA (siRE).(C) Binding of de novo (siRE unique), common, and lost (siMM unique) transcription factors (C/EBPα (top) and RUNX1 (bottom) to regions of increased (DHS up), unchanged (DHS invariant), or reduced DNaseI hypersensitivity.See also Figure S5.
Mentions: We next examined how the t(8;21) core transcriptional network changed 2 days after RUNX1/ETO depletion. Depletion had no immediate influence on the expression levels of any of the other factors studied above, with the notable exception of C/EBPα (Figure 3A). Nevertheless, loss of RUNX1/ETO had a profound effect on the binding of these transcription factors (Figure S5A). As exemplified by the CEBPE locus, depletion led to increased RUNX1 occupancy at several thousand sites, confirming that RUNX1/ETO and RUNX1 binding are in equilibrium (Figures 5A, top left, 5B, S5B, and S5C). Furthermore, increased RUNX1 occupancy, including RUNX1 sites that were not previously bound by RUNX1/ETO, was associated with a strong increase in p300 binding (Figure 3D). In contrast, more than 3,000 LMO2 binding sites were lost, mainly outside the regions bound by RUNX1/ ETO and RUNX1 (Figures 5A, bottom-right panel, and S5C). Furthermore, whereas 80% of all PU.1 binding sites remained unchanged, the number of sites bound by C/EBPα increased 4-fold. Interestingly, 65% of all C/EBPα de novo sites colocalized with PU.1 (Figures 5A, top left, S5B, and S5D). In agreement with these results, C/EBPα binding sites clustered more strongly with both RUNX1 and PU.1 sites upon depletion of RUNX1/ETO (Figure S5E).

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