The effect of BCR-ABL translocation and subsequent TKI treatment on the heterogeneity of the CML LSC population. (A) Distribution of BCR-ABL^pos and/or BCR-ABL^neg cells within the 7 Lin⁻CD34⁺CD38^−/low subpopulations in nBM, CP-CML at diagnosis (CML Dx), and following TKI treatment (CML TKI). (B) Fold change in the proportion of BCR-ABL^pos cells from patients where analysis was performed both at diagnosis (Dx) and following TKI treatment (TKI). (C) PCA plots of the single-cell gene expression data displaying how Lin⁻CD34⁺CD38^−/low heterogeneity is changed in CP-CML at diagnosis (Dx) compared with healthy nBM, and how cells with more myeloid or Meg/E molecular signatures are eradicated during treatment (TKI). Each dot represents a single cell that has been color coded according to the RFC. The legend on top of the plots (ALL CELLS, nBM, BCR-ABL^pos-Dx, BCR-ABL^pos-TKI) indicates cells that are colored; other cells are depicted as gray. (D) PCA plots and distribution of BCR-ABL^pos cells according to RFC (colored bar) for 4 individual patients. Black dots represent cells from the specific patient at the indicated point of analysis (diagnosis [Dx], following TKI treatment [TKI]); the rest of the data set is depicted in gray.