Poster Presentation 47th Lorne Genome Conference 2026

Dosage-dependent activation of the endothelial gene expression program in human ES-cell derived myeloid precursor cells by the leukaemic oncoprotein RUNX1-ETO (132996)

Constanze Bonifer 1 , Katherina Terrolli 1 , Floyd Hassenrueck 1 , Alexander Maytum 1 , Peter Keane 2 , Lea Flippe 1 , Edouard Stanley 1 , Elizabeth Ng 1 , Andrew Elefanty 1
  1. Murdoch Children's Research Institute / University of Birmingham, Parkville, VICTORIA, Australia
  2. School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK

In t(8;21) Acute Myeloid Leukaemia (AML) the DNA binding domain of the master regulator of haematopoiesis, RUNX1 is fused to the RUNX1T1 (ETO) protein producing the RUNX1-ETO onco-fusion protein which interferes with RUNX1 by binding to the same genomic sites1. In AML, a consequence of mutations affecting gene regulation is the derailing of differentiation causing compensatory cellular changes in gene regulatory networks (GRNs), which can result in the aberrant activation of genes unrelated to blood cell development2. This feature is also true for cells in patients carrying the t(8;21) AML and other Core Binding Factor AML subtypes. We recently showed that t(8;21) progenitor cells activate ectopic signalling pathways to kick-start the production of proliferating blast cells3. One of these aberrantly activated pathways is specific for endothelial cells, including the gene encoding Vascular Endothelial Growth Factor Alpha (VEGFA) and its receptor FLK1 encoded by the KDR gene. 

To test whether RUNX1-ETO directly causes aberrant signalling pathway activation or whether rewiring is a result of AML progression, we employed a human Embryonic Stem Cell (ESC) line expressing an inducible RUNX1-ETO transgene4. Using an advanced in vitro differentiation system capable of generating multi-lineage engrafting haematopoietic stem cells5 followed by single cell analyses we show that RUNX1-ETO induction in ESC-derived myeloid progenitors causes a dosage-dependent reprogramming of their GRN by irreversibly activating an endothelial cellular phenotype and a cell cycle block, creating cells with rewired signalling features. Integrated data analysis demonstrates (i) that endothelial reprogramming is irreversible and (ii) that a sub-population of blood progenitors escapes reprogramming when RUNX1-ETO expression levels balance those of RUNX1.

In summary, our study demonstrates that our human embryonic stem cell system faithfully dissects the earliest stages of cellular reprogramming by oncogenic transcription factors and provides important insights into the activation of aberrant gene expression patterns in AML.

  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 Sep 25;8(6):1974-1988
  2. Subtype-specific regulatory network rewiring in acute myeloid leukemia. Assi SA, Imperato MR, Coleman DJL, Pickin A, Potluri S, Ptasinska A, Chin PS, Blair H, Cauchy P, James SR, Zacarias-Cabeza J, Gilding LN, Beggs A, Clokie S, Loke JC, Jenkin P, Uddin A, Delwel R, Richards SJ, Raghavan M, Griffiths MJ, Heidenreich O, Cockerill PN, Bonifer C. Nat Genet. 2019 Jan;51(1):151-162
  3. Leukemic stem cells activate lineage inappropriate signalling pathways to promote their growth. Kellaway SG, Potluri S, Keane P, Blair HJ, Ames L, Worker A, Chin PS, Ptasinska A, Derevyanko PK, Adamo A, Coleman DJL, Khan N, Assi SA, Krippner-Heidenreich A, Raghavan M, Cockerill PN, Heidenreich O, Bonifer C. Nat Commun. 2024 Feb 14;15(1):1359
  4. Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells. Nafria M, Keane P, Ng ES, Stanley EG, Elefanty AG, Bonifer C. Cell Rep. 2020 May 26;31(8):107691
  5. Long-term engrafting multilineage hematopoietic cells differentiated from human induced pluripotent stem cells. Ng ES, Sarila G, Li JY, Edirisinghe HS, Saxena R, Sun S, Bruveris FF, Labonne T, Sleebs N, Maytum A, Yow RY, Inguanti C, Motazedian A, Calvanese V, Capellera-Garcia S, Ma F, Nim HT, Ramialison M, Bonifer C, Mikkola HKA, Stanley EG, Elefanty AG. Nat Biotechnol. 2025 Aug;43(8):1274-1287