CD34⁻ non-LSC populations are more differentiated compared with LSC populations. (A, left) PCA of normal populations and CD34⁻ AML LSCs and non-LSC populations using the ANOVA 500 gene set (Fig. 4 A). The arrow shows the axis of normal myelomonocytic differentiation. (Right) PCA comparing LSCs and non-LSCs within five individual patients showing just the area shaded in gray on the main PCA plot on the left. CMP, common myeloid progenitor; Ery-Pre, erythroid precursor; MEP, megakaryocyte-erythroid progenitor. (B) Heat map of the normalized enrichment score (NES) from GSEA of normal HSC/MPP, GM-pre, and GM-mat signatures in profiles of LSC versus non-LSC populations in four patients (#001, #230, #875, and #880). Representative GSEA plots are from patient #001. (C) PCA showing the position of normal HSCs/MPPs, LMPPs, GM-pre, GM-mat, and CD34⁻ AML LSCs and non-LSCs using 300 genes differentially expressed between CD34⁻ LSCs and non-LSCs (from rank product analysis; PFP <0.05). (Top right and bottom) PCA of LSC and non-LSC populations in individual patients (#001, #059, #230, #875, and #880) analyzed with normal HSPC, GM-pre, and GM-mat cell populations. (D) Loadings plot of PCA in C. (E) Heat map of expression pattern of 125 genes with increased expression in CD34⁻ AML LSC versus non-LSC populations (top) and 175 genes with increased expression in non-LSC versus CD34⁻ AML LSC populations (bottom) in normal HSC/MPP, LMPP, GMP, GM-pre, and GM-mat populations. The color bar scale is as in Fig. 5 (B and D). (Right) Mean expression of the two gene sets in each population. Error bars represent SD. CPM, counts per million.