Hematopoiesis generates various cell types in the blood through a structured hierarchical process. In acute myeloid leukemia (AML), the process of hematopoiesis goes terribly wrong: Leukemic cells follow an altered hierarchy during development—the extent of differences depends on the specific mutations and the cell type of origin.1 Unfortunately, current tools can only provide a rough idea of what stages of differentiation are present in an AML sample, and biomarkers to predict treatment responses remain unavailable.
Now, a team of researchers has used single-cell RNA-sequencing (scRNA-Seq) to comprehensively map the process of hematopoiesis and determine all the ways this process can go wrong in AML.2 In a study published in Blood Cancer Discovery, the authors showcase their reference atlas of normal hematopoiesis and a computational tool, called BoneMarrowMap, for mapping and classifying leukemic cells.
In a presentation at the American Association for Cancer Research (AACR) Annual Meeting 2025, author Andy Zeng of the University of Toronto revealed that their approach could distinguish 12 distinct patterns of differentiation across AML samples—this level of granular information could not be achieved using current methods. “You can see that despite having the same diagnosis, they differ profoundly in terms of the regions of hematopoiesis that are implicated,” said Zeng.
The team used their reference map for normal hematopoiesis, comprised of 263,159 single-cell transcriptomes across 55 cell states, as a North Star. They mapped over 1.2 million cells from more than 300 leukemia samples to this reference atlas to determine patterns of aberrant differentiation.
Among the different cell differentiation stages that the team identified, some were characterized by early blocks in differentiation, and some by the enrichment of differentiation states from many stages of hematopoiesis. Others were characterized by the enrichment of differentiation states from a specific progenitor, such as an erythroid, lymphoid, or myeloid progenitor. Erythroid and lymphoid enrichment were unexpected because AML is typically characterized by a differentiation trajectory toward myeloid cells.
This made the team curious about the clinical implications of these unconventional differentiation patterns, so they subjected hundreds of AML patient samples to bulk RNA sequencing to determine if the abundance of these specific cell types had an effect on the overall survival rates observed in those patients. The analysis showed that “having more of these lymphoid progenitor-like cells is adverse, and having more erythroid involvement is actually favorable,” said Zeng. They next wanted to explore options for patients with lymphoid-enriched lineages in whom overall survival was lower. Drug sensitivity tests ex vivo revealed that the lymphoid-enriched samples are more likely to respond to tyrosine kinase inhibitor drugs, highlighting the potential for the authors’ cell-mapping approach in identifying targeted treatments for AML.
Zeng and his colleagues also decided to explore the relationships between these AML differentiation patterns and 45 genetic mutations that are known to drive the disease. This yielded another key finding. “Even with patients that were genetically identical in terms of their driver [mutations], there was still variation in terms of the differentiation hierarchies that we could see,” Zeng said of the results. “This shows us that beyond the driver alone, it's the cellular context in which transformation occurs that can determine that ultimate phenotype.”
According to Zeng, their scRNA-Seq reference atlas and the BoneMarrowMap tool can be used by other researchers to potentially develop more tailored treatment plans for patients. “You can map [your samples] in 10 minutes onto our atlas and see exactly what cell states are implicated,” Zeng concluded.
- Zeng AGX, et al. A cellular hierarchy framework for understanding heterogeneity and predicting drug response in acute myeloid leukemia. Nat Med. 2022;28(6):1212-1223.
- Zeng AGX, et al. Single-cell transcriptional atlas of human hematopoiesis reveals genetic and hierarchy-based determinants of aberrant AML differentiation. Blood Cancer Discov. 2025:1-18.
