A stem cell model identifies two alternative cell fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation (ChIP-seq)

CBFA2T3::GLIS2 (CG) is an oncogenic fusion protein found in high-risk pediatric acute megakaryoblastic leukemia (AMKL). To gain insight into its leukemogenic mechanism, we developed a disease model based on genetically modified human induced pluripotent stem cells. We found that in this model CG expression disrupts myeloid differentiation via two alternate paths: either by delaying differentiation of aberrant megakaryocytes (aMK) or by locking aberrant megakaryocyte progenitors (aMKP) in a proliferative state akin to AMKL tumor cells. We defined the gene-regulatory networks characterizing both cell states by single-cell transcriptome and epigenome analysis and observed that CG sustains aMKP self-renewal along with cooperators like GATA2 and ERG, while repressing differentiation factors such as SPI1, CEBPA, NFE2, and LYL1. In contrast, in aMKs, CG downregulated drivers of self-renewal and upregulated most but not all lineage-specific differentiation factors. Our findings may contribute to strategies selectively targeting the aMKP state in CG-AMKL patients. We established a new hiPSC lines harboring an endogenous conditional CG allele and equipped with a degradation tag. We generated gene expression (RNA-seq, scRNA-seq), chromatin (ChIP-seq, ATAC-seq), and multimodal (scRNA-seq+scATAC-seq) profilings in longitudinal fashion (early = Day 12-13, intermediate = Day 22-25, longterm = Day 72-115 ) for a comprehensive benchmark and characterization of our model.