RUNX1::RUNX1T1 Depletion Eliminates Stemness and Induces Bidirectional Differentiation of Acute Myeloid Leukemia

Derevyanko, P. K.; Swart, L. E.; Casimiro, L. D. M.; van den Brink, L.; van Oort, A. T.; Ashtiani, M.; Zwaan, C. M.; Krippner-Heidenreich, A.; Bonifer, C.; Schiffelers, R.; Vormoor, H. J.; Kellaway, S. G.; Heidenreich, O.

doi:10.1101/2025.02.13.637937

bioRxiv · 10.1101/2025.02.13.637937

RUNX1::RUNX1T1 Depletion Eliminates Stemness and Induces Bidirectional Differentiation of Acute Myeloid Leukemia

Derevyanko, P. K.·Swart, L. E.·Casimiro, L. D. M.·van den Brink, L.·van Oort, A. T.·Ashtiani, M.·Zwaan, C. M.·Krippner-Heidenreich, A.·Bonifer, C.·Schiffelers, R.·Vormoor, H. J.·Kellaway, S. G.·Heidenreich, O.

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Abstract

Chromosomal rearrangements that generate novel fusion genes are a hallmark of acute myeloid leukemia (AML). Depletion experiments in cell line models have suggested that continued expression is required for maintaining their leukemic phenotype and they therefore represent ideal cancer-specific therapeutic targets. However, to which extent this result holds true for the different stages of hematopoietic development in primary cells and whether therapeutic agents can be efficiently delivered to those cells is still unclear. In this study, we demonstrate that primary AML cells harboring the chromosomal translocation t(8;21) are critically dependent on the corresponding fusion gene, RUNX1::RUNX1T1, to suppress differentiation and maintain stemness. Silencing RUNX1::RUNX1T1 expression using siRNA-loaded lipid nanoparticles induces substantial changes in chromatin accessibility, thereby redirecting the leukemia-associated transcriptional network towards a myeloid differentiation program. Single-cell analyses reveal that this transcriptional reprogramming is associated with the depletion of immature stem and progenitor-like cell populations, accompanied by an expansion of granulocytic and eosinophilic/mast cell-like populations with impaired self-renewal capacity. These findings underscore the essential role of RUNX1::RUNX1T1 in sustaining AML and highlight the therapeutic potential of targeting fusion gene expression in primary AML cells. O_FIG O_LINKSMALLFIG WIDTH=167 HEIGHT=200 SRC="FIGDIR/small/637937v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@cf4838org.highwire.dtl.DTLVardef@8e6d90org.highwire.dtl.DTLVardef@bb46c5org.highwire.dtl.DTLVardef@12357e4_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Derevyanko, P. K., Swart, L. E., Casimiro, L. D. M., van den Brink, L., van Oort, A. T., Ashtiani, M., Zwaan, C. M., Krippner-Heidenreich, A., Bonifer, C., Schiffelers, R., Vormoor, H. J., Kellaway, S. G., Heidenreich, O.. 2025-02-17. RUNX1::RUNX1T1 Depletion Eliminates Stemness and Induces Bidirectional Differentiation of Acute Myeloid Leukemia. https://doi.org/10.1101/2025.02.13.637937

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