Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia

Single-cell whole transcriptome analysis of chronic myeloid leukemia stem cells, defined as Lin-CD34+CD38-. Overall design: We developed a method that combines high-sensitivity mutation detection with whole-transcriptome analysis of the same single cell. We applied this technique to analyze more than 2,000 single cells from patients with chronic myeloid leukemia (CML) throughout the disease course, revealing heterogeneity of CML stem cells, including the identification of a subgroup of CML stem cells with a distinct molecular signature that selectively persisted during prolonged therapy. We performed differential gene expression and the gene set enrichment analyses of BCR-ABL+ vs BCR-ABL- single cells from either patients or normal donors, analyzed at different stages of the disease.