High-dimensional phenotype analysis of leukemias induced by gene-edited HSPCs. (A) Bar graphs summarize protein levels, as determined by CyTOF analysis of human patient MLLr leukemias and gene-edited leukemias. Control, Cas9-only treated human cells engrafted in mouse BM. (B) PCA plot shows the effective separation of patient leukemias into AML vs ALL lineages and a comparable separation in gene-edited leukemias. MPALs show overlapped clustering with AMLs. (C) UMAP plots show that the distributions of individual leukemia cells depend on the sample origins (left panel) and lineage phenotypes (right panel). Patient and gene-edited ALL cells reside mostly UMAP2 < 0, whereas patient AMLs, gene-edited AMLs, and MPALs cells reside UMAP2 > 0. (D) Hierarchical clustering of patient ALLs and AMLs based on their median protein expression. Two ALL and 4 AML reference groups are indicated at the bottom. Diagnostic phenotypes of patient leukemia samples are indicated on top of the heat map. (E) Hierarchical clustering of the percentage of cells in each sample associated with patient ALL and AML reference groups. The 6 colors represent the 2 ALL and 4 AML reference groups identified in Figure 5D. Flow cytometry–determined phenotypes in gene-edited leukemias are indicated on top of the bar graph; blue, ALLs; red, AMLs; green, MPALs. Lineages determined by protein expression pattern in CyTOF are listed at the bottom of each bar graph.