Figure 1.
ZMIZ1 is important for human and murine immature T-ALL population growth. (A)ZMIZ1 expression according to ETP status (n = 19 ETP; n = 24; near-ETP; n = 146 not-ETP) in the TARGET database (Liu et al., 2017). Horizontal lines indicate medians. (B and C) The proportion of ETP, near-ETP, and non-ETP T-ALL blasts in four key T-cell developmental stages based on scRNA (B) and scATAC (C) projections to healthy reference. P values are based on two-sided Mann–Whitney test. BMP stage encapsulates multipotent progenitors: HSPC/LMPP/CLP/ETP. (D) Identification of LOUCY and CUTLL3 cell lines as experimental models for BMP-like blasts based on transcriptome similarity with BMP developmental subsets identified in scRNA-seq data (Xu et al., 2024). 19 T-ALL cell lines were examined. Pearson correlation was calculated for over 971 lineage-determinant genes. Row-based Z-score normalized correlations and hierarchical clustering (k = 2 nodes) are shown. Cell states with maximum correlation to LOUCY and CUTLL3 are boxed. (E) Identification of LOUCY and CUTLL3 cell lines as experimental models for BMP-like blasts using BMP-like transcriptomic signatures—BMP-119 (BMP-like DEGs) and BMP-like transcription factor (BMP-like-TFs) (Xu et al., 2024). See also Table S1. DepMap 22Q4, GSE138659, GSE59810, and GSE164928. (F) Volcano plot of significance versus log(fold change) RNA-seq expression of transcription factors in BMP-like ETP-ALLs compared to T-specified ETP-ALL blasts (Xu et al., 2024). Elevated expression of BMP-like transcription factors (red) and reduced expression of NOTCH1-induced transcription factors (blue) are highlighted. ZMIZ1 was added as a reference. (G–J) LOUCY cells (G and I) and CUTLL3 cells (H and J) were transduced with shZMIZ1 and analyzed for ZMIZ1 protein expression by western blot (G and H) or population growth assay by trypan-blue exclusion cell count; n = 3/group. (I–L) Immature T-ALL PDX cells were transduced with shZMIZ1 and analyzed for population growth by flow cytometry during co-culture on OP9-DL1 stromal cells; n = 3/group. (M–P) Representative peripheral blood GFP+ flow cytometric analysis (M), peripheral blood GFP+ blast counts (N), H&E liver sections at 10× magnification at day 131 after transplant (100 μm scale bar, O), and survival (P) were measured after transplantation of primary tumor per experimental design described in Fig. S2 A; n = 9/group (Experiment #321). Unless noted otherwise, P values were based on two-sided t tests for two samples and one-way ANOVA for more than two samples. **P < 0.01; ***P < 0.001. Source data are available for this figure: SourceData F1. Refer to the image caption for details.

ZMIZ1 is important for human and murine immature T-ALL population growth. (A) ZMIZ1 expression according to ETP status (n = 19 ETP; n = 24; near-ETP; n = 146 not-ETP) in the TARGET database (Liu et al., 2017). Horizontal lines indicate medians. (B and C) The proportion of ETP, near-ETP, and non-ETP T-ALL blasts in four key T-cell developmental stages based on scRNA (B) and scATAC (C) projections to healthy reference. P values are based on two-sided Mann–Whitney test. BMP stage encapsulates multipotent progenitors: HSPC/LMPP/CLP/ETP. (D) Identification of LOUCY and CUTLL3 cell lines as experimental models for BMP-like blasts based on transcriptome similarity with BMP developmental subsets identified in scRNA-seq data (Xu et al., 2024). 19 T-ALL cell lines were examined. Pearson correlation was calculated for over 971 lineage-determinant genes. Row-based Z-score normalized correlations and hierarchical clustering (k = 2 nodes) are shown. Cell states with maximum correlation to LOUCY and CUTLL3 are boxed. (E) Identification of LOUCY and CUTLL3 cell lines as experimental models for BMP-like blasts using BMP-like transcriptomic signatures—BMP-119 (BMP-like DEGs) and BMP-like transcription factor (BMP-like-TFs) (Xu et al., 2024). See also Table S1. DepMap 22Q4, GSE138659, GSE59810, and GSE164928. (F) Volcano plot of significance versus log(fold change) RNA-seq expression of transcription factors in BMP-like ETP-ALLs compared to T-specified ETP-ALL blasts (Xu et al., 2024). Elevated expression of BMP-like transcription factors (red) and reduced expression of NOTCH1-induced transcription factors (blue) are highlighted. ZMIZ1 was added as a reference. (G–J) LOUCY cells (G and I) and CUTLL3 cells (H and J) were transduced with shZMIZ1 and analyzed for ZMIZ1 protein expression by western blot (G and H) or population growth assay by trypan-blue exclusion cell count; n = 3/group. (I–L) Immature T-ALL PDX cells were transduced with shZMIZ1 and analyzed for population growth by flow cytometry during co-culture on OP9-DL1 stromal cells; n = 3/group. (M–P) Representative peripheral blood GFP+ flow cytometric analysis (M), peripheral blood GFP+ blast counts (N), H&E liver sections at 10× magnification at day 131 after transplant (100 μm scale bar, O), and survival (P) were measured after transplantation of primary tumor per experimental design described in Fig. S2 A; n = 9/group (Experiment #321). Unless noted otherwise, P values were based on two-sided t tests for two samples and one-way ANOVA for more than two samples. **P < 0.01; ***P < 0.001. Source data are available for this figure: SourceData F1.

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