Single-cell transcriptional atlas of hematopoiesis reveals genetic and hierarchy-based determinants of aberrant differentiation in AML

Therapeutic targeting of acute myeloid leukemia (AML) is hampered by intra- and inter-tumoral cell state heterogeneity. To develop a more precise understanding of AML cell states, we constructed a reference atlas of human hematopoiesis from 263,159 single cell transcriptomes spanning 55 cellular states. Using this atlas, we mapped over 1.2 million cells spanning 318 leukemia samples, revealing twelve recurrent patterns of aberrant differentiation in AML. Notably, this uncovered unexpected AML cell states resembling lymphoid and erythroid progenitors that were prognostic within the clinically heterogeneous context of normal karyotype AML, independent of genomic classifications. Systematic mapping of genotype-to-phenotype associations revealed specific differentiation landscapes associated with >45 genetic drivers. Importantly, distinct cellular hierarchies can arise from samples sharing the same genetic driver, potentially reflecting distinct cellular origins for disease-sustaining leukemia stem cells. Thus, precise mapping of malignant cell states provides insights into leukemogenesis and refines disease classification in acute leukemia. Frozen mononuclear cells from 13 genetically diverse AML samples (12 primary AML samples, 1 xenograft sample) were obtained from the Munich Leukemia Laboratory (MLL) and were subject to scRNA-seq with 10x 5’ v1.1 technology at the St Jude Children's Research Hospital (SJCRH).