Single cell transcriptomics derived combinatorial markers distinguished leukemic stem cells from hematopoietic stem cells in acute myeloid leukemia.

Leukemic stem cells (LSCs) play a critical role in relapse and chemoresistance in acute myeloid leukemia (AML). These LSCs originate from Hematopoietic stem cells (HSCs) after acquiring genetic and molecular aberrations. Both HSCs and LSCs predominantly reside in CD34 +CD38- fraction of the bone marrow and their phenotypic similarities poses a challenge in distinguishing between them. In addition, the phenotypic heterogeneity of LSCs limits the precise quantitation of this population in clinical studies. Delineation of LSCs from HSCs and quantification of LSC burden is crucial as it is correlated with survival rates and treatment outcomes in AML. In this study, we employed single cell transcriptomic analysis to identify differentially expressed cell surface markers that can discriminate LSCs from HSCs. Our data revealed several candidate markers, including CD48, CD52, CD96 and CD88 with distinct expression patterns in LSCs compared to HSCs. We further validated the expression levels of these markers as potential biomarkers for the identification of LSCs in both CD34 + and CD34- AML. Among these cell surface markers, CD52, CD96 and CD48 were significantly over-expressed in LSCs relative to HSCs. Incorporating these markers in combination with established aberrant markers can enhance the identification of LSCs and help distinguish them from HSCs in both CD34 + and CD34- AML. Our findings support the use of an expanded combinatorial marker panel and warrants its further evaluation in a larger AML cohort, particularly in the context of measurable residual disease (MRD) assessment, prognostication and correlation with treatment response and survival outcomes.