Figure 6. Sphingolipid genes including S1PR3 predict prognosis in human AML.

A, GSEA analysis of 10 S1P genes in AML LSC+ and LSC^– gene expression data shows enrichment of S1PR1, S1PR3, S1PR5, the S1P kinase (SPHK1) in LSC^– samples. See Supplementary Table 12 for LSC ranking. B, GSEA analysis of 23 lipid-stem genes, previously shown to be enriched in HSC subsets relative to committed progenitor populations, in AML LSC+ and LSC– gene expression data shows enrichment in LSC+ samples. C, A uniform manifold approximation and projection (UMAP) plot for the sphingolipid composition of samples measured by LC/MS spectrometry in functionally defined individual LSC+ (n=7) and LSC^–(n=7) fractions from 10 patient AMLs as determined by xenotransplantation and normal stem (CD34⁺CD38^-) and progenitor (CD34⁺CD38⁺) fractions (CB, n=3). LSC+ (red circles), LSC^– (blue circles), CB stem (red triangles), CB progenitor (blue triangles). LSC+ subpopulation from AML9, which is high for S1PR3 gene expression, clusters away from other 6 LSC+ samples. See Supplementary Figure 9C-G for sphingolipid composition distribution of individual samples and quantification of specific sphingolipid species and Supplementary Table 9 for patient AML data. D, Sparse regression analysis, as described in Ng, et al. al(7), to derive a weighted sphingolipid gene score predictive of overall survival (OS) applied to a large training cohort of n=495 AML patients yielded a set of 8 genes with their associated scores which were then validated on GSE12417 and TCGA-AML cohorts in univariate analysis. These included 3 genes associated with S1P production and signaling and 5 genes encoding sphingolipid enzymes. E, Kaplan-Meier estimates of OS based on above versus below median values of a weighted sphingolipid gene score. A low score is associated with greater OS. F, GSEA plot for sphingolipid 8-gene OS signature shows negative enrichment in patient samples at relapse.