Inducible MLL-AF9 expression drives an AML program during human pluripotent stem cell-derived hematopoietic differentiation

Abstract

A t(9;11)(p22;q23) translocation produces the MLL-AF9 fusion protein, which is found in up to 25% of de novo AML cases in children. Despite major advances, obtaining a comprehensive understanding of context-dependent MLL-AF9-mediated gene programs during early hematopoiesis is challenging. Here, we generated a human inducible pluripotent stem cell (hiPSC) model with doxycycline dose-dependent MLL-AF9 expression. We exploit MLL-AF9 expression as an oncogenic hit to uncover epigenetic and transcriptomic effects on iPSC-derived hematopoietic development and the transformation into (pre-)leukemic states. In doing so, we observed disruption of early myelomonocytic development and expansion of a CD34+ early hematopoietic progenitor compartment upon MLL-AF9 activation. In agreement, we identified gene profiles consistent with primary MLL-AF9 AML and uncovered highly confident MLL-AF9-associated core genes that faithfully represent primary MLL-AF9 AML, including known and thus far unknown factors. Our system allows for careful chemically controlled and stepwise in vitro hiPSC-derived differentiation under serum-free and feeder-free conditions. For a disease that currently lacks effective precision medicine, our system provides a novel entry-point into exploring potential novel biomarkers and targets for personalized therapeutic strategies.