HSPC-like leukemic blasts are resistant to chemotherapy in acute leukemias. (A-C) Frequencies of developmental arrest stages of leukemia blasts across leukemia subtypes. Each developmental pseudotime trajectory from HSC/MPP to terminally differentiated population is ordered in 20 bins. Heat maps show the frequencies of each bin from individual patients: AML (n = 10) (A), B-ALL (n = 35) (B), and T-ALL (n = 40) (C). Dashed vertical lines delineate the division between multipotent stem/progenitor-like population and lineage-like populations for each lineage. Bottom line plots show the frequency of each developmental stage along the pseudotime trajectories using HD data: myeloid lineage (A), B-cell lineage (B), and T-cell lineage (C). Legends on the right side show the percentage of MRD for AML and T-ALL or genetic subtypes for B-ALL. (D) Box plots showing the frequencies of HSPC-like blasts in MRD⁺ vs MRD^– patients (AML and T-ALL) or in high-risk vs low-risk subtype (B-ALL) patients in the single-cell data of this study. P values were computed using the Student t test. (E) Association between frequency of HSPC-like/lineage-like blasts and EOI MRD values after induction chemotherapy in AML, B-ALL, and T-ALL based on multiple linear regression (supplemental Methods). Error bars show the 95% confidence interval of regression coefficient. The frequencies of HSPC-like and lineage-like blasts were computed using CIBERSORT and bulk RNA-seq data from the National Cancer Institute’s TARGET (AML, B-ALL) project, and the Children’s Oncology Group AALL0434 trial (T-ALL). (F) Association between frequency of HSPC-like/lineage-like blasts and LC50 of 9 conventional chemotherapy drugs. The color of the dots represents regression coefficients and the size of the dots represents the –log₁₀(adjusted P value of regression coefficient). The frequencies of HSPC-like and lineage-like blasts were computed using CIBERSORT. LC50 data and corresponding bulk RNA-seq data sets were downloaded from Lee et al.³⁹ P values were computed using the Student t test and adjusted for multiple testing using the Benjamini-Hochberg method. Significant associations are indicated with a circle with thicker borders. (G) Drug response curves showing the different response to conventional chemotherapy drugs between HSPC-like derived (n = 2) and lineage-like derived PDX cells (n = 2). (H) Frequencies of HSPC-like blasts from PDX treatment groups based on PDX treatment scRNA-seq data. Sample numbers: dexamethasone (Dex) n = 5; vincristine (VCR) n = 2; untreated controls n = 7. P values were computed using the Student t test. (I) Volcano plot showing the DEGs comparing dexamethasone-treated PDXs and control PDXs based on scRNA-seq data. Red dots represent the genes with adjusted P value <.05 and abs(log₂FC) > 0.25; purple dots represent the genes with adjusted P value < .05 only; black dots represent the nonsignificant genes. CLP, common lymphoid progenitor; Ctrl, control; DP, double positive T cells; GMP, granulocyte monocyte progenitor; LC50, lethal concentration 50%; LMPP, lympho-myeloid primed progenitor; MPP, multipotent progenitor; NK, natural killer; TNF, tumor necrosis factor.