Fig 2: Validation of the enrichment of QSCs in refractory and early-relapsed AML patients by flow cytometry based on the markers identified by single-cell data.A Bar plots showing the percentage of each leukemia-like cellular state in CD99+ITGA4+ and CD99+ITGA4+CD52+LGALS1+ cells of single-cell transcriptomic data in this study. B Comparison of the percentage of CD99+CD49d+CD52+Galectin-1+ (QSCs) cells in viable CD45dimSSClow blasts among diagnosis (DX) sensitive patients, diagnosis (DX) resistant patients, and refractory/early-relapsed AML patients by flow cytometry. C Flow cytometric analysis of the percentage of QSCs in matched bone marrow samples from primary refractory AML patients (Pt#27, Pt#28, Pt#29, and Pt#30) before and after chemotherapy. D Comparison of the percentage of QSCs in viable CD45dimSSClow blasts at diagnosis and refractory bone marrow samples of Pt27, Pt#28, Pt#29, and Pt#30.

Fig 3: Longitudinal scRNA-seq analyses for the identification of cellular and molecular reprogramming induced by chemotherapy in AML patients.A Left: t-SNE visualization of scRNA-seq data of primary refractory patient Pt#3 before and after chemotherapy. Right: Sankey plot showing the dynamic changes of cellular states after chemotherapy in Pt#3. B Left: t-SNE visualization of scRNA-seq data of primary refractory patient Pt#9 before and after chemotherapy. Right: Sankey plot showing the dynamic changes of cellular states after chemotherapy in Pt#9. C Left: t-SNE visualization of scRNA-seq data of Pt#10 who achieved partial remission. Right: Sankey plot showing the dynamic changes of cellular states after chemotherapy in Pt#10. D Sankey plot showing the dynamic changes of cellular states during chemotherapy in samples from the study of Galen et al. E Heatmap for differentially expressed genes after chemotherapy in Pt#3. F Principal component analysis (PCA) of the cellular states in Pt#3 based on the differentially expressed genes during chemotherapy. The dot shape represents the cellular states before or after chemotherapy. G, H Ridge plots showing the activity scores of transcriptional factors GATA2 and TAL1 in QSCs and PSPs during chemotherapy in Pt#3. I The enrichment of GATA2 and TAL1 peaks on gene CD52 based on the ChIP‐Seq data of K562 cell line.