Multicolor detection of chronic myeloid leukemia stem cells, including novel marker CD69, predicts survival and early hematological toxicity

Chronic myeloid leukemia stem cells (LSCs) drive disease initiation, persistence, and relapse. To improve LSC-based prognostication and patient stratification, we evaluated six LSC markers (CD26, CD25, IL1-RAP, CD56, CD93, and CD69) using a single-tube analysis of CD34+CD38- cells in a cohort of 48 chronic phase chronic myeloid leukemia patients at diagnosis, month 3, or month 6. We demonstrate that these markers (including the novel marker CD69) are co-expressed, and their combination enhances LSC detection, especially during follow-up when marker expression is reduced. Furthermore, LSC data from month 3 and month 6 predict patient outcomes. We also show that quantifying residual normal hematopoietic stem cells at diagnosis enables early hematological toxicity prediction. Our findings provide technological LSC detection advancements and highlight the potential of these data for prognostic applications.