Capturing single-cell mRNA expression before and after TKI therapy. This is a highly simplified presentation of the experimental design. First, bulk mononuclear cells from CP-CML patients at diagnosis and after TKI therapy (A) were flow cytometry sorted into single cells based on a group of surface antigens associated with the leukemia stem cell state (B). In this figure, LSCs are in shades of red, whereas normal stem cells are in shades of blue. Gene mRNA levels for 95 genes were performed on each cell (C). From these gene expression patterns, 7 different cell subtypes were inferred, including 4 myeloid groups (from less to more differentiated), and 1 group each with erythroid, lymphoid, and quiescence expression patterns. After therapy, residual CML cells were biased toward some pathways (schematically shown by size of font), the largest with inferred quiescence state, with the CD45RA⁻cKIT⁻CD26⁺ phenotype appearing to be the population mostly associated with TKI resistance.