Dissecting leukemic stem cells at single-cell resolution: A proteogenomic approach

Acute myeloid leukemia (AML) remains one of the most heterogeneous hematologic malignancies, both at the genetic and phenotypic levels. Despite initial responses to therapy, relapse is frequent and largely driven by a rare population of leukemic stem cells (LSC), which persist in up to 70–80% of AML cases and act as a reservoir for disease propagation and resistance. Traditional bulk approaches have provided key insights into AML biology but inherently obscure the cellular diversity that shapes disease evolution and therapeutic escape.

Here, we leveraged single-cell proteogenomics to dissect the heterogeneity of LSC at unprecedented resolution. By combining high-dimensional genotyping with a custom-designed antibody panel, we were able to simultaneously capture mutational landscapes and phenotypic profiles of stem and progenitor compartments. This approach uncovered unexpected subclonal architectures, revealed co-existing immunophenotypic states within genetically defined clones, and highlighted rare but clinically relevant LSC subsets that would have been invisible using conventional methods.

Our work illustrates how single-cell proteogenomics can bridge the gap between genotype and phenotype in AML, offering a powerful framework to better understand LSC biology, monitor minimal residual disease, and ultimately inform precision therapeutic strategies.