Molecular remodeling of Lama4^+/+ and Lama4^−/− MSCs post-AML exposure. BM MSCs initially sorted from 3 to 4 month-old Lama4^+/+ and Lama4^−/− mice were sorted for RNA sequencing 48 hours post coculture with MLL-AF9 AML cells. Data are from 3 independent experiments. (A) Experimental setup. (B) PCA plot of Lama4^+/+ and Lama4^−/− MSCs with or without being exposed to the AML cells. (C) Venn diagram summarizing differentially expressed genes in Lama4^+/+ and Lama4^−/− MSCs after being exposed to the AML cells. (D) Volcano plot showing uniquely altered genes in Lama4^−/− MSCs after AML exposure. Data shown are padj vs Log2(FC) of each gene tested between Lama4^−/− and Lama4^+/+ MSCs from RNA sequencing data. (E) Radar plot showing selected gene sets highly enriched in Lama4^−/− MSCs in comparison with Lama4^+/+ MSCs, before (green) and after (purple) AML exposure. (F-H) GSEA plots showing enrichment of genes related to focal adhesion (F), cytokine-receptor interaction (G), and glutathione metabolism (H) in Lama4^−/− MSCs relative to Lama4^+/+ MSCs post-AML exposure and the heatmap of genes in the leading edge (red frame). FDR-q value (adjusted P value). NES, normalized enrichment scores. (I) Gene expression of the selected cytokines and growth factors in Lama4^−/− MSCs compared with Lama4^+/+ MSCs before and after AML exposure. The data are extracted from RNA-sequencing analysis. The P values in the panels were determined by unpaired 1-tailed or 2-tailed parametric Student t test depending on the data distribution. (J) Gene expression in the AML cells cocultured with Lama4^+/+ or Lama4^−/− MSCs. The data are extracted from RNA-sequencing analysis. The top panels show the expression of cell proliferation-related genes, and the lower panel is the GSEA plot showing the downregulation of genes related to arachidonic acid metabolism. The P values in the panels were determined by unpaired 1-tailed parametric Student t test.